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Published by soedito, 2017-07-28 05:58:50

ANIMAL GENETIC RESOURCES FOR_524

ANIMAL GENETIC RESOURCES FOR_524

THE STATE OF THE WORLD'S ANIMAL GENETIC RESOURCES FOR FOOD AND AGRICULTURE

PART 3

Agriculture119. Egypt has a General Union of associations in various production areas – the dairy
Poultry Producers120. Cameroon mentions its agro-industry122, bird raising123, and meat124.
Société du Développement et de l’Exploitation
des Productions Animales121. Nicaragua reports

119 Decree No. 5/78 creating the National Institution of Poultry 122 Decree 364. Law of the Corporación Nicaragüense de la
Breeding (AVICOLA), 1978 (Legal Questionnaire, 2003). Agroindustria Láctea, 31/05/88; Decree No. 82. Creating a
120 Ministerial Resolution No. 97 implementing Law No. 96 of Development Fund for the Dairy Industry, 23/07/66
1998 regarding the creation of the General Union of Poultry (CR Nicaragua, 2004).
Producers (FAOLEX). 123 Decree 357, Law creating the Corporación Avícola
121 Decree No. 81/395 of 9 September 1981, modifying and Nicaragüense, 31/05/88 (CR Nicaragua, 2004).
completing Decree No. 75 of 8 March 1976 124 Decree 360, Law creating the Corporación Nicaragüense de la
(CR Cameroon, 2003). Carne, 31/05/88 (CR Nicaragua, 2004).

TABLE 93
Instruments for promoting trade in livestock products

Instruments Africa Near & Southwest Europe Asia Latin North
Middle Pacific & the America America
Caucasus & the
East Caribbean

Legislation to foster trade in AnGR products

Marketing in general 2 [1] 2 [1] [2] 1

Specific products 1 [1] 3 [1] 1

Organic/niche [2] 3 [3] 1 1

Institutions 3 [1] 1 33

Protective measures, and subsidies 2 1 21

Number of CRs 42 7 11 39 25 22 2

[n] = policies or legal basis unclear.
Note that institutions may promote specific products or marketing of products in general. These cases are indicated under both,
“institutions” and “laws to foster trade”.

TABLE 94
Instruments regulating import and export of genetic material

Regulations relating to Africa Near & Southwest Europe Asia Latin North
Middle Pacific & the
Caucasus America America
East
& the

Caribbean

Import 7 3 3 26 6 5
Export 4 2 0 23 1 0
CBD implementation 1 11

Number of CRs 42 7 11 39 25 22 2

326

THE STATE OF CAPACITIES IN ANIMAL GENETIC RESOURCES MANAGEMENT

Box 63 Regulations on import and export of genetic
Russian Federation – Veterinary and material are motivated by a variety of objectives,
Sanitary Requirements No. 13-8-01/1-8 which vary from country to country. Preventing the
(1999) introduction of livestock disease is an important
motivation. Other objectives may include ensuring
For boar semen to be admitted to the territory of the that the imported genetic material is adapted
Russian Federation, it must have been collected at AI to local ecosystems, or increasing the output of
centres that are kept under permanent supervision by national livestock production. There may also be
the state veterinary service of the exporting country. legislation in place implementing the provisions of
Animals must be kept, and semen must be collected, the CBD related to the need to obtain governments’
in compliance with the veterinary and sanitary prior informed consent for the export of genetic
requirements currently in force. Boars supplying resources.
sperm for export must not be vaccinated against
classical swine fever. Boars must be kept at the AI In Europe in particular, there is a high density
centres for six months before collection of sperm, and of regulation related to the import and export
must not be used for natural insemination during this of genetic material. Box 63, which describes
period. Boars must not have been fed on feedstuffs regulations controlling semen imports to the
produced using genetically modified additives or Russian Federation, provides an illustrative
other genetically modified products. Semen must example.
be free of pathogenic and toxic micro-organisms.
Compliance with these veterinary and sanitary Some Country Reports mention the possibility
requirements must be certified by a veterinary of preventing the import of semen for ecological
certificate, signed by the state veterinary inspector of reasons. CR Algeria (2003) indicates that in
the exporting country, and drawn up in the language certain cases the government can exercise its
of the country of origin and in Russian. The veterinary regulatory powers to ensure that inappropriate
certificate must contain the date and the results of exotic semen is not imported or promoted to the
diagnostic examinations. Semen destined for export detriment of local breeds that are better adapted
must be packed and transported in special containers to local conditions and the production objectives
(vessels) filled with liquid nitrogen. Dispatch of of small producers. CR Ecuador (2003) mentions
semen to the Russian Federation is possible only after that improved seeds, animals, technologies and
authorization issued to the importer by the Veterinary equipment can be freely imported if they are not
Department of the Ministry of Agriculture and Food. deemed harmful to local ecosystems125. Colombia
has a constitutional regulation126 stating that “the
Source: Legal Questionnaire (2003). state will regulate the entry and exit of genetic
resources from the country, and their utilization,
Import and export of genetic material in accordance with national interests”.
Under this heading, legislation on the import and
export of genetic material in the narrow sense CR Burkina Faso (2003) mentions the country’s
(semen and embryos) is presented. Import and participation in a number of regional agreements
export of live animals is discussed below under relating to the management, utilization and
livestock movement and trade. In several cases it is exchange of genetic material, but indicates that
not clear from the information available whether these have not yet been implemented.
import/export of semen and embryos is included
under regulations covering livestock trade, or 125 Law of Agricultural Development the codification of which
on the import/export of livestock products. was published in the Official Register No. 55 of 30 April 1997.
126 Political Constitution of Colombia, 1991, Article 81
(CR Colombia, 2003).

327

THE STATE OF THE WORLD'S ANIMAL GENETIC RESOURCES FOR FOOD AND AGRICULTURE

PART 3

Box 64 barriers to the international exchange of AnGR.
India – rules for transportation Instruments mentioned in the Country Reports
include the definition of health standards for the
The rules provide for the transportation of poultry import of live animals, requirements related to the
and pigs by rail, road or plane. Containers must be animal health status of exporting countries, and
properly fitted for transportation – providing shelter quarantine requirements for imported animals.
from sun, heat, rain or cold, and allowing poultry
and pigs to be comfortable during the journey. A Some countries indicate zoosanitary
table details the rules regarding the containers and regulations for both import and export of live
the timing of journeys according to the size and age animals in general – for example, Mali127, or for
group of the animals. Vaccination and other health specific species – for example, Myanmar128 (pigs,
requisites are listed. horses, sheep, goats, and cattle and buffaloes).
Conversely, some countries indicate zoosanitary
Source: FAOLEX. requirements and control for the import of live
animals only129. See Section E: 3.2 for a discussion
Box 65 of EU laws covering health-related restrictions on
West Africa – pastoralists crossing trade in livestock and livestock products.
borders
Quarantine measures are mentioned by many
Decision A/DEC.5/10/98, taken in Abuja in 1998 by countries. Provisions for further quarantine
the heads of state and government of the Economic measures to be applied in the case of disease
Community of West African States (ECOWAS) relates epidemics are also often mentioned (see below).
to the use of transhumance certificates by mobile Some countries have instruments in place related
pastoralists within Member States. In Nigeria, efforts to the import of animals from countries of regions
have been made to, inter alia, stipulate conditions for particularly affected by animal health problems.
movement of nomadic livestock, i.e. their arrival to Botswana’s, Diseases of Animals Act 1977, for
and departure from Nigeria. example, allows the prohibition of the import
of animals from areas that are known to be
Source: E-mail Consultation Nigeria (2005). affected by major diseases (CR Botswana, 2003).
Other examples include El Salvador’s legislation
prohibiting the import of animals from countries
affected by FMD130 and Cape Verde’s legislation
prohibiting bovine imports from areas infected
by BSE131.

Import and export of live animals 127 Decree 372/P-RM regulating sanitary control of animals on the
Controls on the international exchange of livestock territory of the Republic of Mali (Legal Questionnaire, 2003).
are of great importance for the control of livestock 128 In the case of pigs: Regulation for importation and exportation
disease. The introduction of diseases across a of breeding swine into Myanmar, 2003; similar laws for the other
country’s borders can have severe consequences species were also passed in 2002 (FAOLEX).
for the livestock sector. CR Kenya (2004) for 129 Kiribati’s Importation of Animals Regulation, 1965 (FAOLEX);
example, mentions that cross-border movement Palau’s Plant and Animal Control – Chapter 20 of Title 25 of the
of livestock has caused the re-introduction of Palau National Code, 1966 (FAOLEX).
some previously eradicated notifiable diseases, 130 Accord No. 54 – 2001. Prohibiting the import of bovine, ovine,
which has led to the loss of disease-free zones caprine and porcine livestock and other cloven-hoofed species
in the country and the loss of external markets. from countries affected by foot-and-mouth disease (FAOLEX).
Zoosanitary regulations are, however, significant 131 Order No. 10/2001 (FAOLEX).

328

THE STATE OF CAPACITIES IN ANIMAL GENETIC RESOURCES MANAGEMENT

TABLE 95
Instruments regulating livestock movements and import and export of live animals and livestock
products

Legislation on trade Africa Near & Southwest Europe Asia Latin North
Middle Pacific & the
Caucasus America America
East
& the

Caribbean

Import (health standards) 2 2 (1) 4 (3) 8 (5) 5 6 (4) (1)
Export 3
Products 31 3
1
42

Number of CRs 42 7 11 39 25 22 2

[n] = policies or legal basis unclear.

There are countries that have regulations to transportation to and from cattle shows.
regarding import and export of breeding animals. Similarly, in the United Kingdom, the Animal
Chad, for example, prohibits the export for Gatherings (England) Order of 2003 specifies the
slaughter of female animals of breeding age132. zoosanitary measures that have to be included
CR China (2003) notes that the country’s Ministry when organizing events such as shows or markets
of Agriculture formulated an Administrative (Legal Questionnaire, 2003). In Japan, a health
Regulation on Exportation of Breeding Animals certificate is required for livestock to cross the
during the 1980s, which was updated and adjusted border of a province (E-mail Consultation Japan,
in 1993. Examples from Europe include Hungary, 2005). In the event of a disease epidemic, stricter
which reports regulations covering exports and regulations are implemented. Several countries
imports (E-mail Consultation Hungary, 2005), and have regulations regarding the welfare of
Germany133 which reports legislation regulating transported live animals. One example is India
the import of breeding animals. Ecuador’s Law (Box 64).
on Agricultural Development (1997) enables the
import of breeding animals deemed unsuitable African countries where pastoralist production
for local ecosystems to be restricted (CR systems are widespread have adopted the use of
Ecuador, 2003). transhumance certificates at both national and
regional levels.

Livestock movement internal and regional Instruments related to animal health
Livestock movement is one issue usually covered by The number of countries that have developed and
legislation related to animal health. In countries implemented legislation related to animal health
where risks of disease outbreaks are high, separate is larger than in any other field (see previous
laws tend to be adopted setting out strict rules on subchapter for further discussion of measures
stock movement within the country and measures related to animal movement and trade). Animals’
to enforce their observation (FAO, 2005). health status has enormous impact on individual
performance, on the production output and
Several countries indicate specific requirements efficiency of the livestock sector, and on trade
related to livestock shows. CR Mozambique in products of animal origin. Most countries
(2005), for example, reports provisions related report some regulation (or at least institutions or
programmes) related to animal health. However,
132 Decree No. 138 bis /PR/MEHP/88 regulating the unlimited some countries explicitly state that they do not
export of and livestock products with the exception of yet have adequate regulation in place. Some of
reproductive females (CR Chad, 2003).
133 Animal Breeding Import Ordinance (Legal
Questionnaire, 2003).

329

THE STATE OF THE WORLD'S ANIMAL GENETIC RESOURCES FOR FOOD AND AGRICULTURE

PART 3

TABLE 96
Regulations in the field of animal health

Types of measures Africa Near & Southwest Europe Asia Latin North
Middle Pacific & the
Caucasus America America
East
& the

Caribbean

Legislation or policy in place 23 [2] 4 [2] 10 32 [1] 18 [4] 13 [1] 1
Veterinary Services 8 [4] 2 0 10 [9] 7 [6] 0 2
Epidemics general 1 35 1
Epidemics specific 0 0 19 3 7
Number of CRs 5 7 11 39 5 22
[n] = policies 42 25

these countries mention the difficulties that they Box 66
face in generating the necessary political will to The Islamic Republic of Iran’s Act of
ensure adequate regulation. Specific reference to National Veterinary System (1971)
the management of AnGR within national-level
animal health legislation is rare in most parts of The act encompasses overall sanitary regulations, and
the world. regulates quarantine measures and transboundary
movement of animals. The act also covers the
Legislation in this field may address disease following measures:
surveillance and reporting, vaccination or vector
control programmes, emergency measures to be • prevention and control of animal diseases;
taken in the event of epidemics, food hygiene • hygiene certificates for animals and animal
and traceability of livestock products, inspection
of livestock holdings and food processing products for export;
establishments, production of livestock feed • hygienic supervision of pastures, watering
and veterinary products, and regulation of the
qualifications, competences and duties of the places, stables and other breeding
veterinary profession. A country may have broad establishments;
laws that regulate many aspects of animal health • monitoring of feed plants, slaughterhouses and
(Box 66), or there may be specific legislation processing units; and
related to a particular aspect of animal health or • control of the production, import, export and
to a specific disease. marketing of various biological materials
(e.g. drugs, vaccines and serums).
It can probably be assumed that nearly
every country has some laws on animal health Source: CR Islamic Republic of Iran (2004).
in place. Differences exist with regard to the
comprehensiveness of the legal provision, and Act134 (Legal Questionnaire, 2003). Legislation
whether the issue is handled within a regional- of this type may specify a list of notifiable
level framework. diseases. Responses to epidemics may include
the declaration and designation of epidemic-
Measures to be implemented in the event of
epidemics 134 Other reported examples include Australia, China, Costa Rica,
A number of countries report general legislation Ecuador, El Salvador, Estonia, Fiji, Germany, Guatemala, Honduras,
outlining response measures to be taken in Iraq, Ireland, Jamaica,the Philippines, the Republic of Korea, Serbia
the event of an epidemic. One such example is and Montenegro, Switzerland, the United Kingdom and Vanuatu.
Denmark’s Infectious Animal Diseases Control

330

THE STATE OF CAPACITIES IN ANIMAL GENETIC RESOURCES MANAGEMENT

free zones and establishments – countries eradication measures are rare, but have begun to
reporting such legislation include Viet Nam135 be put in place in Europe for some diseases (see
and Zambia136. Eradication and control zones Section E: 3.2).
may be declared – countries reporting such
legislation include El Salvador137, Australia138 and Regional cooperation
the United Kingdom139. Uruguay, in its efforts There tends to be a greater amount of regional or
to combat scabies in sheep obliges farmers to bilateral cooperation in the field of animal health
declare outbreaks or even the suspicion of an than in other areas of AnGR-related legislation.
outbreak, and to contribute to the control of the Reported examples of cooperation agreements
disease140. between neighbouring states, include those
existing between Egypt and Algeria147, Turkey and
Measures may include quarantine – examples Kazakhstan148, members of the Commonwealth of
include Zambia’s Livestock Diseases Act (Legal Independent States149, and Lusophone countries
Questionnaire, 2003). There may also be in Africa150. There are also examples of bilateral
regulations regarding the disposal of infected international cooperation agreements between
animals – countries reporting such measures more distant countries – for example between
include Malawi141, Zambia142, the Netherlands143 Argentina and Hungary151.
and Chile144. There may be payment of
compensation for losses – reported, for example, Institutions and animal health services
by Estonia145 and Switzerland146. Strategies A number of countries report legislation related to
to safeguard valuable AnGR in the event of institutional aspects of the delivery of veterinary
services. These measures may include licensing
135 Regulation on animal epidemic-free zones and establishments requirements for veterinary practice – an example
2002 (FAOLEX). being reported by Kazakhstan152, or define the
136 Cattle Cleansing Act of 1930 amended 1994 (Legal duties and powers153, or responsibilities and
Questionnaire, 2003). obligations of veterinarians154. CR India (2004)
137 Accord 194, declaring the geographical areas of the reports the existence of veterinary councils
departments Usulután, San Miguel, Morazán and La Unión
as control and erradication zones for bovine tuberculosis and 147 Algeria: Official Gazette No. 14, 5 April 2001 (FAOLEX).
brucellosis (CR El Salvador, 2003). 148 Agreement between the Government of Kazakhstan and the
138 Animal Health Act, 1995 (Legal Questionnaire, 2003). Government of Turkey on cooperation in the sphere of animal
139 Diseases of Poultry (England) Order, 2003 (S.I. No. 1078 of health, 1995 (FAOLEX).
2003); Disease Control (England) Order, 2003 (S.I. No. 1729 of 149 Armenia, Belarus, Kazakhstan, Kyrgyzstan, Moldova, Russian
2003) (Legal Questionnaire, 2003). Federation, Tajikistan, Turkmenistan, Ukraine, Uzbekistan;
140 Law No. 16.339 – declaring sheep scab a plague and making Agreement on cooperation of CIS member-states in the veterinary
efforts to erradicate it compulsory (FAOLEX). sphere (FAOLEX).
141 Control and Diseases of Animals Act 2000 (Legal 150 Angola, Cape Verde, Guinea-Bissau, Mozambique, Sao Tome
Questionnaire, 2003). and Principe; Guinea-Bissau’s Decree No 351/73, Boletin Official
142 Stock Diseases Act 1963 (amended 1994) (Legal No. 89 (FAOLEX).
Questionnaire, 2003). 151 Governmental Decree No. 4 of 2002 ratifying and publishing
143 Decree No. 403 of 2001 to amend the Decree implementing the Agreement stipulated on 10 December 1999 in Budapest
provisions of the Animal Destruction Act, 16 July 2001 (Legal between Hungary and Argentina on animal health (FAOLEX).
Questionnaire, 2003). 152 Ministerial Decree No. 1972 of 1997 regarding the validation
144 Law No. 18.617 – norms for compensation for the slaughter for the regulation on licensing of veterinary practice,
of animals for the control of foot-and-mouth disease (Legal 20 August 1997 (Legal Questionnaire, 2003).
Questionnaire, 2003). 153 Georgia’s Veterinary Act (CR Georgia, 2004).
145 Infectious Animal Disease Control Act, 16 June 1999 (Legal 154 Estonia’s Veterinary Activities Organization Act, 1999 (Legal
Questionnaire, 2003). Questionnaire, 2003).
146 Law on Epizootics, 1966 (amended 2002) (Legal
Questionnaire, 2003).

