32 Quantitative Genomics of Reproduction
Genetic recombination takes place during Inheritance of the functional mutation is
meiosis at relatively random positions now in LD with those nearby alleles in his
throughout the genome (although recombi- descendants until recombination breaks up
nation hotspots have been described) and the relationship. Now suppose another
therefore occurs more frequently between mutation occurs in the same region in a
distant genetic loci than adjacent loci. On sibling male, who shares the same original
average within a population, genetic loci on alleles in the region. The new mutation is
the same chromosome that are distant from also in LD with the shared alleles in his
each other are in less LD than those close descendants, but not with the functional
together. The degree of LD in a population mutation in descendants of the original sire,
depends on the number of generations its even though they are located right next to
members have been free to mate at random, each other in the genome. Finally, suppose
whether any reduction in the overall popula- a third nearby mutation occurs in a descen-
tion size took place in its history, and when dant of the original sire. This third mutation
mutations occurred relative to one another. will also be in LD with the functional
Genetic selection of individuals in a popula- mutation. Over generations, recombination
tion will tend to preserve LD surrounding events may disrupt any of these relation-
genes inﬂuencing the selected trait. A reduc- ships over time. In this way, varying degrees
tion in population size increases the related- of LD can result between nearby loci, because
ness of offspring of the remaining individuals, mutations that are close in distance but
which increases LD until sufﬁcient genera- separated in time may vary in LD with
tions pass to allow recombination to mix up each other. To exploit LD, one needs to have
the linked chromosomal regions. In humans, sufﬁcient markers in a region that are suf-
regions of LD, called “haplotype blocks,” ﬁciently close to the functional polymor-
are relatively small (50 kb [Dunning et al. phism. How close depends on the structure
2000; Abecasis et al. 2001; Shifman et al. of LD for that region of the genome within
2003; Tsunoda et al. 2004]) compared with the population. Within the region of sub-
livestock (pig 250–1000 kb [Nsengimana stantial LD, dividing the genetic variation
et al. 2004; Harmegnies et al. 2006; Du et al. into three or four roughly equal portions
2007], sheep 5000–10,000 kb [McRae et al. using genetic markers will give a reasonable
2002], and cattle 500 kb [McKay et al. 2007]). assessment of the effect of a chromosomal
The larger regions of LD in livestock are region on a trait. Figures 2.1 and 2.2 illus-
likely a reﬂection of periodic reductions in trate how this can work for a high-frequency
population size as well as the cumulative and a low-frequency functional polymor-
effect of genetic selection for various traits. phism and surrounding SNP. Adjacent SNP
The existence of LD means that alleles of illustrated in Figures 2.1 and 2.2 are hypo-
nearby SNP are often inherited together. If a thetical situations meant to represent pos-
functional polymorphism is sufﬁciently sible arrangements. In practice, one must
near other SNP, inheritance of the adjacent examine sufﬁcient adjacent SNP to provide
loci can be used to track inheritance of the a good division of the genetic variation
functional polymorphism. To understand within the locus, but not so many that the
how this can work, suppose a functional variation is divided up so much that indi-
mutation occurs on a chromosome within vidual effects of haplotypes are no longer
a region in a sire with nearby alleles. detectable.
a. b. c. SNPA d.
01 new 0 1
e. f. g. h. SNPB
1 QTN 1 1 new
0 1 new 0 SNPA 0
Figure 2.1 The pie charts illustrate an additive genetic effect in a population of animals in a hypothetical
QTL region of the genome. In (a), two alleles of a functional SNP (quantitative trait nucleotide or QTN) with
a frequency of 0.5 each exist at a locus. One allele does not change the phenotype (and is therefore 0);
the other increases the phenotype by 1. This gives an allele substitution effect for this locus of 1; thus, in
this population, this genomic region contributes from 0 (homozygous for the 0 allele) to 2 (homozygous for
the 1 allele) units to the phenotypic trait. In (b), a genetic marker based on the QTN is illustrated. In (c), a
nearby mutation occurs on a chromosome containing allele 1 of the QTN, creating an SNPA with alleles in
linkage disequilibrium with the QTN. Overtime, half of the chromosomes with QTN allele 1 have the new
allele of SNPA, and half have the old allele of SNPA, and all of the chromosomes with allele 0 of the func-
tional SNP have the old allele of SNPA. For SNPA, the new allele is always present with allele 1 of the
functional SNP; the old SNPA allele is a mixture of QTN alleles 0 and 1. In this arrangement, a commonly
used measure of linkage disequilibrium (r 2) is 0.33 and is calculated as the squared correlation between
the incidences of the alleles at each locus. The substitution effect of SNPA alleles would be 0.67, two-thirds
that of the QTN. In (d), three adjacent SNPs are illustrated together, SNPA (from c) and SNPB, along with
the QTN. SNPB in this case now occurred on a chromosome with allele 0 of the functional SNP, and over-
time two-thirds of allele 0 has the new allele at SNPB, and one-third of allele 0 and all of allele 1 at the
functional SNP have the old allele at SNPB. The r 2 = 0.5 for SNPB, and it can be calculated that SNPB
will have a substitution effect of 0.75. This marker arrangement creates three haplotypes: SNPA old allele
with SNPB new allele, SNPA old allele with SNPB old allele, and SNPA new allele with SNPB old allele.