331

THE STATE OF THE WORLD'S ANIMAL GENETIC RESOURCES FOR FOOD AND AGRICULTURE

PART 3

established by a Veterinary Council Act; similar and poverty alleviation are key objectives.
measures are reported from Nepal155. Although there is often considerable focus on
promoting intensive production, a number of
A number of countries report legislation countries, particularly in Africa, report measures
defining their animal health systems. Examples to regulate and support the sustainability of
include the Act of Veterinary System mentioned extensive grazing systems. Given the unique
in CR Islamic Republic of Iran (2004), and the adaptive traits of many dryland breeds and the
Russian Federation’s Federal Law on Veterinary many pressures faced by these production systems,
Service, which involves a scheme for state effective policy and legislation in this field are of
veterinary inspection of collective farms, state great importance. Nonetheless, devising measures
agricultural enterprises, and big livestock farms that are appropriate to the needs of pastoral
and complexes (Legal Questionnaire, 2003). groups, who are often politically marginalized,
Some countries have decentralized institutions remains a major challenge. Other reported
– Peru, for example, reports local committees legislative measures that have been put in place
for animal health (CR Peru, 2004). Brazil reports to support small-scale livestock production
regional Animal Health Inspectorates156 within include those related to the provision of credit
the Ministry of Agriculture to carry out control and the establishment of producer organizations
of animal health at regional level. and cooperative groups.

4.5 Conclusions The implementation of specific measures
aimed at the conservation of AnGR is greatly
The analysis presented above clearly indicates dependent on the economic means of the country
that AnGR management is a complex matter, in question, and this is reflected in the greater
comprising a wide range of technical, policy density of legislation and policy in the more
and logistical operations. Many policy areas developed areas of the world. However, it is also
are involved – including agricultural and rural clear that the importance of sustainable use and
development, animal health, environmental and conservation of AnGR has in many cases not been
landscape conservation, culture, trade, research adequately accommodated in the development of
and education. Cooperation between many legal and policy frameworks at the national level.
diverse stakeholders is required. Inventory and registration systems, for example,
are of great importance for the planning and
The decline of traditional livestock production implementation of conservation measures, but
systems is significant threat to many livestock many countries report that policy and legislation
breeds. Legislative and policy measures that, for in this field remains weak. A further step that
whatever motivation, seek to support this type can facilitate the administration of conservation
of production are potentially of importance to schemes is the legal definition of criteria for the
the maintenance of AnGR diversity. Countries in inclusion of breeds in such programmes, but
industrialized parts of the world are increasingly measures of this type remain rare.
concerned about the conservation of rural
environments and landscapes. There is a trend Where regulations related to conservation
towards the introduction of regulations and exist, they are often isolated, and not integrated
policies aimed at the promotion of extensive into a strategy which takes account of the cross-
farming practices – which tend to require cutting character of the issue. For example,
breeds that are well adapted to local conditions. measures aimed at increasing food security often
Conversely, in developing countries, food security focus almost exclusively on high-output breeds,
without an adequate assessment of the potential
155 Nepal’s Veterinary Council Act, 2055 (1999) (FAOLEX). contribution of local breeds, and without a
156 Law No. 1.052 creating the Animal Health Inspectorate within strategy for their conservation. Another example
the Ministry of Agriculture (1950) (Legal Questionnaire, 2003).

332

THE STATE OF CAPACITIES IN ANIMAL GENETIC RESOURCES MANAGEMENT

is the field of animal health, which is the most policy decisions and strategies, complemented
highly regulated aspect of livestock management by a clear legal definition of the competences
on a global scale. While effective disease control and duties of institutions, and a well-organized
is essential for the use and development of AnGR, monitoring and evaluation system, might be more
restrictions on movement and trade can present effective than an elaborate legal framework.
problems for AnGR management. Slaughter
policies implemented in the event of epidemics References
pose a potential threat to rare breed populations.
It is a matter of concern that throughout most CR (Country name). year. Country report on the state of
of the world, very little attention has been animal genetic resources. (available in DAD-IS library
paid to this threat in the development of legal at http://www.fao.org/dad-is/).
frameworks and policies for disease control.
E-mail Consultation (Country name). 2005. E-mail
The extent to which legal frameworks for the consultation with National Coordinators during the
management of AnGR have been put in place at preparation of this chapter. (unpublished).
the national level varies greatly. Many countries
in Europe have extensive legislation. Conversely, FAO. 2005, The legal framework for the management
in other regions, in particular in Africa, countries of animal genetic resources, by A. Ingrassia, D.
generally seem to rely on policy measures, Manzella & E. Martynuik, for the Development Law
which may be backed by legal mandates for the Service, FAO Legal Office. FAO Legislative study
implementing institutions. This contrast raises No 89. Rome.
the question of whether the establishment of
elaborate legislative instruments regulating AnGR FAOLEX. (available at http://faolex.fao.org/faolex/index.
management is the most appropriate objective htm).
in developing countries. In some cases, countries
clearly indicate that improved legislation is Legal Questionnaire. 2003. Questionnaire survey con-
considered necessary. CR Kenya (2004), for ducted by FAO in 2003, (see FAO, 2005 for details).
example, states that:

“a suitable legal framework is ... required for
operationalization of the [existing] policies.
Once the right policies and legislation have
been formulated, it will be necessary to review
and revise them regularly to make them
respond to the changes that occur with time.”
Some countries are increasingly relying on
market mechanisms or on private institutions
for specific aspects of AnGR management, but
have only limited legislation in place to regulate
the field. It is possible that this could give rise to
problems with regards to public goods aspects
of AnGR management, and a close evaluation
of the need for improved regulation is likely to
be necessary. The decision, as to the appropriate
solution for a given situation will depend on the
political and legislative culture of the country
in question, and on the structures available for
implementation. In some circumstances, sound

333

Part 4

STATE OF THE ART IN
THE MANAGEMENT
OF ANIMAL GENETIC

RESOURCES

PART 4

Introduction

This part of the report gives an overview of the state of the art in methodologies and
techniques for the management of animal genetic resources for food and agriculture
(AnGR). As AnGR management is not an established scientific discipline, Section A
outlines basic concepts that underlie FAO’s understanding of the term. These concepts
are the outcome of a series of expert meetings. Methodological developments in relevant
fields of research are then highlighted, and important findings are illustrated through
case studies. Finally, gaps in current knowledge are identified, and priorities for future
research are proposed.

STATE OF THE ART IN THE MANAGEMENT OF ANIMAL GENETIC RESOURCES

Section A

Basic concepts

1 Animal genetic resources and In developed countries, breeds are relatively
breeds clearly delineated. The role of breed societies,
normally voluntary organizations, which supervise
AnGR are here defined as those animal species breeding standards, provide for the registration
that are used, or may be used, for food production of animals, and promote the utilization of the
and agriculture1, and the populations within each. breed, is important in this respect. A pattern of
Distinct populations within species are usually breed development based on recorded breeding
referred to as breeds. The broad definition of the and shared pedigrees emerged in western
term “breed” used by FAO (Box 67) is a reflection Europe during the late eighteenth century, with
of the difficulties involved in establishing a strict the first breed societies being established in
definition of the term. England during the nineteenth century. Under
the auspices of such organizations, a breed has
Box 67 come to be distinguished as a population sharing
Definition of breed adopted by FAO common ancestry, which has been subjected to
similar selection objectives, and which conforms
Either a subspecific group of domestic livestock with to certain established “breed standards”.
definable and identifiable external characteristics
that enable it to be separated by visual appraisal Breeds are generally not completely isolated
from other similarly defined groups within the same in genetic terms. They are constantly required
species or a group for which geographical and/or to change in response to changes in market
cultural separation from phenotypically similar groups demand, and will at times be supplemented
has led to acceptance of its separate identity. with bloodlines from other breeds (FAO, 2003).
Moreover, despite the existence of societies
Source: FAO (1999). ostensibly associated with specific breeds, the
precepts to be followed when establishing criteria
1 Fish are excluded as management requirements and breeding for the delineation of a breed remain vague.
techniques are very different. The term “farm animal genetic Definitions of breeds within a developed-country
resources”, which had been used by FAO in relation to the Global context have included “animals which share a
Strategy for the Management of Farm Animal Genetic Resources, common pattern of use in agriculture, a degree
has been criticized on the grounds that it appeared to exclude of uniformity of phenotype, and a common gene
animals not kept on farms, but in mobile systems. pool” (FAO, 1995) and “distinct intraspecific
groups, the members of which share particular
characteristics that distinguish them from other
such groups” (FAO, 2003). Discussing the situation
in the United States of America, Hammak (2003)
notes that all that is required to start a breed

339

THE STATE OF THE WORLD'S ANIMAL GENETIC RESOURCES FOR FOOD AND AGRICULTURE

PART 4

registry is “to adopt specific requirements as a means of identifying populations that merit
for eligibility and start to record ancestry.” being treated as separate breeds. The following
Similarly, under European Union (EU) legislation, definition is an example of such an approach:
there is no definition of a “breed” beyond the
requirement that in order to be registered as a “A domestic animal population may be
pure-bred animal, an animal’s pedigree should be regarded as a breed, if the animals fulfil the
traceable to “parents and grandparents ... which criteria of (i) being subjected to a common
are entered or registered in a herd-book of the utilization pattern, (ii) sharing a common
same breed ... [and the animal itself should be] ... habitat/distribution area, (iii) representing
either entered or registered and eligible for entry largely a closed gene pool, and (iv) being
in such a herd-book” (the quotation, from Council regarded as distinct by their breeders”
Directive 77/504/EEC, relates to bovine animals, (Köhler-Rollefson, 1997).
but similar rules apply to other species). Thus, in the absence of breed association records
or molecular studies, the views of the livestock
There may, indeed, be little benefit in seeking keepers themselves perhaps provide the best
a perfect definition. In the words of Jay Lush, a indicator of breed identity. It may be possible to
prominent figure in the field of animal breeding identify groups of farmers who claim to be raising
and genetics, an animal of a distinct type; can reliably recognize
the type; exchange germplasm only with other
“A breed is a group of domestic animals, termed breeders dedicated to holding the same type; and
such by common consent of the breeders, ... a indicate that such breeding practices have been
term which arose among breeders of livestock, ongoing for many generations (FAO, 2003).
created one might say, for their own use, and Within a breed there may be “stocks”, “strains”,
no one is warranted in assigning to this word a “varieties”, or “lines”; these terms which are often
scientific definition and in calling the breeders used interchangeably describe populations within
wrong when they deviate from the formulated breeds that are phenotypically distinct as a result
definition. It is their word and the breeders’ of human selection. The term “ecotype” refers to
common usage is what we must accept as the a population within a breed that is genetically
correct definition” (Lush, 1994). adapted to a specific habitat.
In the developing regions of the world, the
situation is even more complex, and the term 2 Management of animal genetic
“breed” often has little meaning. Populations resources
that are isolated from others, whether on
geographical, ecological or cultural grounds, will Management of AnGR focuses on maintaining
tend to become distinct as a result of natural and genetic diversity. However, most scientific methods
artificial selection, and genetic drift (FAO, 2003). and techniques within the animal sciences (e.g.
However, the names used to distinguish livestock animal husbandry, animal breeding or genetics)
populations do not necessarily correspond to have not been developed with this focus. Thus,
the underlying genetic diversity. In many cases, there is no well-defined set of methodologies
animals will not correspond to any recognized encompassed by the phrase “management of
breed, although there may be local terms AnGR”. The overview presented here, therefore,
referring to different populations. selects the methodologies most relevant to the
Where distinguishing genetically diverse topic, guided by FAO’s definition:
populations is difficult, molecular studies may
contribute to the delineation of separate breeds “AnGR management encompasses all
and breed groups. Studying the cultural and technical, policy, and logistical operations
ecological aspects of livestock keeping also serves

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STATE OF THE ART IN THE MANAGEMENT OF ANIMAL GENETIC RESOURCES

involved in understanding (characterization), – AnGR are dynamic resources, changing with
using and developing (utilization), each generation in interaction with the physical
maintaining (conservation), accessing, environment and according to the selection criteria
and sharing the benefits of animal genetic of their keepers. The proposed approach for
resources” (FAO, 2001). genetic improvement is to base breeding efforts
As such, this part of the report includes on locally adapted genetic resources. This will help
descriptions of methodologies for characterization to avoid the loss of breeds with unique attributes.
and conservation (Sections B and F); because Existing genetic variation in animals’ ability to use
of their increasing importance, methods for locally available resources, survive, produce and
molecular characterization are presented reproduce under the conditions of medium-to-
separately from other aspects of characterization low input farming should be exploited by well-
(Section C). However, when it comes to utilization designed breeding programmes. Complementary
– using and developing AnGR for agriculture measures such as improvement in the provision
and food production – no clear concept has of feed and water, treatment of diseases and
emerged. It is, therefore, not possible to present parasites, and the management of reproduction
a comprehensive description of the state of the will also need to be considered in strategies to
art in utilization. Nonetheless, FAO has started improve the performance of these breeds.
to identify key elements of such a concept, using
as a starting point the definition of sustainable Thus, genetic improvement methods are central
use proposed by the Convention on Biological to the development of breeds. Scientific methods
Diversity (CBD): for breeding programmes have, however, been
“Sustainable use is the use of components developed mainly in higher-input production
of biological diversity in a way and at a rate systems, and under favourable infrastructural
that does not lead to the long-term decline conditions. Breeding programmes do not usually
of biological diversity, thereby maintaining its include maintaining genetic diversity within and
potential to meet the needs and aspirations of between breeds as an explicit goal. The state of
present and future generations” (Article 2 of knowledge in the field of genetic improvement is
the CBD). described in Section D.
To meet this objective FAO has proposed that:
• wise use of AnGR is possible without Ideally, breeding programmes should be part
of a holistic strategy with the goal of sustainably
depleting domestic animal diversity; intensifying production systems to improve
• AnGR with high levels of adaptive fitness to the livelihoods of the producers. Sustainable
intensification has been put forward as the ideal
the environment concerned should be used, way of improving production systems, and is
and sound genetic principles deployed; and defined as follows:
• development of AnGR includes a broad
mix of ongoing activities that must be well “Sustainable intensification of production
planned and executed for success, and systems is the manipulation of inputs to, and
compounded over time. outputs from, livestock production systems
Thus, an important element of (sustainable) use aimed at increasing production and/or
of AnGR is to ensure that locally adapted breeds productivity and/or changing product quality,
remain a functional part of production systems. while maintaining the long-term integrity of the
Adaptive fitness traits, some of which may not yet systems and their surrounding environment,
have been discovered, are of particular importance, so as to meet the needs of both present
as they are genetically complex and cannot easily and future human generations. Sustainable
be achieved by selection over a short period of agricultural intensification respects the needs
time. Use of AnGR inevitably includes development and aspirations of local and indigenous people,
takes into account the roles and values of their

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PART 4

locally adapted genetic resources, and considers development. Interdependencies among regions
the need to achieve long-term environmental in terms of access to AnGR, and past and present
sustainability within and beyond the agro- patterns of exchange are described in Part 1
ecosystem” (FAO, 2001). – Section C. Developments in biotechnology
Addressing these general principles for the use (described in Sections C and F) have facilitated
and development of AnGR is not merely a matter exchange and use of genetic resources, have
of scientific methodology, but requires an effective begun to detect genes regulating functional
combination of methodologies and techniques traits, and present new opportunities for the
with appropriate development policies. To support use of genetic material. Thus, they will play an
policy development, economic analyses are needed important role in future patterns of access and
to describe the economic importance of locally benefit sharing (ABS). The contribution that
adapted breeds, in particular from the perspective methodologies developed in the social and
of the smallholder; to define the value of livestock political sciences can make to the formulation of
genetic diversity; and to compare different adequate policies for ABS is, however, beyond the
management strategies. An overview of economic scope of this discussion.
valuation methods is presented in Section E.
Another difficulty related to the concept of 3 Risk status classification
utilization, is that of clearly distinguishing it from
in vivo conservation. This problem arises due to An assessment of the risk status of livestock breeds
the fact that sustainable use is considered the or populations is an important element in the
preferred method of maintaining AnGR. Thus, planning of AnGR management. The risk status
when conservation is defined in the broad sense of a breed informs stakeholders whether, and
of ensuring maintenance of all relevant AnGR, how urgently, actions need to be taken. Gandini
it includes sustainable use. However, a more et al. (2004) define “degree of endangerment” as
operational definition, which allows a clearer “a measure of the likelihood that, under current
delineation of the subject, and which is used in circumstances and expectations, the breed will
Section F on methods for conservation, is that become extinct.” Accurately estimating degrees
conservation comprises actions that are required of risk is a difficult undertaking and incorporates
because the continued use of a particular genetic both demographic and genetic factors.
resource is threatened. The role of conservation
is to ensure that unique genetic resources are Clearly, current population size is an important
available to farmers and breeders in the future, factor in determining risk status. A small
and consequently, conservation can be considered population is at greater risk of being wiped out
as part of an overall strategy to use AnGR in a by natural disasters, disease or inappropriate
sustainable manner to meet current and future management. However, a mere headcount of
human needs. To inform decisions regarding animals, or even of animals of breeding age, does
conservation strategies, it is important to have an not give the whole picture with regard to risk
estimate of current risk status (see below), and also status.
to identify threats likely to affect the breed in the
near future. The latter allows interventions, such as Breeding between individuals sharing common
any breed development necessary to maintain the ancestors tends to reduce the rate of allelic
breed, to take place at a sufficiently early stage. variation in the next generation. The genetic
Accessing and sharing the benefits of diversity of the population is, thus, reduced.
AnGR (also components of FAO’s definition of The accumulation of deleterious recessive alleles
AnGR management) are key areas for policy may threaten the fitness of the population and
negatively affect reproductive rates, thereby

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STATE OF THE ART IN THE MANAGEMENT OF ANIMAL GENETIC RESOURCES

increasing the risk of extinction (Gandini et and 500, respectively (ibid.). Additionally, it can
al., 2004; Woolliams, 2004). The extent of the be seen from the above equation that the value
risk is commonly expressed in terms of the rate of Ne is far more readily influenced by changes
of inbreeding (ΔF) in the population, which affecting the male (smaller) breeding population
is a measure of the expected changes in gene than the female. This underlines the importance
frequencies in the population due to genetic drift of considering the number of breeding males in
(Woolliams, 2004). The rate of inbreeding is often any assessment of risk status.
inferred from the effective population size (Ne).
As Ne goes up ΔF decreases, or more formally, In addition to the current effective population
Ne = 1/(2 ΔF). size, degree of risk is related to population growth
trends. As noted above, where populations are
The value of Ne in a population is often small there is a greater likelihood that adverse
approximated on the basis of the equation events or trends will lead rapidly to extinction.
Ne = 4MF/(M+F) where M and F are number of Above a certain population size the risk of such
reproducing males and females. The method is an outcome can be regarded as small (see below
based on the assumption that matings between for discussion of the thresholds used in various
these breeding animals are random. However, risk status classifications). The more rapidly a
this assumption is rarely applicable in livestock population builds up to reach the critical size,
populations, as some individuals contribute the less it is exposed to the risk of extinction.
disproportionate numbers of progeny to the Obviously, if population figures are low and the
next generation. The way in which breeding is growth trend is negative, the prospects for the
managed, for example the implementation of breed are not good. A complicating factor is
selective breeding programmes, influences the that breed population growth rates often show
effective population size. Various techniques considerable fluctuations over time, particularly
for adjusting the calculation to account for such where production conditions cannot be strictly
factors have been developed, but require further controlled (Gandini et al., 2004). Factors which may
data inputs (Gandini et al., 2004). Collecting influence the variance of the population growth
the demographic data needed to calculate Ne is rate include the variability of market demand,
often problematic: there may be inconsistencies patterns of disease, the existence of programmes
in census data and registration of females and for and awareness of AnGR conservation, the
offspring, some females may be used in crossing general economic stability of the agricultural
programmes, and not all females may be bred each sector, and the spatial distribution and density of
year (Alderson, 2003). Another element that can the population (ibid.). Calculating the probability
influence the outcome of risk status estimations that the population size will lie within a given
is the time interval over which risk is calculated. range at a given time in the future is, thus, fraught
Because of the different generation intervals in with theoretical and data-related difficulties.
different livestock species, calculations performed Despite such problems, current population trends
on the basis of the number of generations will are clearly a factor to be considered in assessing
produce different priorities from those calculated risk status. In addition to overall population size
on the basis of years (ibid.). and growth rates, the risk status of a population
is affected by other factors such as the number of
Some implications of changes to the effective herds, and the geographical concentration of the
population size are important to note. At low population, which influence exposure to threats
levels of Ne, particularly below 100, the rate of loss such as disease epidemics; and by sociological
of genetic diversity increases dramatically (FAO, factors such as the age of the farmers keeping the
1992a). For example, approximately 18, 10, 4, 1.6 breed (Woolliams, 2004).
and 0.8 percent of genetic diversity is lost in ten
generations, when Ne is equal to 25, 50, 125, 250

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In 1992, FAO convened an Expert Consultation breed. Extinction is absolute when there
to develop recommendations for the assessment are no breeding males (semen), breeding
of risk status. The preference was for a breed risk females (oocytes), nor embryos remaining.
status classification based on the concept of Ne, • Critical breed: A breed where the total
adjusted by trends in population size, extent of number of breeding females is less than
cross-breeding, extent of cryoconservation, and 100 or the total number of breeding
variability of family size. It was also suggested that males is less than or equal to five; or the
the number of herds and trends in the number of overall population size is close to, but
herds should be included (FAO, 1992a). However, slightly above 100 and decreasing, and the
data limitations and the necessity of a consistent percentage of pure-bred females is below
approach on a global scale meant that a simpler 80 percent.
approach was adopted, based on the number • Endangered breed: A breed where the total
of breeding females and males, and trends in number of breeding females is between 100
population size (see below for details). In the and 1000 or the total number of breeding
future, as more complete data become available it males is less than or equal to 20 and greater
may be possible to refine the method of calculation than five; or the overall population size
to account for the above factors, and also to adapt is close to, but slightly above 100 and
it to account for the different generation intervals increasing and the percentage of pure-
of different species. bred females is above 80 percent; or the
overall population size is close to, but
For planning and prioritization purposes, it is slightly above 1 000 and decreasing and the
useful to classify breeds into risk status categories. percentage of pure-bred females is below
The numerical boundaries between the different 80 percent.
risk status categories used by FAO are intended to • Critical–maintained breed and endangered–
be indicators of the need to take action. A paper maintained breed: Critical or endangered
presented at the Expert Consultation in 1992 breeds that are being maintained by an
argued that a population size between 100 and active public conservation programme or
1 000 breeding females “implies that the breed is within a commercial or research facility.
in danger of extinction. Without action its effective • Breed not at risk: A breed where the total
populationsizeisinadequateinmostcasestoprevent number of breeding females and males is
continuing genetic loss in future generations. An greater than 1 000 and 20 respectively; or
increase in the degree of inbreeding is unavoidable the population size approaches 1 000 and
and threatens the vitality of animals. There is a real the percentage of pure-bred females is close
danger either of spontaneous loss for example by to 100 percent, and the overall population
sudden disease, or due to neglect by man” (FAO size is increasing.
1992b). Further, a population size of less than 100 The FAO system outlined above is not the
breeding females indicates that “The population only existing classification of risk status. Another
is close to extinction. The first action must be to classification was developed for the European
increase the population size. At this level of threat, Association of Animal Production–Animal Genetic
the genetic variability is often already reduced so Data Bank (EAAP–AGDB), and is now used by the
that the population cannot be considered the same European Farm Animal Biodiversity Information
as the ancient breed” (ibid.). System (EFABIS) (http://efabis.tzv.fal.de/). It covers
breeds of buffalo, cattle, goat, sheep, horse,
As such, the following classification is used donkey, pig and rabbit in 46 European countries,
by FAO to describe the degrees of risk faced by and is based on genetic risk – as represented
livestock breeds: by expected cumulative rates of inbreeding in

• Extinct breed: The case when it is no longer
possible to recreate a population of the

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STATE OF THE ART IN THE MANAGEMENT OF ANIMAL GENETIC RESOURCES

50 years (ΔF–50). Calculations are based on the References
familiar equation Ne = 4MF/(M+F) (see above) with
its inherent assumptions (EAAP–AGDB, 2005). Alderson, L. 2003. Criteria for the recognition and pri-
Breeds are classified into one of five categories oritisation of breeds of special genetic importance.
according to ΔF–50: not endangered, <5 percent; Animal Genetic Resources Information, 33: 1–9.
potentially endangered, 5–15 percent; minimally
endangered, 16–25 percent; endangered, 26–40 Convention on Biological Diversity (CBD). Convention
percent; and critically endangered, >40 percent. Text. Article 2. Use of Terms. Concluded at Rio de
Breeds may be shifted to a higher risk class based Janeiro, 5 June 1992. (available at www.biodiv.
on a set of additional risk factors: a high rate of org/convention/convention.shtml).
incrossing with other breeds; a downward trend
in the number of breeding females; or a low EAAP–AGDB. 2005. Factors used for assessing the
number of breeding herds (ibid.). status of endangerment of a breed. European
Association of Animal Production – Animal Genetic
The EU, under Commission Regulation (EC) Data Bank. (available at www.tiho-hannover.
No. 817/2004, sets out risk status thresholds for de/einricht/zucht/eaap/).
the purposes of providing incentive payments to
farmers keeping threatened breeds. Calculations FAO. 1992a. Monitoring animal genetic resources and
are based on the number of breeding females criteria for prioritization of breeds, by K. Maijala. In
summed across all EU countries. Separate J. Hodges, ed. The management of global animal
thresholds are established for each species: cattle genetic resources, Proceedings of an FAO Expert
– 7 500, sheep – 10 000, goats – 10 000, equidae Consultation, Rome, Italy, April 1992, Animal
– 5 000, pigs – 15 000 and avian species – 25 000. Production and Health Paper No. 104. Rome.
Some arguments can be put forward in support
of these rather high thresholds. Gandini et al. FAO. 1992b. The minimum number of preserved popula-
(2004) note that while in the European context tions, by I. Bodó, In J. Hodges, ed. The management
a breed with 1 000 or more breeding females can of global animal genetic resources. Proceedings of
generally be self-sustainable, this is not always the an FAO Expert Consultation, Rome, Italy, April 1992,
case, and that it is easier to prevent a population Animal Production and Health Paper No. 104. Rome.
from losing self-sustainability than to restore it.
FAO. 1995. Global impact domain – animal genetic
The NGO Rare Breeds International has also resources, by E.P. Cunningham. Rome.
developed a system based on the number of
registered pure-bred breeding females, which FAO. 1999. The global strategy for the management
classifies priority breeds into four categories: of farm animal genetic resources. Executive Brief.
critical, endangered, vulnerable and at risk Rome.
(Alderson, 2003). Other factors (number of
breeding units, number of unrelated sire lines, FAO. 2001. Preparation of the first report on the state of
population trends, distance between major the world’s animal genetic resources. Guidelines for
breeding units), which would ideally be included the development of country reports. Rome.
in an estimation of risk status, are disregarded in
the interests of avoiding excessive complexity in FAO. 2003. Defining livestock breeds in the context of
the calculations (ibid.). community-based management of farm animal ge-
netic resources, by J.E.O. Rege. In Community-based
management of farm animal genetic resources.
Proceedings of the workshop held in Mbabane,
Swaziland, 7–11 May 2001. Rome.

345

THE STATE OF THE WORLD'S ANIMAL GENETIC RESOURCES FOR FOOD AND AGRICULTURE

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Gandini, G.C., Ollivier, L., Danell, B., Distl, O.,
Georgoudis, A., Groeneveld, E., Martyniuk, E.,
van Arendonk, J.A.M. & Woolliams, J.A. 2004.
Criteria to assess the degree of endangerment of
livestock breeds in Europe. Livestock Production
Science, 91(1-2): 173–182.

Hammak, S.P. 2003. Creating cattle breeds and com-
posites. College Station Texas. Texas Cooperative
Extension, Texas A & M University.

Köhler-Rollefson, I. 1997. Indigenous practices of
animal genetic resource management and their
relevance for the conservation of domestic animal
diversity in developing countries. Journal of Animal
Breeding and Genetics, 114: 231–238.

Lush, J.L. 1994. The genetics of populations. Iowa
Agriculture and Home Economics Experiment
Station. Special Report 94. Ames, Iowa, USA. Iowa
State University.

Woolliams, J.A. 2004. Managing populations at risk. In
G. Simm, B. Villanueva, K.D. Sinclair & S. Townsend,
eds. Farm animal genetic resources, pp. 85–106.
British Society for Animal Science, Publication 30.
Nottingham, UK. Nottingham University Press.

European legislation cited

COMMISSION REGULATION (EC) No 817/2004 of 29
April 2004 laying down detailed rules for the ap-
plication of Council Regulation (EC) No 1257/1999
on support for rural development from the European
Agricultural Guidance and Guarantee Fund (EAGGF).
http://europa.eu.int/eur-lex/pri/en/oj/dat/2004/l_153/
l_15320040430en00300081.pdf

COUNCIL DIRECTIVE 77/504/EEC of 25 July 1977 on
pure- bred breeding animals of the bovine species.
http://europa.eu.int/smartapi/cgi/sga_doc?smartapi!
celexapi!prod!CELEXnumdoc&lg=EN&numdoc=319
77L0504&model=guichett

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Section B

Methods for characterization

1 Introduction 2 Characterization – as the basis
for decision-making
Characterization of AnGR encompasses all
activities associated with the identification, A key consideration for the management of AnGR
quantitative and qualitative description, and at the national level is whether, at a given point
documentation of breed populations and the in time, a particular breed population is self-
natural habitats and production systems to which sustainable or whether it is at risk. This primary
they are or are not adapted. The aim is to obtain assessment (baseline survey2) of breed/population
better knowledge of AnGR, of their present and status is based on information on:
potential future uses for food and agriculture in
defined environments, and their current state • population size and structure;
as distinct breed populations (FAO, 1984; Rege, • geographical distribution;
1992). National-level characterization comprises • within-breed genetic diversity; and
the identification of the country’s AnGR and the • the genetic connectedness of breeds when
surveying of these resources. The process also
includes the systematic documentation of the populations are found in more than one
information gathered so as to allow easy access. country (e.g. the Djallonke sheep of West
Characterization activities should contribute Africa).
to objective and reliable prediction of animal If a breed/population is not as risk, no immediate
performance in defined environments, so as to steps to implement conservation measures are
allow a comparison of potential performance necessary. Nevertheless, as part of national
within the various major production systems livestock development plans, decisions have to
found in a country or region. It is, therefore, more be taken as to whether a genetic improvement
than the mere accumulation of existing reports. programme is needed – in response, for example,
to changing market conditions. Decisions
The information provided through the regarding such improvement programmes are
characterization process enables a range of mainly guided by information on long-term
interest groups, including farmers, national benefits to livestock keepers and society.
governments and regional as well as global
bodies to make informed decisions on priorities 2 Baseline information is related to a particular target animal
for the management of AnGR (FAO, 1992; FAO/ population at a given time and within a given production
UNEP, 1998). Such policy decisions aim to promote environment. Depending on the degree of change, these
further development of AnGR while ensuring descriptions may need to be updated about once a generation.
that these resources are conserved for the needs The baseline study should characterize phenotypic and molecular
of present and future generations. attributes of the breeding females and males in the population.
About 100 adult females and about 30 adult males are needed for
phenotypic characterization, but about a third of this size may be
sufficient for molecular diversity estimation.

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PART 4

When a breed/population is found to be to be conserved are found in more than one
at risk, active conservation strategies have to country, decisions should be taken at the regional
be implemented or the potential loss of the level. Thus, regional coordinating institutions/
breed must be accepted. To allocate the limited organizations, and supporting national policies,
resources that are available for conservation are required to facilitate such decisions and to
programmes, breeds need to be prioritized. implement actions. To date, only a few examples
These decisions may be based on the genetic of multi-country actions in AnGR management
distinctiveness, adaptive traits, relative value for have been reported.
food and agriculture, or historical and cultural
values of the breeds in question. This information
is also needed to decide, whether in vivo or in
vitro strategies or a combination of both appears
to be the most promising approach. If the breeds

FIGURE 47
Information required to design management strategies

Breed population within a country

Status of the breed:

• population size and structure
• geographical distribution within the country
• populations of same breed in other countries

Breeds at risk Breeds potentially at risk Breeds not at risk

“Value” of the breed: Potential for improvement:

• genetic distinctiveness • target traits (genetic diversity within
• adaptive traits population)
• relative utility value for food and agriculture
• historical or cultural use • preference of market and society

No conservation Conservation Genetic No planned
programme programme improvement genetic
programme changes

High risk In vitro In vivo Pure/straight Cross-breeding
of extinction conservation conservation breeding

Risk Criteria Elements of
status action plans

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STATE OF THE ART IN THE MANAGEMENT OF ANIMAL GENETIC RESOURCES

For decisions on conservation strategies and genetic diversity among the breeds under
on development programmes for self-sustainable consideration (in order to maximize the
breeds, comprehensive information is needed, diversity conserved for the benefit of future
and should include: human generations);
• origin and development of the breeds; and
• description of the typical phenotypic • unique genetic (or phenotypic if genetic
characteristics of the breed population, attributes are not known) characteristics
including physical features and and their significance in current or
appearance, economic traits (e.g. growth, anticipated production settings.
reproduction and product yield/quality) National decision-makers need to identify
and some measures (e.g. range) of the breeds in which genetic improvement
variation in these traits – the focus is programmes would be most beneficial. Such
generally on the productive and adaptive programmes could include breeds classified as at
attributes of the breed; risk, and form part of a conservation programme.
Investments in breed improvement should be
• description of the production environments justified by adequate returns to investment.
(Box 68), both the original habitat and the These are determined by performance levels,
current production system in which the special adaptive characteristics and/or specific uses
population is kept – some breeds are kept and values of the breeds in a given production
in more than one production environment, environment or in relation to anticipated changes
in a number of countries, and sometimes in the production environment (including market
outside their original geographical area; conditions). Thus, performance data, description
of particularly useful attributes and values, and
• documentation of any special characteristics a detailed description of the general production
(unique features) of the population in terms environment are essential to guide decisions on
of adaptation and production – including breed development programmes.
responses to environmental stressors The set of information needed for the
(disease and parasite challenge, extremes of development of appropriate breeding
climate, poor feed quality, etc.); programmes also allows the choice of breed to
be reconsidered as the production environment
• images of typical adult males and females in evolves, whether through changes to husbandry
their typical production environment; practices, market conditions, cultural preferences,
or biophysical (e.g. climatic stress or disease
• relevant indigenous knowledge (including challenge) factors. Similarly, this information is
but not limited to gender-specific needed in the design of AnGR restocking schemes
knowledge) of traditional management undertaken following natural disasters (drought,
strategies used by communities to utilize floods, etc.), disease outbreaks or civil unrest.
the genetic diversity of their livestock; Restocking may be based on AnGR available
within the country, from other countries in the
• description of ongoing management region, or from another region of the world.
(utilization and conservation) actions and In all cases, restocking schemes should seek to
the stakeholders involved; and obtain the animals that are best adapted to the
production environment into which they will be
• description of any known genetic introduced.
relationships between breeds within or Management decisions may differ in type and
outside the country. scope at subnational, national, regional and

In addition to the information listed for both
pathways (conservation and development), the
following supplementary information is useful to
guide the choice of priority breeds and geographic
areas for conservation programmes:

• genetic distinctiveness of the breeds and
their significance with respect to the total

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Box 68
Production environment descriptors for animal genetic resources

A comprehensive description of the production indicator. The workshop noted that many developing
environment is essential to make use of performance countries had very little capacity to collect and
data and to understand the special adaptations of analyse production environment variables, and that,
breeds/populations. Adaptive fitness of breeds is a less complex descriptive system would, therefore,
complex and difficult to measure directly, but can be preferable as it would be more likely to be used.
be characterized indirectly by describing the primary Despite these concerns, the system proposed required
variables (criteria) which have affected an animal very detailed information. A less detailed and more
gene pool (breed) over time, and have probably pragmatic approach to describing production systems
maximized its adaptive fitness for that environment. would probably facilitate efforts to begin to fill the
Thus, an (improved) description of production current large gaps in breed documentation. However,
environments would be extremely valuable, in order a detailed approach should be encouraged whenever
to better understand the comparative adaptive fitness this is possible.
of specific AnGR.
The system devised at the meeting in Armidale
In January 1998, an expert group met in Armidale, appears to be the first attempt to develop a structured
Australia, and devised a very detailed and well- set of production environment descriptors (PEDs)
structured approach, using five main criteria to for use in the characterization of livestock breeds.
characterize most, if not all, production environments, The Domestic Animal Genetic Resources Information
for all animal species used for food and agriculture. System (DAGRIS) database, developed by the
The five criteria were: climate; terrain; disease, disease International Livestock Research Institute (ILRI)
complexes and parasites; resource availability; and includes a field devoted to the “habitat” of each
management interventions (FAO, 1998). At a second breed, but there is no set structure to the entries,
level of hierarchy, three to seven indicators for and the information provided to date is quite limited.
each criterion were formulated to characterize (i.e. Oklahoma State University’s “Breeds of Livestock”
describe and measure variables in) the production database provides some information on production
environments. For each indicator two or more environments, but this is again not based on a
verifiers were identified to specify or measure each systematic set of descriptors.

international levels. It is, therefore, important 3 Tools for characterization
that relevant information on breed characteristics
is made accessible to decision-makers at all levels. 3.1 Surveying
For example, it may happen that a country decides
not to invest in the conservation of a specific local Surveys are undertaken to systematically collect
breed, but a regional or international organization data needed to identify breed populations
decides that the breed is a unique genetic resource, and describe their observable characteristics,
and that it is in the global interest to conserve it. geographical distribution, uses and general
husbandry, as well as their production
environments. Full baseline surveys need to be
undertaken once; some elements of the survey
may be repeated when significant changes are
observed in the livestock sector.