The r 2 for the haplotypes is 0.59, better than either SNP alone. The substitution effects of these three
haplotypes are 0.6 for the substitution of SNPA old, SNPB old for SNPA old, SNPB new; 0.4 for the sub-
stitution of SNPA new, SNPB old for SNPA old, SNPB old; and 1 for the substitution of SNPA new, SNPB
old for SNPA old, SNPB new. In this case, the haplotypes regenerate the substitution effect of the original
QTN because the SNPA new, SNPB old haplotype is only present with the QTN 1 allele, and the SNPA
old, SNPB new haplotype is only present with the QTN 0 allele. In (e), a different hypothetical QTN is
illustrated that has an allele 1 with a frequency of 0.1 that increases the phenotype by 1 and an alternate
allele 0 with a frequency of 0.9 that does not change the phenotype. In (f), a marker based on the new
QTN is illustrated. In (g), a mutation generating a new allele for SNPA occurred sometime before the muta-
tion resulting in the QTN and overtime results in a frequency of 40%, which will eventually be present only
with QTN allele 0. The old SNPA allele (60%) will be present with a mixture of QTN alleles 0 and 1. In (h),
another SNPB occurred sometime before the QTN on a chromosome with the old allele of SNPA, and
overtime the frequency of the new allele is 25% and the old allele is 75%. This SNP arrangement results
in three haplotypes as before: new allele SNPA with old allele SNPB (frequency 0.4), old allele SNPA with
old allele SNPB (frequency 0.35), and old allele SNPA with new allele SNPB (frequency 0.25). Later in the
history of the population, a mutation occurs on a chromosome with the old SNPA, new SNPB allele haplo-
type generating QTN allele 1, which rises in frequency to 0.1, representing 40% of chromosomes with the
old SNPA, new SNPB haplotype. One can calculate r 2 and the substitution effects for SNPA, SNPB, and
the three haplotypes. The r 2’s are 0.07, 0.33, and 0.23, respectively. In this case, the haplotypes are in less
linkage disequilibrium than SNPB. The substitution effects are 0.17 for SNPA, 0.4 for SNPB, and 0 for
replacing SNPA old, SNPB old with SNPA new, SNPB old and 0.4 for replacing either alternative haplotype
with SNPA old, SNPB new. In this example, the three haplotypes do not provide better detection of the
additive effect of the genetic locus than SNPB alone. Both examples illustrate the potential advantage of
exploiting linkage disequilibrium for the examination of genetic locus effects on a trait.
34 Quantitative Genomics of Reproduction
a. SNPA QTN 0 SNPB b. SNPA SNPB
old new new QTN 0 old
SNPA QTN 0 SNPB SNPA QTN 0 SNPB
old old old old
SNPA QTN 1 SNPB SNPA QTN 0 SNPB
old old old new
SNPA QTN 1 SNPB SNPA QTN 1 SNPB
new old old new
Figure 2.2 The arrangement of haplotypes described in Figure 2.1a through d is illustrated in (a); the
arrangement of haplotypes described in Figure 2.1e through h is illustrated in (b). Without linkage disequi-
librium, three loci, each with two alleles, would have 23 or 8 combinations of alleles. Linkage disequilibrium
reduced the number of combinations to four in each case and broadened the range over which the effect
of the QTL could be observed.
LD analysis is most useful when pheno- lation for a genome scan if genotyping using
typed animals represent a diverse sampling genetic markers that are sufﬁciently dense
of the population of interest. Unrelated to assess genetic variation within the natu-
animals can be advantageous because linkage rally occurring “haplotype blocks” alluded
between adjacent loci is smaller and similar to earlier is available. Given that natural LD
to that of the livestock population at large. within livestock populations only occurs
Diverse and extensive sampling from the within 100 kb or so, a genomic scan capable
population of interest typically means that of assessing the genetic variation across the
only those female reproductive traits that entire genome (i.e., a genome scan using
are routinely and easily obtained in live- naturally occurring LD) requires the geno-
stock will be available for this type of analy- typing of thousands of SNP for each animal
sis. Thus, the examination of difﬁcult to in a population. It is only recently that this
collect reproductive phenotypes is at odds technology has become available for live-
with the sampling necessary to reduce the stock. Discovering the location of thousands
size of regions associated with those traits. of SNP in livestock is a monumental task.