As part of the effort to develop global
databanks for the management of AnGR, FAO

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STATE OF THE ART IN THE MANAGEMENT OF ANIMAL GENETIC RESOURCES

developed a comprehensive list of animal and first computer-based information system known
environment descriptors to serve as a guide as EAAP–AGDB. ILRI, in collaboration with FAO
for standardized characterization activities at (Rowlands et al., 2003) has developed and tested
various levels (FAO, 1986a,b,c). However, these an approach for collecting and analysing on-
descriptors were far too complex for universal farm breed-level information in Zimbabwe. The
application. In recognition of this fact, FAO same approach has been applied in Ethiopia.
developed simplified formats for data collection A key lesson from this work was that logistic
for mammalian and avian species (see summary and time requirements for extensive livestock
of data items in Tables 97 and 98). This was based surveys, data management and analysis, can be
on the experience of the EAAP, which started grossly underestimated. It was also found that
collecting data in the 1980s and later built the the outcomes of multivariate survey techniques

TABLE 97
Information recorded for mammalian species in the Global Databank for Animal Genetic Resources

• GENERAL INFORMATION • SPECIAL QUALITIES

Species Specific quality of products
Breed name (most common name and other local names) Specific health characteristics
Distribution Adaptability to specific environment
Special reproductive characteristics
• POPULATION DATA Other special qualities

Basic Population Information: • MANAGEMENT CONDITIONS
Year of data collection
Total population size (range or exact figure) Management system
Reliability of population data Mobility
Population trend (increasing, stable, decreasing) Feeding of adults
Population figures based on (census/survey at species/breed level Housing period
or estimate) Specific management conditions

Advanced Population Information: • IN SITU CONSERVATION

Number of breeding females and males Description of in situ conservation programmes
Percentage of females bred to males of the same breed and
percentage of males used for breeding • EX SITU CONSERVATION
Number of females registered in herd book/register
Artificial Insemination usage and storage of semen and embryos Semen stored and number of sires represented
Number of herds and average herd size Embryos stored and number of dams and sires represented in embryos
Description of ex situ conservation programmes
• MAIN USES
• PERFORMANCE
Listed in order of importance
Birth weight
• ORIGIN AND DEVELOPMENT Age at sexual maturity
Average age of breeding males
Current domestication status (domestic/wild/feral) Age at first parturition and parturition interval
Taxonomic classification (breed/variety/strain/line) Length of productive life
Origin (description and year) Milk yield and lactation length (mammals)
Import Milk fat
Year of herd book establishment Lean meat
Organization monitoring breed (address) Daily gain
Carcass Weight
• MORPHOLOGY Dressing percentage
Management conditions under which performance was measured
Adult height and weight
Number and shape/size of horns Source: FAO/UNEP (2000).
Colour
Specific visible traits
Hair and/or wool type

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TABLE 98
Information recorded for avian species in the Global Databank for Animal Genetic Resources

• GENERAL INFORMATION • SPECIAL QUALITIES

Species Specific quality of products
Breed name (most common name and other local names) Specific health characteristics
Distribution Adaptability to specific environment
Special reproductive characteristics
• POPULATION DATA Other special qualities

Basic Population Information: • MANAGEMENT CONDITIONS
Year of data collection
Total population size (range or exact figure) Management system
Reliability of population data Mobility
Population trend (increasing, stable, decreasing) Feeding of adults
Population figures based on (census/survey at species/breed level or Housing period
estimate) Specific management conditions

Advanced Population Information: • IN SITU CONSERVATION
Number of breeding females and males
Percentage of females bred to males of the same breed and Description of in situ conservation programmes
percentage of males used for breeding.
Number of females registered in herd book/register • EX SITU CONSERVATION
Artificial Insemination usage and storage of semen and embryos
Number of herds and average herd size Semen stored and number of sires represented
Description of ex situ conservation programmes
• MAIN USES
• PERFORMANCE
Listed in order of importance
Age at sexual maturity
• ORIGIN AND DEVELOPMENT Age at first egg and clutch interval
Length of productive life
Current domestication status (domestic/wild/feral) Number of eggs per year
Taxonomic classification (breed/variety/strain/line) Daily gain
Origin (description and year) Carcass Weight
Import Dressing percentage
Year of herd book establishment Management conditions under which performance was measured
Organization monitoring breed (address)
Source: FAO/UNEP (2000).
• MORPHOLOGY

Adult live weight
Patterns within feathers
Plumage pattern
Skin colour
Shank and foot colour
Comb type
Egg shell colour
Specific visible traits

need to be verified by complementary molecular the breed, typical morphological features, average
genetic studies (Ayalew et al., 2004). performance levels, special characteristics, and
ongoing conservation activities.
Based on the Global Strategy for the
Management of AnGR, ten categories of variables 3.2 Monitoring
are covered in AnGR surveys, including basic and
advanced breed population information, main uses Changes in population size and structure need
of the breed, origin and development/evolution of to be documented regularly for all breeds. This

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STATE OF THE ART IN THE MANAGEMENT OF ANIMAL GENETIC RESOURCES

should be carried out on a yearly or biennial and reporting of actual population sizes by those
basis, as the application of modern reproductive directly involved may be adequate and achievable.
technologies, global trade, market demands, and Large and widely dispersed populations may
policies favouring particular breeds, can lead to require the establishment of stratified samples,
rapid changes in the size and structure of breed where a portion of the population in each major
populations. geographical region of the country is monitored.
Lack of easy-to-apply tools for collecting such
Monitoring should be conducted at least once data, general lack of trained persons to undertake
per generation of the species, particularly for assessments, and lack of awareness on the part
breeds classified as at risk or potentially at risk. of policy-makers and implementers regarding
This requires surveys at intervals of about eight the importance of such information, represent
years for horses and donkeys, five years for cattle, important challenges.
buffalo, sheep and goats, three years for pigs and
two years for poultry species. In every country there may be opportunities to
monitor AnGR by taking advantage of existing
At present, most national livestock censuses activities, and thereby avoiding significant
do not contain breed-level data, and so regular additional costs. National livestock censuses offer
reporting of breed population numbers does not good opportunities. It may also be possible to
take place. Species and breeds that have been set up effective monitoring stations in locations
classified as at risk should be monitored on a where livestock are sold or traded, such as
regular basis. This monitoring should serve as the auctions and local markets. This approach can
basis for national early warning. greatly reduce costs by bringing the livestock to
the monitors. However, a focus on traded animals
Information collected during monitoring may not accurately reflect the structure of the
activities enables adjustments to be made target populations on the farms. In countries
to management plans for AnGR. Monitoring where farmer groups, breed societies, or herd
programmes need to be carefully designed so or stud books exist, tracking registrations can
that they provide feedback to farmers, managers be a very effective means to monitor particular
and other stakeholders. Monitoring approaches breeds. There may also be opportunities to
need to be flexible, and activities by different combine monitoring activities with the tasks
players need to be well coordinated, as different of existing government offices. For example,
groups will monitor different parameters. wildlife biologists could assist in monitoring
For example, farmers may wish to monitor livestock populations as part of wildlife surveys.
production parameters; resource managers may Health officials could record livestock population
wish to monitor completion of breed inventories; numbers by breed when conducting food-
and administrators may wish to monitor the cost- processing inspections or delivering veterinary
effectiveness of various programmes. Monitoring services. All these options, however, have to be
is also necessary to evaluate progress in the treated with caution and potential biases need
implementation of action plans, and to identify to be considered. The value of the information
new priorities, issues and opportunities. obtainable on the basis of existing activities has to
be weighed against the additional information,
Monitoring can be an extremely expensive but also greater costs, associated with surveys
aspect of AnGR management. However, if countries specifically designed and conducted to monitor
are strategic in their approaches to monitoring, AnGR.
and take advantage of existing resources, it can
be cost effective. For managing genetic resources As a step towards the inclusion of breed-level
at high risk, data on current population size data in national livestock censuses, the next World
and geographic location are required. For such
populations, regular and simple quantification

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Programme for Census of Agriculture (produced • identify parentage and genetic relationships
by FAO every ten years to guide countries (e.g. DNA fingerprinting) within populations;
in conducting of their agricultural census)
(FAO, 2006) encourages countries to collect and • support marker assisted genetic
report livestock data at breed level. improvement of animal populations; and

3.3 Molecular genetic characterization • develop DNA repositories for research and
development (FAO, 2005).
Molecular genetic characterization explores
polymorphism in selected protein molecules • In populations with limited or no
and DNA markers in order to measure genetic information on pedigrees and population
variation at the population level. Because of the structure, molecular markers can also be used
low level of polymorphism observed in proteins, to estimate the effective population size (Ne).
and hence limited applicability in diversity studies,
DNA-level polymorphisms are the markers of In the absence of comprehensive breed
choice for molecular genetic characterization (see characterization data and documentation of
Section C). the origin of breeding populations, molecular
marker information may provide the most easily
The process of molecular genetic characterization obtainable estimates of genetic diversity within
comprises field sampling of biological material and between a given set of populations.
(often blood or hair root samples), laboratory
extraction of DNA from the samples, DNA 3.4 Information systems
storage, laboratory assaying (e.g. genotyping or
sequencing), data analysis, report writing, and Information systems or databases can serve a
maintenance of a molecular genetic information variety of different purposes, but collectively
database. Sampling for molecular analysis may be they contain important information for
combined with surveying and/or monitoring, as decision-making, research, training, planning
molecular information on its own cannot be used and evaluation of programmes, progress
for utilization and conservation decisions. reporting and public awareness. An information
system normally includes hardware, software
Characterization at the molecular genetic level (applications), organized data (information) and
is undertaken mainly to explore genetic diversity facilities for communication. It can be operated
within and between animal populations, and either manually, electronically using computers, or
to determine genetic relationships among such through a combination of both. The information
populations. More specifically, the results from may be on a single desktop machine, or a network
the laboratory work are used to: of computers. Alternatively, it may be on the
Internet, allowing external access to view or, in
• determine within and between-breed case of interactive dynamic systems, update the
diversity parameters; information.

• identify the geographical locations of The overall purpose of information systems is
particular populations, and/or of admixture to enable and support decision-making regarding
among populations of different genetic the present value and potential future uses of
origins; AnGR, by a range of stakeholders, including
policy-makers, development practitioners, farmers
• provide information on evolutionary and researchers. Thus, they need to incorporate
relationships (phylogenetic trees) and clarify essential decision-support tools to meet the
centres of origin and migration routes; needs of stakeholders at subnational, national,
subregional, regional and global levels. However,
• implement gene mapping activities, users operating at these different hierarchies or
including identification of carriers of known levels will each have different objectives, and
genes;

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STATE OF THE ART IN THE MANAGEMENT OF ANIMAL GENETIC RESOURCES

be interested in different aspects of the data State University’s Breeds of Livestock information
contained within the information system. For system provides brief summaries of breed origins,
instance, users operating at regional or global characteristics and uses. The content of these
levels will be more interested in the cross-border information systems is described in Box 69.
distribution of breeds, cross-border livestock
markets, transboundary disease risks, and Currently, the information resources have
germplasm exchange across borders. Conversely, facilities for simple searches by country or breed
more relevant issues for users at national and only. Ideally, they should have as much research
subnational (local) levels are breed population information as is available, and enable users to
size, herd/flock structures, production levels, make informed judgements about the value
and stressors associated with local environments. of each item of information. If researchers and
Linkages and information exchange between the decision-makers are to have the information
hierarchies, as well as with external information they require, the functionality of the existing
sources can add value to information systems. information systems will need to be greatly
Complementary databases may exchange increased, to allow extraction and customized
information through a system of data transfer, or analysis of various categories of information
can serve as “gateways” to each other through within and between data sources. The scope of
electronic links via the Internet. For instance, data acquisition also needs to be expanded so that
national and subnational AnGR databases could breed information can be linked to geographical
be linked to geophysical databases (climate, soils, information system (GIS)-based environment and
water or landscape). Functional linkages between production system mapping. This will allow poorly
these sets of data could lead to the generation documented adaptation traits such as disease
of animal disease risk maps, and information resistance to be predicted from past and current
on specific adaptations of particular breeds to breed distribution and use (Gibson et al., 2007).
stressful environments.
Information systems for AnGR have been
National databases of domestic animal diversity developed and administered as global public
are essential planning tools. They present goods, and have limited ability to attract
the current state of knowledge on the size, investment from the private sector or major
distribution, status, and utility value of AnGR. funding agencies. This explains the very limited
They allow access to information on planned and information that the systems contain compared to
ongoing management activities. Moreover, they that which is potentially possible and which would
facilitate the identification of gaps in existing be necessary for them to effectively achieve their
information. stated purposes. One possibility to circumvent
such limitations is to establish functionalities for
At present, a number of public-domain electronic interconnectivity and interoperability between
information systems for animal genetic diversity information systems. This has been achieved
are globally accessible and contain data from more with FABISnet (a distributed information system
than one country. Two of these – the Domestic for AnGR) which enables countries to set up
Animal Diversity Information System (DAD-IS) and national Web-based information systems that can
the European Farm Animal Biodiversity Information exchange core data with the higher levels of the
System (EFABIS) (previously EAAP–AGDB) – are network – regional systems (such as EFABIS) and
related to the FAO global information system for the global system (DAD-IS).
AnGR. The Domestic Animal Genetic Resources
Information System (DAGRIS), managed by ILRI is
a database of synthesized research information
from published and grey literature. Oklahoma

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Box 69 synchronization. Countries and regions are provided
Information systems at global level with tools to set up their own Web-based information
systems. Information content and interface can be
DAD-IS [http://www.fao.org/dad-is] translated to any local language. The appearance of
The Domestic Animal Diversity Information System the interface can be adapted to reflect local flavours.
(DAD-IS) developed by FAO is the first globally Outside the core data structure, countries and regions
accessible dynamic multilingual database of may further define data structures that specifically
AnGR. It was initiated as a key communication reflect their needs. These specificities would not
and information tool for implementing the Global be synchronized with the higher-level information
Strategy for the Management of AnGR, to assist systems. Poland set up the first national information
countries and country networks in their respective system under this new framework (http://efabis.
programmes (FAO, 1999). Apart from country-level izoo.krakow.pl), and defined additional structures to
breed information and images, DAD-IS provides a accommodate data on farmed fish and bees. NCs can
virtual library containing a large number of selected enter breed information, images, publications, links to
technical and policy documents, including tools and external Web sites, contact addresses and news into
guidelines for research related to AnGR. It offers Web- the system.
links to relevant electronic information resources. It
also has a facility for the exchange of views and for DAGRIS [http://dagris.ilri.cgiar.org/]
addressing specific information requests, by linking a The Domestic Animal Genetic Resources Information
range of stakeholders: farmers, scientists, researchers, System (DAGRIS) is developed and managed by the
development practitioners and policy-makers. International Livestock Research Institute (ILRI). It
DAD-IS provides a summary of national breed-level was initiated in 1999 as a tool to collate research
information on the origin, population, risk status, information available on global AnGR. In addition to
special characteristics, morphology and performance containing information, obtained from a synthesis
of breeds, as provided by FAO member countries. of the literature on the origin, distribution, diversity,
Currently, the database contains more than 14 000 characteristics, present uses and status of indigenous
national breed populations from 35 species and breeds. DAGRIS is unique in that it includes complete
181 countries. A key feature of DAD-IS is that it references and abstracts of published or unpublished
provides a country-secure information storage and scientific literature pertaining to the breeds in the
communication tool. Each country decides when and system. DAGRIS is designed to support research,
what breed data are released through their officially training, public awareness, genetic improvement and
designated contact person (the National Coordinator conservation. Version I of the database was released
(NC) for the Management of AnGR). See Tables 97 on the Web in April 2003, and is also available on
and 98 for a summary of information recorded, stored CD-ROM. Currently, the database contains over
and disseminated in the global breeds database 19 200 trait records on 154 cattle, 98 sheep, and 62
contained in DAD-IS. goat breeds of Africa, plus 129 chicken ecotypes/
breeds and 165 pig breeds of Africa and some Asian
DAD-IS:3 has been rebuilt based on the same countries. The breed information pages in DAGRIS
software and functionality as EFABIS (European provide a Web link to the page for the corresponding
Farm Animal Biodiversity Information System breed in the FAO’s DAD-IS system and vice versa.
– http://efabis-eaap.tzv.fal.de), and with a similar
interface. The software was developed within a • continues
European Union project in order to overcome the
problem of incompatibility between EAAP–AGDB
(an earlier European system) and DAD-IS. The new
system allows for the creation of a network of
distributed information systems with automatic data

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STATE OF THE ART IN THE MANAGEMENT OF ANIMAL GENETIC RESOURCES

Box 69 cont. 4 Conclusions
Information systems at global level
Adequate characterization of AnGR is a
The scope of DAGRIS is being expanded so that it prerequisite for successful management
will, in the near future, cover more species (turkeys, programmes and for informed decision-making
geese and ducks) and countries in Asia (Ayalew et al., in national livestock development. Tools
2003). The priority next-steps for DAGRIS are: developed in the field of characterization should
allow a strategic and coherent approach to
1. development of a new module to allow all users identification, description and documentation
to upload relevant research information into of breed populations. Interest in such an
the database so that database administrators approach is slowly emerging. Some aspects
can capture and collate otherwise unavailable of characterization are increasingly being
breed-level information; addressed. Molecular characterization has
received particular attention. However, there is
2. development of GIS linkages in the database to still a need for methods and tools to organize
allow georeferencing of as much of the breed- surveying and monitoring.
level information as possible; and
An important missing element in breed
3. development of a template for a country descriptions in many countries/regions, is a
module of DAGRIS to assist interested countries clear definition of the respective breeds to give
to further develop and customize the database. them unique identity, and a description of the
production environments to which they are
Breeds of Livestock – Oklahoma State University adapted. A basic structure for the definition of
[http://www.ansi.okstate.edu/breeds] production environments has been proposed,
The Department of Animal Science of Oklahoma State but needs to be reviewed and implemented.
University, in the United States of America, manages The existing breed-related information systems
this information resource which was established need to be further developed to allow easy
in 1995. It provides a brief description of breeds in information capture, processing, accessibility
terms of origin, distribution, typical features, uses, and interconnectivity.
and population status, along with photographs/
images and key references for breed information. It Ideally, tools and methods for decision-
presents a list of breeds from all over the world, with making on AnGR management, as well as early
options to sort by region. As of January 2006, the warning and response tools, would be based on
database displayed a total of 1 063 breeds including comprehensive information obtained using the
280 sheep, 262 cattle, 217 horse, 100 goat, 72 pig, methods described above. However, given that
8 donkey, 8 buffalo, 6 camel, 4 reindeer, 1 llama, immediate action is required, there is a need for
1 yak, 64 chicken, 10 duck, 7 turkey, 7 goose, 1 tools and methods that make effective use of
guinea fowl and 1 black swan breeds. It also provides incomplete information.
links to relevant information in its virtual livestock
library. The aim is to expand the scope of the system,
in terms of the number of breeds and the educational
and scientific information it contains, through
collaboration with individuals and universities from
around the world. The submission of information
(written material or images) on breeds not included
in the list, or additional information on those already
included, is welcome.

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References

Ayalew, W., Rege, J.E.O., Getahun, E., Tibbo, M. & FAO. 2005. Genetic characterization of livestock popula-
Mamo, Y. 2003. Delivering systematic information tions and its use in conservation decision making, by
on indigenous animal genetic resources – the devel- O. Hannotte & H. Jianlin. In J. Ruane & A. Sonnino,
opment and prospects of DAGRIS. In Proceedings eds. The role of biotechnology in exploring and
of the Deutscher Tropentag 2003, Technological protecting agricultural genetic resources, pp. 89–96.
and Institutional Innovations for Sustainable Rural Rome. (also available at www.fao.org/docrep/009/
Development, held 8–10 October 2003. Göttingen, a0399e/a0399e00.htm).
Germany. (also available at www.tropentag.de/2003/
abstracts/full/28.pdf). FAO. 2006. A system of integrated agricultural censuses
and surveys, volume 1, World Programme for the
Ayalew, W., van Dorland, A. & Rowlands, J. 2004. Census of Agriculture 2010. Statistical Development
Design, execution and analysis of the livestock breed Series No. 11. (also available at www.fao.org/es/ess/
survey in Oromia Regional State, Ethiopia. Addis census/default.asp).
Ababa and Nairobi. OADB (Oromia Agricultural
Development Bureau) and ILRI (International FAO/UNEP. 1998. Primary guidelines for development of
Livestock Research Institute). national farm animal genetic resources management
plans. Rome.
DAGRIS. 2004. Domestic Animal Genetic Resources
Information System (DAGRIS). J.E.O. Rege, FAO/UNEP. 2000. World watch list for domestic animal
W. Ayalew & E. Getahun, eds. Addis Ababa. diversity, 3rd edition. Edited by B.D. Scherf. Rome.
International Livestock Research Institute.
Gibson, J.P., Ayalew, W. & Hanotte, O. 2007.
FAO. 1984. Animal genetic resource conservation by Measures of diversity as inputs for decisions in con-
management, databanks and training. Animal servation of livestock genetic resources. In D.I. Jarvis,
Production and Health Paper No. 44/1. Rome. C. Padoch & D. Cooper, eds. Managing biodiversity
in agroecosystems. New York, USA. Columbia
FAO. 1986a. Animal genetic resources data banks - 1. University Press.
Computer systems study for regional data banks.
Animal Production and Health Paper No. 59, Oklahoma State University. 2005. Breeds of livestock.
Volume 1. Rome. Stillwater, Oklahoma, USA. Department of Animal
Science, Oklahoma State University. (available at
FAO. 1986b. Animal genetic resources data banks - 2. http://www.ansi.okstate.edu/breeds/).
Descriptor lists for cattle, buffalo, pigs, sheep and
goats. Animal Production and Health Paper No. 59, Rege, J.E.O. 1992. Background to ILCA’s animal genetic
Volume 2. Rome. resources characterization project, objectives and
agenda for the research planning workshop. In J.E.O.
FAO. 1986c. Animal genetic resources data banks - 3. Rege & M.E. Lipner, eds. Animal genetic resources:
Descriptor lists for poultry. Animal Production and their characterization, conservation and utilization.
Health Paper No. 59, Volume 3. Rome. Research planning workshop, ILCA, Addis Ababa,
Ethiopia, 19-21 February, 1992, pp. 55–59. Addis
FAO. 1992. The management of global animal genetic Ababa. International Livestock Centre for Africa.
resources. Proceedings of an Expert Consultation,
Rome, Italy, April 1992. Edited by J. Hodges. Animal Rowlands, J., Nagda, S., Rege, E., Mhlanga, F.,
Production and Health Paper No.104. Rome. Dzama, K., Gandiya, F., Hamudikwanda, H.,
Makuza, S., Moyo, S., Matika, O., Nangomasha,
FAO. 1998. Report: Working group on production E. & Sikosana, J. 2003. The design, execution and
environment descriptors for farm animal genetic analysis of livestock breed surveys - a case study in
resources. Report of a Working Group, held in Zimbabwe. A report to FAO. Nairobi. International
Armidale, Australia, 19 – 21 January 1998. Rome. Livestock Research Institute.

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Section C

Molecular markers – a tool for
exploring genetic diversity

1 Introduction

DNA markers are useful in both basic (e.g. selection, paternity testing and food traceability).
phylogenetic analysis and search for useful This section focuses mainly on their application
genes) and applied research (e.g. marker assisted in characterization of AnGR diversity, and in the

Box 70 polypeptide (an entire protein or one of the chains
DNA, RNA and protein of a protein complex). The mRNA molecule is read
or translated three nucleotides (a codon) at a time.
DNA (deoxyribonucleic acid) is organized in pairs of Complementarity between the mRNA codon and the
chromosomes, each inherited from one of the parents. anti-codon of a transfer RNA (tRNA) molecule which
Each gene in an individual, therefore, has two copies, carries the corresponding amino acid to the ribosome
called alleles, one on each chromosome of a pair. In ensures that the newly formed polypeptide contains
mammals, genes are scattered along chromosomes, the specific sequence of amino acids required.
separated by long, mainly repetitive, DNA sequences.
Genes are formed by coding sequences (exons) Not all genes are translated into proteins; some
separated by introns. The latter carry no protein- express their function as RNA molecules (such as the
coding information, but sometimes play a role in the rRNA and tRNA involved in translation). Recently,
regulation of gene expression. The instruction encoded new roles of RNA in the process of mRNA editing
by genes is put into action through two processes. and in the regulation of gene expression have been
The first is transcription (copy) of genetic information discovered (Storz et al., 2005; Aravin and Tuschl, 2005;
into another type of nucleic acid, RNA (ribonucleic Wienholds and Plasterk 2005). Indeed, non-coding
acid). Both exons and introns are transcribed into RNAs appear to be key players in various regulatory
a primary messenger RNA (mRNA) molecule. This processes (Bertone et al., 2004; Clop et al., 2006).
molecule is then edited, a process which involves Thus, three types of molecules are available for
removing the introns, joining the exons together, and investigating genetic characteristics at cellular, tissue
adding unique features to each end of the mRNA. A and whole organism levels: the DNA which contains
mature mRNA molecule is, thereby, created, which is the encoded instruction; the RNA which transfers the
then transported to structures known as ribosomes instructions to the cell “factory”; and the proteins
located in the cell cytoplasm. Ribosomes are made of which are built according to the instructions, and
ribosomal RNA (rRNA) and proteins, and provide sites make functioning cells and organisms.
for the second process – translation of the genetic
information, previously copied to the mRNA, into a

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PART 4

search for functional variants of relevant genes. expressing proteins in specific tissues at different
It is important to note that RNA and proteins development or physiological stages.
also contain key information, and therefore
deserve parallel study; their role in the search for Although analysis of single types of biomolecules
functional variants is also explored below. has proven extremely useful in understanding
biological phenomena, the parallel large-scale
Diversity among organisms is a result of investigation of DNA, RNA and proteins opens
variations in DNA sequences and of environmental up new perspectives in the interpretation and
effects. Genetic variation is substantial, and modelling of the complexity of living organisms.
each individual of a species, with the exception New scientific disciplines with the suffix “–omics”
of monozygotic twins, possesses a unique DNA are coming into existence. In these fields, recent
sequence. DNA variations are mutations resulting advances in the preparation, identification and
from substitution of single nucleotides (single sequencing of DNA, RNA and proteins, and in
nucleotide polymorphisms – SNPs), insertion or large-scale data storage and analysis, are bringing
deletion of DNA fragments of various lengths about a revolution in our understanding. A global,
(from a single to several thousand nucleotides), integrated view of an entire set of biological
or duplication or inversion of DNA fragments. molecules involved in complex biological processes
DNA variations are classified as “neutral” when
they cause no change in metabolic or phenotypic Box 72
traits, and hence are not subjected to positive, Recent developments in molecular
negative, or balancing selection; otherwise, they biology
are referred to as “functional”. Mutations in key
nucleotides of a coding sequence may change the Current revolutionary developments in molecular
amino acid composition of a protein, and lead to biological research relevant to livestock breeding
new functional variants. Such variants may have and genetic diversity conservation include:
an increased or decreased metabolic efficiency
compared to the original “wild type”, may lose 1. establishment of the entire genome sequence
their functionality completely, or even gain a of the most important livestock species;
novel function. Mutations in regulatory regions 2. development of technology to measure
may affect levels and patterns of gene expression; polymorphisms at loci spread all over the genome
for example, turning genes on/off or under/over- (e.g. methods to detect SNPs); and
3. development of microarray technology to
Box 71 measure gene transcription at a large scale.
The new “–omics” scientific disciplines Information obtained through the sequencing
of the entire genome (achieved for chickens and
Genomics charts genes and the genetic variations almost complete for pigs and cattle), integrated
among individuals and groups. It provides an with SNP technology, will speed up the search
insight into the translation of genetic information for genes. Quantitative trait loci (QTL) mapping
to metabolic functions and phenotypic traits. It to identify chromosome regions influencing a
unveils biological processes and their interactions target trait, the presence of candidate genes
with environmental factors. Genomics involves located in the same region, and investigation of
the combination of a set of high-throughput their patterns of expression (e.g. by microarray
technologies, such as proteomics and metabolomics, and proteomic analyses) and their function across
with the bioinformatic techniques that enable species, will come together to identify key genes
the processing, analysis and integration of large and to unravel the complexity of physiological
amounts of data. regulation for target traits.

See below for further discussion of these developments.

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is emerging. Structural genomics, transcriptomics of functional variations. Molecular techniques
and proteomics are followed by metabolomics, have also proved useful in the investigation
and interactomics among others, and at a still of the origin and domestication of livestock
higher level of complexity, systems biology (Hood species, and their subsequent migrations, as
et al., 2004; Box 71). well as providing information on evolutionary
relationships (phylogenetic trees), and
Investigation of biological complexity is a new identifying geographical areas of admixture
frontier which requires high-throughput molecular among populations of different genetic origins.
technology, high computer speed and memory, Subchapter 3.1 presents an outline of molecular
new approaches to data analysis, and integration techniques for the assessment of genetic diversity
of interdisciplinary expertise (Box 72). within and between breeds.

2 The roles of molecular Second role. Effective population size (Ne) is
technologies in characterization an index that estimates the effective number
of animals in a population that reproduce and
Information on genetic diversity is essential in contribute genes to the next generation. Ne is
optimizing both conservation and utilization closely linked to the level of inbreeding and
strategies for AnGR. As resources for conservation genetic drift in a population, and therefore is
are limited, prioritization is often necessary. New a critical indicator for assessing the degree of
molecular tools hold the promise of allowing the endangerment of populations (see Sections
identification of genes involved in a number of A and F). Traditional approaches to obtaining
traits,includingadaptivetraits,andpolymorphisms reliable estimates of Ne for breeding populations
causing functional genetic variation (QTN are based on pedigree data or censuses. The
– Quantitative Trait Nucleotides). However, we necessary data on variability of reproductive
do not have sufficient knowledge to prioritize success and generation intervals are often not
conservation choices on the basis of functional reliably available for populations in developing
molecular diversity, and alternative measures countries. Molecular approaches may, therefore,
are still needed. Phenotypic characterization be a promising alternative (see subchapter 3.2 for
provides a crude estimate of the average of the further details).
functional variants of genes carried by a given
individual or population. However, the majority Third role. A top priority in the management
of phenotypes of the majority of livestock species of AnGR is the conservation of breeds that have
are not recorded. unique traits. Among these, the ability to live and
produce in challenging conditions, and to resist
First role. In the absence of reliable phenotype infectious diseases are of major importance,
and QTN data, or to complement the existing particularly for developing countries. Complex
data, the most rapid and cost-effective measures traits, such as adaptation and disease resistance,
of genetic diversity are obtained from the assay are not visible or easily measurable. They can be
of polymorphisms using anonymous molecular investigated in experiments in which the animals
genetic markers. Anonymous markers are likely are submitted to the specific environmental
to provide indirect information on functional conditions or are infected with the relevant
genes for important traits, assuming that agent. However, such experiments are difficult
unique populations that have had a particular and expensive to perform, and raise concerns
evolutionary history at the neutral markers (e.g. about animal welfare. This is the reason why
because of ancient isolation or independent researchers are extremely interested in identifying
domestication) are likely to carry unique variants genes controlling complex traits. Such genes can
be sought by a number of different approaches.

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Tools being developed to target functional Box 73
variation are described in subchapter 3.3. Extraction and multiplication of DNA
and RNA
3 Overview of molecular
techniques The first step in DNA, RNA and protein analysis is
extraction and purification from biological specimens.
This section describes the most important Several protocols and commercial kits are available.
molecular techniques currently being utilized and The strategies applied depend on the source material
developed for the assessment of genetic diversity, and the target molecule. For example, DNA extraction
and for targeting functional variation. Box 73 from whole blood or white cells is relatively easy,
describes how DNA and RNA are extracted from while its extraction from processed food is rather
biological material and prepared for analysis. The difficult. RNA extraction from pancreatic tissue
attributes of commonly used molecular markers is difficult because of very rapid post-mortem
are outlined in Box 74, and sampling (a very degradation in this organ. Purity of DNA, RNA and
important aspect of molecular studies) is discussed proteins is often a key neglected factor in obtaining
in Box 75. reliable results.

Protein polymorphisms were the first markers After isolating DNA (or RNA) from cells, the next
used for genetic studies in livestock. However, the step is to obtain thousands or millions of copies of
number of polymorphic loci that can be assayed, a particular gene or piece of DNA. DNA fragment
and the level of polymorphisms observed at multiplication can be delegated to micro-organisms,
the loci are often low, which greatly limits their typically E. coli, or accomplished in vitro using a
application in genetic diversity studies. With polymerase chain reaction (PCR). This technique,
the development of new technologies, DNA which won the Nobel Prize for its inventor, Cary
polymorphisms have become the markers of Mullis, exponentially amplifies any DNA segment
choice for molecular-based surveys of genetic of known sequence. The key component in a PCR
variation (Box 74). reaction is the DNA polymerase isolated from
Thermus aquaticus, a micro-organism adapted
3.1 Techniques using DNA markers to to live and multiply at very high temperature.
assess genetic diversity This thermostable Taq- (after Thermus aquaticus)
polymerase permits chain replication in cycles
Nuclear DNA markers and produces a geometric growth in the number
A number of markers are now available to detect of copies of the target DNA. A PCR cycle includes
polymorphisms in nuclear DNA. In genetic diversity three steps: i) DNA denaturation at 90–95 oC to
studies, the most frequently used markers are separate the DNA into two single strands to serve
microsatellites. as a template; ii) annealing of a pair of short single-
strand oligonucleotides (primers) complementary
Microsatellites to the target regions flanking the fragment of
Currently, microsatellites (Box 74) are the interest, at 45–65 oC; iii) extension or elongation of
most popular markers in livestock genetic newly synthesized DNA strands led by primers and
characterization studies (Sunnucks, 2001). Their facilitated by the Taq-polymerase, at 72 oC. This cycle
high mutation rate and codominant nature can be repeated, normally 25 to 45 times, to enable
permit the estimation of within and between- amplification of enough amplicons (a fragment of a
breed genetic diversity, and genetic admixture gene or DNA synthesized using PCR) to be detected.
among breeds even if they are closely related.

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Box 74 recommendations for sets of microsatellite loci to be
Commonly used DNA markers used for diversity studies for major livestock species,
which were developed by the ISAG–FAO Advisory
Restriction fragment length polymorphisms (RFLPs) Group on Animal Genetic Diversity (see DAD-IS library
are identified using restriction enzymes that cleave http://www.fao.org/dad-is/).
the DNA only at precise “restriction sites” (e.g.
EcoRI cleaves at the site defined by the palindrome Minisatellites share the same characteristics as
sequence GAATTC). At present, the most frequent use microsatellites, but the repeats are ten to a few
of RFLPs is downstream of PCR (PCR–RFLP), to detect hundreds bp long. Micro and minisatellites are
alleles that differ in sequence at a given restriction also known as VNTRs (Variable Number of Tandem
site. A gene fragment is first amplified using PCR, and Repeats) polymorphisms.
then exposed to a specific restriction enzyme that
cleaves only one of the allelic forms. The digested Amplified fragment length polymorphisms
amplicons are generally resolved by electrophoresis. (AFLPs) are a DNA fingerprinting technique which
detects DNA restriction fragments by means of PCR
Microsatellites or SSR (Simple Sequence Repeats) amplification.
or STR (Simple Tandem Repeats) consist of a stretch
of DNA a few nucleotides long – 2 to 6 base pairs STS (Sequence Tagged Site) are DNA sequences
(bp) – repeated several times in tandem (e.g. that occur only once in a genome, in a known
CACACACACACACACA). They are spread over a position. They needn’t be polymorphic and are used to
eukaryote genome. Microsatellites are of relatively build physical maps.
small size, and can, therefore, be easily amplified
using PCR from DNA extracted from a variety of SNPs are variations at single nucleotides which do
sources including blood, hair, skin or even faeces. not change the overall length of the DNA sequence in
Polymorphisms can be visualized on a sequencing the region. SNPs occur throughout the genome. They
gel, and the availability of automatic DNA sequencers are highly abundant and are present at one SNP in
allows high-throughput analysis of a large number of every 1000 bp in the human genome (Sachinandam
samples (Goldstein and Schlötterer, 1999; Jarne and et al., 2001). Most SNPs are located in non-coding
Lagoda, 1996). Microsatellites are hypervariable; they regions, and have no direct impact on the phenotype
often show tens of alleles at a locus that differ from of an individual. However, some introduce mutations
each other in the numbers of the repeats. They are in expressed sequences or regions influencing gene
still the markers of choice for diversity studies as well expression (promoters, enhancers), and may induce
as for parentage analysis and Quantitative Trait Loci changes in protein structure or regulation. These
(QTL) mapping, although this might be challenged SNPs have the potential to detect functional genetic
in the near future with the development of cheap variation.
methods for the assay of SNPs. FAO has published

Some controversy has surrounded the choice The mean number of alleles (MNA) per
of a mutation model – infinite allele or step- population, and observed and expected
wise mutation model (Goldstein et al, 1995) – for heterozygosity (Ho and He), are the most common
microsatellite data analysis. However, simulation parameters for assessing within-breed diversity.
studies have shown that the infinite allele mutation The simplest parameters for assessing diversity
model is generally valid for assessment of within- among breeds are the genetic differentiation
species diversity (Takezaki and Nei, 1996). or fixation indices. Several estimators have been

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Box 75 be calculated for the FST values between pairs
Sampling genetic material of populations (Weir and Cockerham, 1984)
to test the null hypothesis of a lack of genetic
Sample collection is the first and the most important differentiation between populations and,
step in any diversity study. Ideally, samples should therefore, the partitioning of genetic diversity
be unrelated and representative of the populations (e.g. Mburu et al., 2003). Hierarchical analysis
under investigation. Generally, the sampling of of molecular variance (AMOVA) (Excoffier
30 to 50 well-chosen individuals per breed is et al., 1992) can be performed to assess the
considered sufficient to provide a first clue as to distribution of diversity within and among groups
breed distinctiveness and within-breed diversity, if a of breeds.
sufficient number of independent markers is assayed
(e.g. 20–30 microsatellites; Nei and Roychoudhury, Microsatellite data are also commonly used to
1974; Nei, 1978). However, the actual numbers assess genetic relationships between populations
required may vary from case to case, and may be and individuals through the estimation of genetic
even lower in the case of a highly inbred local distances (e.g. Beja-Pereira et al., 2003; Ibeagha-
population, and higher in a widely spread population Awemu et al., 2004; Joshi et al., 2004; Sodhi et
divided into different ecotypes. al., 2005; Tapio et al., 2005). The most commonly
used measure of genetic distances is Nei’s standard
The choice of unrelated samples is quite genetic distance (DS) (Nei, 1972). However, for
straightforward in a well-defined breed, where it closely related populations, where genetic drift
can be based on the herd book or pedigree record. is the main factor of genetic differentiation, as
Conversely, it can be rather difficult in a semi-feral is often the case in livestock breeds, particularly
population for which no written record is available. in the developing world, the modified Cavalli-
In this case, the use of a geographic criterion is highly Sforza distance (DA) is recommended (Nei et
recommendable, i.e. to collect a single or very few al., 1983). Genetic relationship between breeds
(unrelated) animals per flock from a number of flocks is often visualized through the reconstruction of
spread over a wide geographic area. The record of a phylogeny, most often using the neighbour-
geographical coordinates, and photo-documentation joining (N-J) method (Saitou and Nei, 1987).
of sampling sites, animals and flocks is extremely However, a major drawback of phylogenetic tree
valuable – to check for cross-breeding in the case reconstruction is that the evolution of lineages
of unexpected outliers, or for identifying interesting is assumed to be non-reticulate, i.e. lineages can
geographic patterns of genetic diversity. A well-chosen diverge, but can never result from crosses between
set of samples is a long-lasting valuable resource, lineages. This assumption will rarely hold for
which can be used to produce meaningful results even livestock, where new breeds often originate from
with poor technology. Conversely, a biased sample cross-breeding between two or more ancestral
will produce results that are distorted or difficult to breeds. The visualization of the evolution of
understand even if the most advanced molecular tools breeds provided by phylogenetic reconstruction
are applied. must, therefore, be interpreted cautiously.

proposed (e.g. FST and GST), the most widely Multivariate analysis, and more recently
used being FST (Weir and Basten, 1990), which Bayesian clustering approaches, have been
measure the degree of genetic differentiation suggested for admixture analysis of microsatellite
of subpopulations through calculation of the data from different populations (Pritchard et
standardized variances in allele frequencies al., 2000). Probably the most comprehensive study
among populations. Statistical significance can of this type in livestock is a continent-wide study
of African cattle (Hanotte et al., 2002), which
reveals the genetic signatures of the origins,

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secondary movements, and differentiation of (2006a) investigated, respectively, chicken and
African cattle pastoralism. pig diversity throughout Europe; Hanotte et al.
(2002) obtained data on cattle at the scale of
Molecular genetic data, in conjunction with, almost the entire African continent; Tapio et al.
and complemented by, other sources such as (2005) assessed sheep diversity at a large regional
archaeological evidence and written records, scale in northern European countries; and Cañon
provide useful information on the origins and et al. (2006) studied goat diversity in Europe and
subsequent movements and developments of the Near and Middle East. However, for most
genetic diversity in livestock species. Mapping species, a comprehensive review is still lacking.
the origin of current genetic diversity potentially Ongoing close coordination between large-scale
allows inferences to be made about where projects promises the delivery of a global estimate
functional genetic variation might be found of genetic diversity in the near future for some
within a species for which only limited data on species such as sheep and goats. In the meantime,
phenotypic variation exist. new methods of data analysis are being developed
to permit the meta-analysis of datasets that have
Combined analysis of microsatellite data only a few breeds and no, or only a few, markers
obtained in separate studies is highly desirable, in common (Freeman et al., 2006). This global
but has rarely been possible. This is because most perspective on livestock diversity will be extremely
population genetic studies using DNA markers valuable to reconstruct the origin and history of
are limited to small numbers of breeds, often domestic animal populations and, indirectly, of
from a single country (Baumung et al., 2004). human populations. It will also highlight regional
Often, different subsets of the FAO-recommended and local hotspots of genetic diversity which may
markers are used, and no standard samples are be targeted by conservation efforts.
genotyped across projects. The application of
different microsatellite genotyping systems causes SNPs
variation between studies in the estimated size SNPs (Box 74) are used as an alternative to
of alleles at the same loci. To promote the use microsatellites in genetic diversity studies. Several
of common markers, FAO is now proposing an technologies are available to detect and type
updated, ranked list of microsatellite loci for the SNP markers (see Syvänen, 2001, for a review).
major livestock species3. FAO recommends the Being biallelic markers, SNPs have rather low
use of the markers in the order of ranking, to information content, and larger numbers have to
maximize the number of markers overlapping be used to reach the level of information obtained
among independent investigations. For some from a standard panel of 30 microsatellite loci.
species, DNA from standard animals is available. However, ever-evolving molecular technologies
For example, aliquots of sheep and goat standard are increasing automation and decreasing the
DNA used in the European Union (EU) Econogene cost of SNP typing. This is likely, in the near
project have been distributed to other large-scale future, to permit the parallel analysis of a large
projects in Asia and Africa, and can be requested number of markers at a lower cost. With this
through the Econogene Website (http://www. perspective, large-scale projects are ongoing in
econogene.eu). several livestock species to identify millions (e.g.
Wong et al., 2004) and validate several thousands
There are only a few examples of large-scale of SNPs, and identify haplotype blocks in the
analyses of the genetic diversity of livestock genome. Like sequence information, SNPs permit
species. Hillel et al. (2003) and SanCristobal et al. a direct comparison and joint analysis of different
experiments.
3 Lists and guidelines can be found in the DAD-IS library at
http://www.fao.org/dad-is.

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SNPs seem to be appealing markers to apply in Mitochondrial DNA markers
the future for genetic diversity studies because they Mitochondrial DNA (mtDNA) polymorphisms
can easily be used in assessing either functional or have been extensively used in phylogenetic and
neutral variation. However, the preliminary phase genetic diversity analyses. The haploid mtDNA,
of SNP discovery or SNP selection from databases carried by the mitochondria in the cell cytoplasm,
is critical. SNPs can be generated through various has a maternal mode of inheritance (individuals
experimental protocols, such as sequencing, inherit the mtDNA from their dams and not from
single-stranded conformational polymorphism their sires) and a high mutation rate; it does not
(SSCP) or denaturing high-performance liquid recombine. These characteristics enable biologists
chromatography (DHPLC), or in silico, aligning to reconstruct evolutionary relationships between
and comparing multiple sequences of the same and within species by assessing the patterns of
region from public genome and expressed mutations in mtDNA. MtDNA markers may also
sequence (EST) databases. When data have not provide a rapid way of detecting hybridization
been obtained randomly, standard estimators between livestock species or subspecies (e.g.
of population genetic parameters cannot be Nijman et al., 2003).
applied. A frequent example is when SNPs
initially identified in a small sample (panel) of The polymorphisms in the sequence of the
individuals are then typed in a larger sample of hypervariable region of the D-loop or control
chromosomes. By preferentially sampling SNPs at region of mtDNA have contributed greatly to the
intermediate frequencies, such a protocol will bias identification of the wild progenitors of domestic
the distribution of allelic frequencies compared species, the establishment of geographic patterns
to the expectation for a random sample. SNPs do of genetic diversity, and the understanding of
hold promise for future application in population livestock domestication (see Bruford et al., 2003,
genetic analyses; however, statistical methods for a review). For example, the Middle Eastern
that can explicitly take into account each method origin of modern European cattle was recently
of SNP discovery have to be developed (Nielsen demonstrated by Troy et al. (2001). The study
and Signorovitch, 2003; Clark et al., 2005). identified four maternal lineages in Bos taurus
and also demonstrated the loss of bovine genetic
AFLPs variability during the human Neolithic migration
AFLPs are dominant biallelic markers (Vos et out of the Fertile Crescent. In the same way,
al., 1995). Variations at many loci can be arrayed multiple maternal origins with three mtDNA
simultaneously to detect single nucleotide lineages were highlighted in goats (Luikart et
variations of unknown genomic regions, in which al., 2001), with Asia and the Fertile Crescent as
a given mutation may be frequently present possible centres of origin. Recently, a third mtDNA
in undetermined functional genes. However, lineage was discovered in native Chinese sheep
a disadvantage is that they show a dominant (Guo et al., 2005), a fourth in native Chinese goats
mode of inheritance; this reduces their power (Chen et al., 2005), and a fifth in Chinese cattle
in population genetic analyses of within-breed (Lai et al., 2006). In Asian chickens, nine different
diversity and inbreeding. Nevertheless, AFLP mtDNA clades have been found (Liu et al., 2006),
profiles are highly informative in assessing the suggesting multiple origins in South and Southeast
relationship between breeds (Ajmone-Marsan Asia. All these results indicate that our current
et al., 2002; Negrini et al., 2006; De Marchi et knowledge of livestock domestication and genetic
al., 2006; SanCristobal et al., 2006b) and related diversity remains far from complete. For further
species (Buntjer et al., 2002). discussion of the origins of domestic livestock
species see Part 1 – Section A.

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3.2 Using markers to estimate Mapping exercises are generally accomplished
effective population size following the co-segregation of polymorphic
markers in structured experimental populations
Hill (1981) suggested using gametic phase (e.g. F2 or backcross) or existing populations
disequilibrium of DNA polymorphisms to estimate
effective population size (Ne). This estimation Box 76
can be based on genotypes for linked markers QTL mapping
(microsatellites or SNPs). The expected correlation
of allele frequencies at linked loci is a function of If a QTL for a target trait exists, the plus- and minus-
Ne and the recombination rate. Ne can, therefore, variant allele of the unknown responsible gene (Q and
be estimated from the observed disequilibrium. q) will co-segregate with the alleles at a nearby M1
Hayes et al. (2003) suggested a similar approach marker (M1 and m1) that we are able to genotype
based on chromosome segment homozygosity, in the laboratory. Let us hypothesize that M1 co-
which, in addition, has the potential to estimate segregates with Q and m1 with q, that is M1 and Q
Ne for earlier generations, and therefore allows are nearby on a same chromosome and m1 and q on
a judgement of whether an existing population the homologous chromosome (M1Q and m1q).
was of increasing or decreasing size in the past.
The study demonstrated, with example data sets, Let us also assume that an F2 population derived
that the Holstein-Friesian cattle breed underwent by the mating of heterozygous F1 individuals is
a substantial reduction of Ne in the past, while genotyped. Following the genotyping, F2 progenies are
the effective population size of the human grouped on the base of their marker genotype (M1M1
population is increasing, which is in agreement and m1m1; M2M2 and m2m2; ... MnMn and mnmn),
with both census and pedigree studies. and afterwards the average phenotype of the groups
is compared. If no QTL is linked to a given marker (e.g.
3.3 Molecular tools for targeting M2), then no significant difference will be detected
functional variation between the average phenotypic value of the M2M2
and m2m2 progenies for the target trait. Conversely,
Approaches based on map position: when progenies are grouped by their genotype at the
quantitative trait loci (QTL) mapping marker M1, then the group M1M1 will mostly be QQ
Genetic markers behave as Mendelian traits; in at the QTL, and the group m1m1 will mostly be qq. In
other words, they follow the laws of segregation this case, a significant difference is observed between
and independent assortment first described by progeny averages, and therefore the presence of a
Mendel. Two genes that are located on the same QTL is detected. In species, such as poultry and pigs,
chromosome are physically linked and tend to be where lines and breeds are commonly interbred
inherited together. During meiosis, recombination commercially, this exercise can be accomplished in
between homologous chromosomes may break experimental populations (F2, BC) while in ruminants
this linkage. The frequency of recombination two (daughter design – DD) or three (grand-daughter
between two genes located on the same design – GDD) generation pedigrees are generally
chromosome depends of the distance between used. In DD the segregation of markers heterozygous
them. Recombination rate between markers in a sire (generation I) is followed in the daughters
is, therefore, an indication of their degree of (generation II) on which phenotypic data are collected.
linkage: the lower the recombination rate, the In GDD, the segregation of markers heterozygous in
closer the markers. The construction of genetic a grand-sire (generation I) are followed in his half-sib
maps exploits this characteristic to infer the sons (generation II), whose phenotype is inferred from
likely order of markers and the distance between those of the grand-daughters (generation III).
them.

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under selection programmes (families of full regions of a model organism for which complete
siblings or half siblings). Medium to high density genome information is available.
genetic maps of a few hundred to a few thousand
markers are available for most livestock species. Occasionally, key information on gene function
arrives from an unexpected source. This was the
To identify a QTL for a given trait, a family case with the myostatin gene, the function of
segregating for the trait is genotyped with which was first discovered in mice and then found
a set of mapped molecular markers evenly to be located in cattle in the chromosomal region
spread over the genome (Box 76). A number of where the double-muscling gene had previously
statistical methods exist to infer the presence of a been mapped (McPherron and Lee, 1997).
significant QTL at a given marker interval, but all
rely on the fact that families possess a high level It is clear that identifying the responsible
of linkage disequilibrium, i.e. large segments gene (quantitative trait genes – QTG) and the
of chromosomes are transmitted without functional mutation (QTN) of a complex trait is
recombination from parents to progeny. still a substantial task, and several approaches
are needed to decrease the number of positional
The result of a QTL mapping experiment is the candidate genes. Information on gene function
identification of a chromosome region, often is fundamental in this respect. However, we are
spanning half of a chromosome, in which a still ignorant about the possible function(s) of the
significant effect is detected for the target trait. majority of genes identified by genome and cDNA
Modern research is actively using mapping to (complementary DNA) sequencing. This is why the
identify QTL influencing adaptive traits. Examples investigation of patterns of gene expression may
of such traits include, in chickens, increased provide useful information, in combination with
resistance to Salmonella colonization and the positional approach previously described, to
excretion (Tilquin et al., 2005), and susceptibility identify candidate genes for complex traits. This
to develop pulmonary hypertension syndrome combined approach is referred to as genetical
(Rabie et al., 2005); and in cattle, trypanotolerance genomics (Haley and de Koning, 2006). New
(Hanotte et al., 2002). advances in the investigation of patterns of gene
expression are described in the next section.
The QTL mapping phase is generally followed by
the refinement of the map position of the QTL (QTL Alternative approaches are presently being
fine mapping). To accomplish this task, additional investigated to detect adaptive genes using
markers, and above all additional recombination genetic markers (Box 77). They are now at the
events in the target area, are analysed. A clever experimental stage, and only further research will
approach has recently been designed and applied permit an evaluation of their efficacy.
to the fine mapping of a chromosome region
on BTA14 carrying a significant QTL for milk fat The ultimate goal of QTL mapping is to identify
percentage and other traits (Farnir et al., 2002). the QTG, and eventually the QTN. Although only
This approach exploits historical recombination in a few examples exist to date in livestock, these
past generations to restrict the map position to are the kind of mutations that could have a
a relatively small 3.8 cM (centimorgan) region, a direct impact on marker assisted breeding and on
size that has permitted the positional cloning of conservation decision-making. Conservation models
the gene (DGAT1) (Grisart et al., 2002). considering functional traits and mutation need to
be developed, as an increasing number of QTG and
Following fine mapping, the genes determining QTN will be uncovered in the near future.
the performance trait can be sought among the
genes that are located in the regions identified. Investigating patterns of gene expression
Candidate genes may be sought in the same species In the past, the expression of specific traits,
(e.g. when a rich EST map is available or when such as adaptation and resistance, could only be
the genome is fully sequenced) or in orthologous measured at the phenotypic level. Nowadays, the

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Box 77 particular, genes involved in adaptation to extreme
The population genomics approach environments, disease resistance, etc. Many of
these traits, which are of great importance to the
An alternative approach to the identification of sustainability of animal breeding, are difficult or
genome regions carrying relevant genes has recently impossible to investigate by classic QTL mapping
been proposed. It consists of the detection of or association study approaches. The potential of
“selection signatures” via a “population genomics” population genomics has recently been investigated
approach (Black et al., 2001; Luikart et al., 2003). from a theoretical point of view (Beaumont and
Three main principles of the population genomics Balding, 2004; Bamshad and Wooding, 2003), and
approach to QTL mapping are that: through experimental work with different types of
markers in natural populations (AFLPs: Campbell
1. neutral loci across the genome will be similarly and Bernatchez, 2004; microsatellites: Kayser et al.,
affected by genetic drift, demography, and 2003; SNPs: Akey et al., 2002). The approach has
evolutionary history of populations; recently been applied within the Econogene project
(http://lasig.epfl.ch/projets/econogene). In preliminary
2. loci under selection will often behave differently analyses, three SNPs in MYH1 (myosin 1), MEG3
and, therefore, reveal “outlier” patterns of (callypige), and CTSB (cathepsin B) genes in sheep
variation, loss of diversity (increase of diversity have shown significant outlier behaviour (Pariset
if the loci were under a balanced selection), et al., 2006).
linkage disequilibrium, and increased/decreased
Gst/Fst indices; and Within the same project, a novel approach based
on Spatial Analysis Method (SAM) has been designed
3. through hitchhiking effects, selection will also to detect signatures of natural selection within the
influence linked markers, allowing the detection genome of domestic and wild animals (Joost, 2006).
of a “selection signature” (outlier effects), Preliminary results obtained with this method are in
which can often be detected by genotyping a agreement with those obtained by the application
large number of markers along a chromosome of theoretical models in population genetics, such as
and identifying clusters of outliers. This those developed by Beaumont and Balding (2004).
approach utilizes phenotypic data at the breed SAM goes a step further compared to classical
level (or subpopulations within a breed), rather approaches, as it is designed to identify environmental
than at the individual level, and thereby nicely parameters associated with selected markers.
complements classical QTL mapping approaches
within pedigrees.

The population genomics approach can also
identify genes subjected to strong selection
pressure and eventually fixed within breeds, and in

transcriptome (the ensemble of all transcripts in genes expressed in a tissue at a given time. Thus,
a cell or tissue), and the proteome (the ensemble the techniques contribute to the decoding of
of all proteins) can be directly investigated by the networks that are likely to underlie many
high-throughput techniques, such as differential complex traits.
display (DD) (Liang and Pardee, 1992), cDNA-
AFLP (Bachem et al., 1996), serial analysis of gene -Omics technologies are often compared to
expression (SAGE) (Velculescu et al., 1995; 2000), turning on the light in front of a Michelangelo
mass spectrometry, and protein and DNA fresco rather than using a torch that permits a
microarrays. These techniques represent a view only of parts of the whole. The overall view
breakthrough in RNA and protein analysis, allows the meaning of the representation to be
permitting the parallel analysis of virtually all understood and its beauty to be appreciated. In
reality, the power of these techniques is paralleled

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at present by the difficulty and cost involved in and sequenced – sequencing of the concatemer
applying them and in analyzing the data produced. clones results in the quick identification of
The isolation of homogeneous cell samples is numerous individual tags; (iii) the expression level
rather difficult, and is an important prerequisite in of the transcript is quantified by the number of
many gene expression profiling studies. The large times a particular tag is observed.
number of parallel assays results in low cost per
assay, but at a high cost per experiment. Equipment Microarrays can be used to compare, in a single
is expensive, and high technical skill is needed in experiment, the mRNA expression levels of several
all experimental phases. This is in addition to the thousands of genes between two biological
general difficulty in analysing RNA compared to systems, for example, between animals in a
DNA. RNA is very sensitive to degradation, and normal environment and animals in a challenging
particular care has to be taken while extracting it environment. Microarray technology can also
from tissues that have a very active metabolism. provide an understanding of the temporal and
Indeed, sample conservation and manipulation spatial patterns of expression of genes in response
is one of the keys to success in RNA analysis to a vast range of factors to which the organism
experiments. The application of nanotechnologies is exposed.
to the analysis of biological molecules is opening
up very promising perspectives in solving these Very small volumes of DNA solution are printed
problems (Sauer et al., 2005). on a slide made of a non-porous material such
as glass, creating spots that range from 100 to
Data handling is a further problem. Molecular 150 μm in diameter. Currently, about 50 000
datasets such as gene expression profiles complementary DNAs (cDNAs) can be robotically
can be produced in a relatively short time. spotted onto a microscope slide. DNA microarrays
However, the standardization of data between contain several hundreds of known genes, and a
laboratories is needed for consistent analysis few thousands of unknown genes. The microarray
of different biological datasets. Agreements is spotted with cDNA fragments or with
on standardization, as well as the creation of prefabricated oligonucleotides. The latter option
interconnected databases, are essential for the has the advantage of a higher specificity and
efficient analysis of molecular networks. reproducibility, but can be designed only when
the sequence is known. Microarray use is based on
Transcript profiling the principle of “hybridization”, i.e. the exposure
This section briefly describes SAGE and microarray of two single-stranded DNA, or one DNA and one
techniques. Descriptions of other techniques RNA, sequences to each other, followed by the
may be found in a number of recent reviews measurement of the amount of double-stranded
(e.g. Donson et al., 2002). SAGE generates molecule formed. The expression of mRNA can
complete expression profiles of tissues or cell be measured qualitatively and quantitatively. It
lines. It involves the construction of total mRNA indicates gene activity in a tissue, and is usually
libraries which enable a quantitative analysis of directly related to the protein production induced
the whole transcripts expressed or inactivated at by this mRNA.
particular steps of a cellular activation. It is based
on three principles: (i) a short sequence tag (9–14 Gene expression profiling contributes to the
bp) obtained from a defined region within each understanding of biological mechanisms, and
mRNA transcript contains sufficient information hence facilitates the identification of candidate
to uniquely identify one specific transcript; (ii) genes. The pool of genes involved in the expression
sequence tags can be linked together to form long of trypanotolerance in cattle, for example, has
DNA molecules (concatemers) which can be cloned been characterized by SAGE (Berthier et al., 2003),
and by cDNA microarray analysis (Hill et al., 2005).
The parallel investigation of the expression of

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STATE OF THE ART IN THE MANAGEMENT OF ANIMAL GENETIC RESOURCES

many genes may permit the identification of Mass spectrometry (an analytical technique
master genes responsible for phenotypic traits for the determination of molecular mass)
that remain undetected by differential expression in combination with chromatographic or
analysis. These master genes may, for instance, electrophoretic separation techniques, is
possess different alleles all expressed at the same currently the method of choice for identifying
level, which promote the expression of downstream endogenous proteins in cells, characterizing
genes with different efficiency. In this case, the post-translational modifications and determining
master gene can be sought either by exploiting protein abundance (Zhu et al., 2003). Two-
current knowledge of metabolic pathways, or dimensional gel electrophoresis is unique
via an expression QTL (eQTL) approach (Lan et with respect to the large number of proteins
al., 2006). In this approach, the level of expression (>10 000) that can be separated and visualized
of the downstream genes is measured in a in a single experiment. Protein spots are cut
segregating population. The amount of transcript from the gel, followed by proteolytic digestion,
of each gene is treated as a phenotypic trait, and and proteins are then identified using mass
QTL that influence the gene expression can be spectrometry (Aebersold and Mann, 2003).
sought using methodologies described above. It is However, standardization and automation of
worth noting that data analysis for the detection two-dimensional gel electrophoresis has proved
of QTL is still quite difficult to master. This is also difficult, and the use of the resulting protein
true for transcript profiling techniques because of patterns as proteomic reference maps has only
the many false signals that occur. been successful in a few cases. A complementary
technique, liquid chromatography, is easier to
Protein profiling automate, and it can be directly coupled to mass
The systematic study of protein structures, post- spectrometry. Affinity-based proteomic methods
translational modifications, protein profiles, that are based on microarrays are an alternative
protein–protein, protein–nucleic acid, and approach to protein profiling (Lueking et al.,
protein–small molecule interactions, and the 2003), and can also be used to detect protein–
spatial and temporal expression of proteins in protein interactions. Such information is essential
eukaryotic cells, are crucial to understanding for algorithmic modelling of biological pathways.
complex biological phenomena. Proteins are However, binding specificity remains a problem
essential to the structure of living cells and their in the application of protein microarrays,
functions. because cross-reactivity cannot accurately be
predicted. Alternative approaches exist for
The structure of a protein can be revealed by detecting protein–protein interactions such as
the diffraction of x-rays or by nuclear magnetic the two hybrid system (Fields and Song, 1989).
resonance spectroscopy. The first requires a However, none of the currently used methods
large amount of crystalline protein, and this is allow the quantitative detection of binding
often restrictive. In order to understand protein proteins, and it remains unclear to what extent
function and protein–protein interactions at the the observed interactions are likely to represent
molecular level, it would be useful to determine the physiological protein–protein interactions.
the structure of all the proteins in a cell or
organism. At present, however, this has not been Array-based methods have also been developed
achieved. Interestingly, the number of different for detecting DNA–protein interaction in vitro
protein variants arising from protein synthesis and in vivo (see Sauer et al., 2005, for a review),
(alternative splicing and/or post-translational and identifying unknown proteins binding to
modifications) is significantly greater than the gene regulatory sequences. DNA microarrays
number of genes in a genome. are employed effectively for screening nuclear
extracts for DNA-binding complexes, whereas

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protein microarrays are mainly used for identifying Box 78
unknown DNA-binding proteins at proteome- Databases of biological molecules
wide level. In the future, these two techniques
will reveal detailed insights into transcriptional A number of databases exist which collect information
regulatory networks. on biological molecules:

Many methods of predicting the function of DNA sequence databases:
a protein are based on its homology to other • European Molecular Biology Lab (EMBL): http://
proteins and its location inside the cell. Predictions www.ebi.ac.uk/embl/index.html
of protein functions are rather complicated, and • GenBank: http://www.ncbi.nlm.nih.gov/
also require techniques to detect protein–protein • DNA Data Bank of Japan (DDBJ): http://www.
interactions, and to detect the binding of proteins ddbj.nig.ac.jp
to other molecules, because proteins fulfil their
functions in these binding processes. Protein databases:
• SWISS-PROT: http://www.expasy.ch/sprot/sprot-
4 The role of bioinformatics top.html
• Protein Information Resource (PIR): http://pir.
Developing high-throughput technologies would georgetown.edu/pirwww/
be useless without the capacity to analyse the • Protein Data Bank (PDB): http://www.rcsb.org/
exponentially growing amount of biological data. pdb/
These need to be stored in electronic databases
(Box 78) associated with specific software Gene identification utility sites Bio-Portal
designed to permit data update, interrogation • GenomeWeb: http://www.hgmp.mrc.ac.uk/
and retrieval. Information must be easily accessible GenomeWeb/nuc-geneid.html
and interrogation-flexible, to allow the retrieval • BCM Search Launcher: http://searchlauncher.
of information, that can be analysed to unravel bcm.tmc.edu/
metabolic pathways and the role of the proteins • MOLBIOL: http://www.molbiol.net/
and genes involved. • Pedro’s BioMolecular Research tools: http://
www.biophys.uni-duesseldorf.de/BioNet/Pedro/
Bioinformatics is crucial to combine information research_tools.html
from different sources and generate new • ExPASy Molecular Biology Server: http://www.
knowledge from existing data. It also has the expasy.ch/
potential to simulate the structure, function and
dynamics of molecular systems, and is therefore Databases of particular interest for
helpful in formulating hypotheses and driving domestic animals:
experimental work.
http://locus.jouy.inra.fr/cgi-bin/bovmap/intro.pl
5 Conclusions http://www.cgd.csiro.au/cgd.html
http://www.ri.bbsrc.ac.uk/cgi-bin/arkdb/browsers/
Molecular characterization can play a role in http://www.marc.usda.gov/genome/genome.html
uncovering the history, and estimating the http://www.ncbi.nlm.nih.gov/genome/guide/pig/
diversity, distinctiveness and population structure http://www.ensembl.org/index.html
of AnGR. It can also serve as an aid in the genetic http://www.tigr.org/
management of small populations, to avoid http://omia.angis.org.au/
excessive inbreeding. A number of investigations http://www.livestockgenomics.csiro.au/ibiss/
http://www.thearkdb.org/
http://www.hgsc.bcm.tmc.edu/projects/bovine/

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STATE OF THE ART IN THE MANAGEMENT OF ANIMAL GENETIC RESOURCES

have described within and between-population high-throughput –omics technologies are
diversity – some at quite a large scale. However, used to this end. The identification of QTN
these studies are fragmented and difficult offers new opportunities and challenges for
to compare and integrate. Moreover, a AnGR management. Information on adaptive
comprehensive worldwide survey of relevant diversity complements that on phenotypic and
species has not been carried out. As such, it is neutral genetic diversity, and can be integrated
of strategic importance to develop methods into AnGR management and conservation
for combining existing, partially overlapping decision-tools. The identification of unique
datasets, and to ensure the provision of standard alleles or combinations of alleles for adaptive
samples and markers for future use as worldwide traits in specific populations may reinforce the
references. A network of facilities collecting justification for their conservation and targeted
samples of autochthonous germplasm, to be utilization. Gene assisted selection also has the
made available to the scientific community under potential to decrease the selection efficiency gap
appropriate regulation, would facilitate the currently existing between large populations
implementation of a global survey. raised in industrial production systems, and small
local populations, where population genetic
Marker technologies are evolving, and it is evaluation systems and breeding schemes cannot
likely that microsatellites will increasingly be be effectively applied. Marker and gene assisted
complemented by SNPs. These markers hold great selection may not, however, always represent
promise because of their large numbers in the the best solution. These options need to be
genome, and their suitability for automation in evaluated and optimized on a case-by-case basis,
production and scoring. However, the efficiency taking into account short and long-term effects
of SNPs for the investigation of diversity in animal on population structure and rates of inbreeding,
species remains to be thoroughly explored. The and cost and benefits in environmental and
subject should be approached with sufficient socio-economic terms – in particular impacts on
critical detachment to avoid the production of people’s livelihoods.
biased results.
As in the case of other advanced technologies,
Methods of data analysis are also evolving. New it is highly desirable that benefits of scientific
methods allow the study of diversity without a advances in the field of molecular characterization
priori assumptions regarding the structure of the are shared across the globe, thereby contributing
populations under investigation; the exploration to an improved understanding, utilization and
of diversity to identify adaptive genes (e.g. conservation of the world’s AnGR for the good of
using population genomics, see Box 77); and the present and future human generations.
integration of information from different sources,
including socio-economic and environmental
parameters, for setting conservation priorities
(see Section F). The adoption of a correct
sampling strategy and the systematic collection
of phenotypic and environmental data, remain
key requirements for exploiting the full potential
of new technologies and approaches.

In addition to neutral variation, research is
actively seeking genes that influence key traits.
Disease resistance, production efficiency, and
product quality are among the traits having
high priority. A number of strategies and new

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Box 79 With this knowledge, it is thought that the
Glossary: molecular markers identification of a few alleles of a haplotype block can
unambiguously identify all other polymorphic sites
For the purpose of this section the following in this region. Such information is very valuable for
definitions are used: investigating the genetics behind complex traits.

Candidate gene: any gene that could plausibly Linkage: The association of genes and/or markers
cause differences in the observable characteristics that lie near each other on a chromosome. Linked
of an animal (e.g. in disease resistance, milk protein genes and markers tend to be inherited together.
production or growth). The gene may be a candidate
because it is located in a particular chromosome Linkage disequilibrium (LD): is a term used
region suspected of being involved in the control of in the study of population genetics for the non-
the trait, or its protein product may suggest that it random association of alleles at two or more loci,
could be involved in controlling the trait (e.g. milk not necessarily on the same chromosome. It is not
protein genes in milk protein production). the same as linkage, which describes the association
of two or more loci on a chromosome with limited
DNA: the genetic information in a genome is recombination between them. LD describes a situation
encoded in deoxyribonucleic acid (DNA), which is in which some combinations of alleles or genetic
stored in the nucleus of a cell. DNA has two strands markers occur more or less frequently in a population
structured in a double helix, which is made of a sugar than would be expected from a random formation of
(deoxiribose), phosphate, and four chemical bases haplotypes from alleles based on their frequencies.
– the nucleotides: adenine (A), guanine (G), cytosine Linkage disequilibrium is caused by fitness
(C) and thymine (T). An A on one strand always interactions between genes or by such non-adaptive
pairs with a T on the other through two hydrogen processes as population structure, inbreeding, and
bonds, while a C always pairs with a G through three stochastic effects. In population genetics, linkage
hydrogen bonds. The two strands are, therefore, disequilibrium is said to characterize the haplotype
complementary to each other. distribution at two or more loci.

Complementary DNA (cDNA): DNA sequences Microarray technology: a new way of studying
generated from the reverse transcription of mRNA how large numbers of genes interact with each other
sequences. This type of DNA includes exons and and how a cell’s regulatory networks control vast
untranslated regions at the 5’ and 3’ ends of genes, batteries of genes simultaneously. The method uses
but does not include intron DNA. a robot to precisely apply tiny droplets containing
functional DNA to glass slides. Researchers then
Genetic marker: a DNA polymorphism that can be attach fluorescent labels to mRNA or cDNA from the
easily detected by molecular or phenotypic analysis. The cell they are studying. The labelled probes are allowed
marker can be within a gene or in DNA with no known to bind to cDNA strands on the slides. The slides are
function. Because DNA segments that lie near each put into a scanning microscope that can measure the
other on a chromosome tend to be inherited together, brightness of each fluorescent dot; brightness reveals
markers are often used as indirect ways of tracking the how much of a specific mRNA is present, an indicator
inheritance pattern of a gene that has not yet been of how active it is.
identified, but whose approximate location is known.
Primer: a short (single strand) oligonucleotide
Haplotype: a contraction of the phrase “haploid sequence used in a polymerase chain reaction (PCR)
genotype”, is the genetic constitution of an individual
chromosome. In the case of diploid organisms, the RNA: Ribonucleic acid is a single stranded nucleic
haplotype will contain one member of the pair of acid consisting of three of the four bases present in
alleles for each site. It may refer to a set of markers DNA (A, C and G). T is, however, replaced by uracil (U).
(e.g. single nucleotide polymorphisms – SNPs) found
to be statistically associated on a single chromosome.

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References

Aebersold, R. & Mann, M. 2003. Mass spectrometry- Berthier, D., Quere, R., Thevenon, S., Belemsaga,
based proteomics. Nature, 422 (6928): 198–207. D., Piquemal, D., Marti, J. & Maillard, J.C. 2003.
Review. Serial analysis of gene expression (SAGE) in bovine
trypanotolerance: preliminary results. Genetics
Ajmone-Marsan, P., Negrini, R., Milanesi, E., Bozzi, Selection Evolution, 35 (Suppl. 1): S35–47.
R., Nijman, I.J., Buntjer, J.B., Valentini, A. &
Lenstra, J.A. 2002. Genetic distances within and Bertone, P, Stolc, V., Royce, T.E., Rozowsky, J.S.,
across cattle breeds as indicated by biallelic AFLP Urban, A.E., Zhu, X., Rinn, J.L., Tongprasit, W.,
markers. Animal Genetics, 33: 280–286. Samanta, M., Weissman, S., Gerstein, M. &
Snyder, M. 2004. Global identification of human
Akey, J.M., Zhang, G., Zhang, K., Jin, L. & Shriver, transcribed sequences with genome tiling arrays.
M.D. 2002. Interrogating a high-density SNP Science, 306: 2242–2246.
map for signatures of natural selection. Genome
Research, 12(12): 1805–14. Black, W.C., Baer, C.F., Antolin, M.F. & DuTeau,
N.M. 2001. Population genomics: genome-wide
Aravin, A. & Tuschl, T. 2005. Identification and charac- sampling of insect populations. Annual Review of
terization of small RNAs involved in RNA silencing. Entomology, 46: 441–469.
Febs Letters, 579(26): 5830–40.
Bruford, M.W., Bradley, D.G. & Luikart, G. 2003. DNA
Bachem, C.W.B., Van der Hoeven, R.S., De Bruijn, markers reveal the complexity of livestock domesti-
S.M., Vreugdenhil, D., Zabeau, M. & Visser, cation. Nature Reviews Genetics, 4: 900–910.
R.G.F. 1996. Visualization of differential gene ex-
pression using a novel method of RNA fingerprinting Buntjer, J.B., Otsen, M., Nijman, I.J., Kuiper, M.T. &
based on AFLP: analyses of gene expression during Lenstra, J.A. 2002. Phylogeny of bovine species
potato tuber development. The Plant Journal, based on AFLP fingerprinting. Heredity, 88: 46–51.
9: 745–753.
Campbell, D. & Bernatchez, L. 2004. Generic scan
Bamshad, M. & Wooding, S.P. 2003. Signatures of using AFLP markers as a means to assess the role of
natural selection in the human genome. Nature directional selection in the divergence of sympatric
Reviews Genetics, 4(2): 99–111. Review. whitefish ecotypes. Molecular Biology and Evolution,
21(5): 945–56.
Baumung, R., Simianer, H. & Hoffmann, I. 2004.
Genetic diversity studies in farm animals – a survey, Cañon, J., Garcıa, D., Garcıa-Atance, M.A., Obexer-
Journal of Animal Breeding and Genetics, Ruff, G., Lenstra, J.A., Ajmone-Marsan, P.,
121: 361–373. Dunner, S. & The ECONOGENE Consortium.
2006. Geographical partitioning of goat diversity in
Beaumont, M.A. & Balding, D.J. 2004. Identifying Europe and the Middle East. Animal Genetics,
adaptive genetic divergence among populations 37: 327–334.
from genome scans. Molecular Ecology,
13(4): 969–80. Chen, S.Y., Su, Y.H., Wu, S.F., Sha, T. & Zhang, Y.P.
2005. Mitochondrial diversity and phylogeographic
Beja-Pereira, A., Alexandrino, P., Bessa, I., Carretero, structure of Chinese domestic goats. Molecular
Y., Dunner, S., Ferrand, N., Jordana, J., Laloe, D., Phylogenetics and Evolution, 37: 804–814.
Moazami-Goudarzi, K., Sanchez, A. & Cañon,
J. 2003. Genetic characterization of southwestern Clark, A.G., Hubisz, M.J., Bustamante, C.D.,
European bovine breeds: a historical and biogeo- Williamson, S.H. & Nielsen, R. 2005.
graphical reassessment with a set of 16 microsatel- Ascertainment bias in studies of human genome-
lites. Journal of Heredity, 94: 243–50. wide polymorphism. Genome Research,
15: 1496–1502.

375

THE STATE OF THE WORLD'S ANIMAL GENETIC RESOURCES FOR FOOD AND AGRICULTURE

PART 4

Clop, A., Marcq, F., Takeda, H., Pirottin, D., Tordoir, Goldstein, D.B. & Schlötterer, C. 1999. Microsatellites:
X., Bibe, B., Bouix, J., Caiment, F., Elsen, J.M., evolution and applications. New York. Oxford
Eychenne, F., Larzul, C., Laville, E., Meish, F., University Press.
Milenkovic, D., Tobin, J., Charlier, C. & Georges,
M. 2006. A mutation creating a potential illegiti- Grisart, B., Coppieters, W., Farnir, F., Karim, L., Ford,
mate microRNA target site in the myostatin gene C., Berzi, P., Cambisano, N., Mni, M., Reid, S.,
affects muscularity in sheep. Nature Genetics, Simon, P., Spelman, R., Georges, M. & Snell, R.
38: 813–818. 2002. Positional candidate cloning of a QTL in dairy
cattle: identification of a missense mutation in the
De Marchi, M., Dalvit, C., Targhetta, C. & Cassandro, bovine DGAT1 gene with major effect on milk yield
M. 2006. Assessing genetic diversity in indigenous and composition. Genome Research, 12: 222–231.
Veneto chicken breeds using AFLP markers. Animal
Genetics, 37: 101–105. Guo, J., Du, L.X., Ma, Y.H., Guan, W.J., Li, H.B., Zhao,
Q.J., Li, X. & Rao, S.Q. 2005. A novel maternal line-
Donson, J., Fang, Y., Espiritu-Santo, G., Xing, W., age revealed in sheep (Ovis aries). Animal Genetics,
Salazar, A., Miyamoto, S., Armendarez, V. & 36: 331–336.
Volkmuth, W. 2002. Comprehensive gene expres-
sion analysis by transcript profiling. Plant Molecular Haley, C. & de Koning, D.J. 2006. Genetical genomics
Biology, 48: 75–97. in livestock: potentials and pitfalls. Animal Genetics,
37(Suppl 1): 10–12.
Excoffier, L., Smouse, P.E. & Quattro, J.M. 1992
Analysis of molecular variance inferred from metric Hanotte, O., Bradley, D.G., Ochieng, J.W., Verjee,
distances among DNA haplotypes: application to hu- Y. & Hill, E.W. 2002. African pastoralism: genetic
man mitochondrial DNA restriction data. Genetics, imprints of origins and migrations. Science,
131: 479–491. 296: 336–339.

Farnir, F., Grisart, B., Coppieters, W., Riquet, J., Berzi, Hayes, B.J., Visscher, P.M., McPartlan, H.C. &
P., Cambisano, N., Karim, L., Mni, M., Moisio, S., Goddard, M.E. 2003. A novel multilocus measure
Simon, P., Wagenaar, D., Vilkki, J. & Georges, M. of linkage disequilibrium to estimate past effective
2002. Simultaneous mining of linkage and linkage population size. Genome Research, 13: 635–643.
disequilibrium to fine map quantitative trait loci in
outbred half-sib pedigrees: revisiting the location of Hill, E.W., O’Gorman, G.M., Agaba, M., Gibson, J.P.,
a quantitative trait locus with major effect on milk Hanotte, O., Kemp, S.J., Naessens, J., Coussens,
production on bovine chromosome 14. Genetics, P.M. & MacHugh, D.E. 2005. Understanding bovine
161: 275–287. trypanosomiasis and trypanotolerance: the promise
of functional genomics. Veterinary Immunology and
Fields, S. & Song, O. 1989. A novel genetic system to Immunopathology, 105: 247–258.
detect protein–protein interactions. Nature,
340: 245–246. Hill, W.G. 1981. Estimation of effective population
size from data on linkage disequilibrium. Genetics
Freeman, A.R., Bradley, D.G., Nagda, S., Gibson, J.P. Research, 38: 209–216.
& Hanotte, O. 2006. Combination of multiple mi-
crosatellite data sets to investigate genetic diversity Hillel, J., Groenen, M.A., Tixier-Boichard, M., Korol,
and admixture of domestic cattle. Animal Genetics, A.B., David, L., Kirzhner, V.M., Burke, T., Barre-
37: 1–9. Dirie, A., Crooijmans, R.P., Elo, K., Feldman,
M.W., Freidlin, P.J., Maki-Tanila, A., Oortwijn,
Goldstein, D.B., Linares, A.R., Cavalli-Sforza, L.L. & M., Thomson, P., Vignal, A., Wimmers, K. &
Feldman, M.W. 1995. An evaluation of genetic Weigend, S. 2003. Biodiversity of 52 chicken
distances for use with microsatellite loci. Genetics, populations assessed by microsatellite typing of DNA
139: 463–471. pools. Genetics Selection Evolution, 35: 533–557.

376

STATE OF THE ART IN THE MANAGEMENT OF ANIMAL GENETIC RESOURCES

Hood, L., Heath, J.R., Phelps, M.E. & Lin, B. 2004. Liu, Y.P., Wu, G.S., Yao, Y.G., Miao, Y.W., Luikart,
Systems biology and new technologies enable pre- G., Baig, M., Beja-Pereira, A., Ding, Z.L.,
dictive and preventative medicine. Science, Palanichamy, M.G. & Zhang, Y.P. 2006. Multiple
306: 640–643. maternal origins of chickens: out of the Asian jun-
gles. Molecular Phylogenetics and Evolution,
Ibeagha-Awemu, E.M., Jann, O.C., Weimann, C. & 38: 12–19.
Erhardt, G. 2004. Genetic diversity, introgression
and relationships among West/Central African cattle Lueking, A., Possling, A., Huber, O., Beveridge, A.,
breeds. Genetics Selection Evolution, 36: 673–690. Horn, M., Eickhoff, H., Schuchardt, J., Lehrach,
H. & Cahill, D.J. 2003. A nonredundant human pro-
Jarne, P. & Lagoda, P.J.L. 1996. Microsatellites, from tein chip for antibody screening and serum profiling.
molecules to populations and back. Tree, Molecular and Cellular Proteomics, 2: 1342–1349.
11: 424–429.
Luikart, G., England, P.R., Tallmon, D., Jordan, S.
Joshi, M.B., Rout, P.K., Mandal, A.K., Tyler-Smith, C., & Taberlet, P. 2003. The power and promise of
Singh, L. & Thangaraj, K. 2004. Phylogeography population genomics: from genotyping to genome
and origin of Indian domestic goats. Molecular typing. Nature Reviews Genetics, 4: 981–994.
Biology and Evolution, 21: 454–462.
Luikart, G., Gielly, L., Excoffier, L., Vigne, J.D.,
Joost, S. 2006. The geographical dimension of ge- Bouvet, J. & Taberlet, P. 2001. Multiple maternal
netic diversity. A GIScience contribution for the origins and weak phylogeographic structure in do-
conservation of animal genetic resources. École mestic goats. Proceedings of the National Academy
Polytechnique Fédérale de Lausanne, Switzerland. of Science USA, 98: 5927–5932.
(PhD thesis)
Mburu, D.N., Ochieng, J.W., Kuria, S.G., Jianlin,
Kayser, M., Brauer, S. & Stoneking, M. 2003. A H. & Kaufmann, B. 2003. Genetic diversity and
genome scan to detect candidate regions influenced relationships of indigenous Kenyan camel (Camelus
by local natural selection in human populations. dromedarius) populations: implications for their clas-
Molecular Biology and Evolution, 20: 893–900. sification. Animal Genetics, 34(1): 26–32.

Lai, S.J., Liu, Y.P., Liu, Y.X., Li, X.W. & Yao, Y.G. McPherron, A.C. & Lee, S.J. 1997. Double muscling
2006. Genetic diversity and origin of Chinese cattle in cattle due to mutations in the myostatin gene.
revealed by mtDNA D-loop sequence variation. Proceedings of the National Academy of Science
Molecular Phylogenetics and Evolution, 38: 146–54. USA, 94: 12457–12461.

Lan, L., Chen, M., Flowers, J.B., Yandell, B.S., Negrini, R., Milanesi, E., Bozzi, R., Pellecchia, M. &
Stapleton, D.S., Mata, C.M., Ton-Keen Mui, Ajmone-Marsan, P. 2006. Tuscany autochthonous
E., Flowers, M.T., Schueler, K.L., Manly, K.F., cattle breeds: an original genetic resource investi-
Williams, R.W., Kendziorski, C. & Attie, A.D. gated by AFLP markers. Journal of Animal Breeding
2006. Combined expression trait correlations and and Genetics, 123: 10–16.
expression quantitative trait locus mapping. PLoS
Genetics, 2: 51–61. Nei, M. 1972. Genetic distance between populations.
The American Naturalist, 106: 283–292.
Liang, P. & Pardee, A.B. 1992. Differential display of eu-
karyotic messenger RNA by means of the polymer- Nei, M. 1978. Estimation of average heterozygosity and
ase chain reaction. Science, 257: 967–997. genetic distance from a small number of individuals.
Genetics, 89: 583–590.

Nei, M. & Roychoudhury, A.K. 1974. Sampling
variances of heterozygosity and genetic distance.
Genetics, 76: 379–390.

377

THE STATE OF THE WORLD'S ANIMAL GENETIC RESOURCES FOR FOOD AND AGRICULTURE

PART 4

Nei, M., Tajima, F. & Tateno, Y. 1983. Accuracy of Group. 2001. A map of human genome sequence
estimated phylogenetic trees from molecular data. variation containing 1.42 million single nucleotide
II. Gene frequency data. Journal of Molecular polymorphisms. Nature, 409: 928–933.
Evolution, 19: 153–170.
SanCristobal, M., Chevalet, C., Haley, C.S., Joosten,
Nielsen, R. & Signorovitch, J. 2003. Correcting for R., Rattink, A.P., Harlizius, B., Groenen, M.A.,
ascertainment biases when analyzing SNP data: Amigues, Y., Boscher, M.Y., Russell, G., Law, A.,
applications to the estimation of linkage disequilib- Davoli, R., Russo, V., Desautes, C., Alderson, L.,
rium. Theoretical Population Biology, 63: 245–55. Fimland, E., Bagga, M., Delgado, J.V., Vega-
Pla, J.L., Martinez, A.M., Ramos, M., Glodek,
Nijman, I.J., Otsen, M., Verkaar, E.L., de Ruijter, C. & P., Meyer, J.N., Gandini, G.C., Matassino, D.,
Hanekamp, E. 2003. Hybridization of banteng (Bos Plastow, G.S., Siggens, K.W., Laval, G., Archibald,
javanicus) and zebu (Bos indicus) revealed by mito- A.L., Milan, D., Hammond, K. & Cardellino,
chondrial DNA, satellite DNA, AFLP and microsatel- R. 2006a. Genetic diversity within and between
lites. Heredity, 90: 10–16. European pig breeds using microsatellite markers.
Animal Genetics, 37: 189–198.
Pariset, L., Cappuccio, I., Joost, S., D’Andrea, M.S.,
Marletta, D., Ajmone Marsan, P., Valentini A. & SanCristobal, M., Chevalet, C., Peleman, J., Heuven,
ECONOGENE Consortium 2006. Characterization H., Brugmans, B., van Schriek, M., Joosten,
of single nucleotide polymorphisms in sheep and R., Rattink, A.P., Harlizius, B., Groenen, M.A.,
their variation as an evidence of selection. Animal Amigues, Y., Boscher, M.Y., Russell, G., Law, A.,
Genetics, 37: 290–292. Davoli, R., Russo, V., Desautes, C., Alderson, L.,
Fimland, E., Bagga, M., Delgado, J.V., Vega-Pla,
Pritchard, J.K., Stephens, M. & Donnelly, P. 2000. J.L., Martinez, A.M., Ramos, M., Glodek, P.,
Inference of population structure using multilocus Meyer, J.N., Gandini, G., Matassino, D., Siggens,
genotype data. Genetics, 155: 945–959. K., Laval, G., Archibald, A., Milan, D., Hammond,
K., Cardellino, R., Haley, C. & Plastow, G. 2006b.
Rabie, T.S., Crooijmans, R.P., Bovenhuis, H., Genetic diversity in European pigs utilizing amplified
Vereijken, A.L., Veenendaal, T., van der Poel, fragment length polymorphism markers. Animal
J.J., Van Arendonk, J.A., Pakdel, A. & Groenen, Genetics, 37: 232–238.
M.A. 2005. Genetic mapping of quantitative trait
loci affecting susceptibility in chicken to develop Sauer, S., Lange, B.M.H., Gobom, J., Nyarsik, L., Seitz,
pulmonary hypertension syndrome. Animal Genetics, H. & Lehrach, H. 2005. Miniaturization in func-
36: 468–476. tional genomics and proteomics. Nature Reviews
Genetics, 6: 465–476.
Saitou, N. & Nei, M. 1987. The neighbor-joining meth-
od: a new method for reconstructing phylogenetic Sodhi, M., Mukesh, M., Mishra, B.P., Mitkari, K.R.,
trees. Molecular Biology and Evolution, 4: 406–425. Prakash, B. & Ahlawat, S.P. 2005. Evaluation of
genetic differentiation in Bos indicus cattle breeds
Sachidanandam, R., Weissman, D., Schmidt, S.C., from Marathwada region of India using microsatel-
Kakol, J.M., Stein, L.D., Marth, G., Sherry, S., lite polymorphism. Animal Biotechnology,
Mullikin, J.C., Mortimore, B.J., Willey, D.L., Hunt, 16: 127–137.
S.E., Cole, C.G., Coggill, P.C., Rice, C.M., Ning,
Z., Rogers, J., Bentley, D.R., Kwok, P.Y., Mardis, Storz, G., Altuvia, S. & Wassarman, K.M. 2005. An
E.R., Yeh, R.T., Schultz, B., Cook, L., Davenport, abundance of RNA regulators. Annual Review of
R., Dante, M., Fulton, L., Hillier, L., Waterston, Biochemistry, 74: 199–217.
R.H., McPherson, J.D., Gilman, B., Schaffner,
S., Van Etten, W.J., Reich, D., Higgins, J., Daly, Sunnucks, P. 2001. Efficient genetic markers for popula-
M.J., Blumenstiel, B., Baldwin, J., Stange- tion biology. Tree, 15: 199–203.
Thomann, N., Zody, M.C., Linton, L., Lander, E.S.
& Altshuler, D.; International SNP Map Working

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