A compromise strategy that could be useful However, SNPs are a natural by-product of
for these phenotypes is to perform continu- livestock genome sequencing efforts. The
ous diverse sampling from the population of individual animals used as a source of DNA
interest (e.g., sample males that are repre- for genome sequencing efforts differ in
sentative of the livestock population of DNA sequence between each other and are
interest by breeding them to a maintained themselves heterozygous at numerous loci,
research population of females such that resulting in a large number of SNP. Thus,
over time sufﬁcient diverse sampling of the availability of the sequenced genome for
livestock population occurs in the progeny cattle has enhanced the effort to discover
of such matings). and map the needed SNP in this species,
and similar efforts are being undertaken
One can skip linkage analysis and use the for swine and sheep. The availability of the
naturally occurring LD in a livestock popu-
Female Reproduction 35
needed SNP in cattle has resulted in the which the animals are related to each other
development of an SNP chip capable of in some degree. These relationships can
simultaneously genotyping ∼60,000 genetic originate from breed differences in animals
loci (Illumina, Inc., San Diego, CA). LD used to generate the populations, or simply
analysis at the appropriate genotyping densi- from parent–offspring (pedigree) relation-
ties will have a signiﬁcant advantage over ships. Often, relationships are extremely
linkage analysis, because if the markers high if the research herds are descended
used are sufﬁciently dense, they can be from populations used for linkage analysis.
used on relatively unrelated animals and In addition, in many cases, analysis at more
will be more predictive and of more utility than a single locus is done. In these cases,
to livestock populations at large. However, association between the phenotype and
these advantages come with signiﬁcant genetic variation at many or all locations
increases in the complexity of the statistical throughout the whole genome is sought.
analysis required to reliably interpret These two issues present some difﬁculties.
A founder animal within a population that
2.4.4 Statistical analysis of is genetically superior at several indepen-
genomic associations dent loci, and is ﬁxed for irrelevant loci on
various chromosomes, would transmit both
Superﬁcially, the association of SNP geno- to its progeny. Separation of the superior loci
types with phenotypes should be a simple from the irrelevant loci occurs in subsequent
task. Two alternate alleles at a locus gener- generations for loci on different chromo-
ate three different genotypes in a population somes, but remains, at least in part, for loci
of animals. Analysis of variance can be used on the same chromosome, because only
to analyze the phenotypes corresponding to recombination can break up the relation-
the three genotypes and to arrive at a test of ship. These associations can lead to errone-
signiﬁcance of the effect of genotype on the ous conclusions about associations between
phenotype. One can use individual contrasts genetic loci and phenotypic traits unless the
between genotypes to arrive at additive polygenic effects between related animals
(comparison between homozygous animals) are accounted for in the analysis (Calus and
and dominance (comparison of the average Veerkamp 2007). This is not trivial; relation-
of the two types of homozygous animals ships between animals must be known, and
with the mean for heterozygous animals) quantitative genetic analysis methods must
effects. This approach can work for an be used to account for the relationships.
unrelated population of animals, but such a Then, an individual genetic locus effect is ﬁt
population is rarely available for genomics simultaneously with the polygenic effects to
research. Indeed, industry populations are distinguish one from the other. If this is not
often sampled under the assumption that done, animals within the population are not
the individuals sampled are unrelated and independent from each other due to their
the results of these studies can produce inac- interrelatedness, and incorrect associations
curate associations when the relationships can be obtained.
between the animals sampled are ignored.
Typically, genotype association studies are This type of analysis is adequate for a few
done on research or commercial herds in SNP in a population, but when the goal is to
determine the effects of genetic variation
throughout the genome, as in a genome
36 Quantitative Genomics of Reproduction
scan, the number of individual tests becomes have more evidence suggesting a real effect
a problem. Typical genome scan analyses than just signiﬁcance at P < 0.05 among
test the effect of genotype at one centimor- multiple tests of candidate genes. This is
gan (∼million base pair) intervals or less. one reason why the effect of a region of
Since the typical livestock genome is 3 the genome on a particular trait should be
billion bases, at least 3000 tests must be examined in different populations to conﬁrm
conducted for a complete genome scan. Use the association. However, because results
of new 50k SNP chips results in even greater of genome scans depend on the founder
numbers of tests. A statistical signiﬁcance animals chosen, failure to obtain a signiﬁ-
level of P = 0.05 for individual genetic loci cant association in any given population
on average results in one false-positive asso- does not mean the association is not present
ciation by chance for every 20 tests per- in another sampled population.
formed. Typically, the problem of multiple
tests is compensated by making analyses Appreciation of interrelatedness among
more stringent, such that the acceptable sig- individuals in a population and control
niﬁcance level is raised to a genome-wide of experiment-wide false-positive/false-
error rate of 1 false positive in 20 genome negative rates is sufﬁcient when the goal is
scans, rather than 1 false positive in 20 tests. to discover genetic loci having a true inﬂu-
Although several QTL have met this crite- ence on a trait, and that has been the goal of
rion, this level of stringency risks missing much of genomics research to date. However,
true genotypic associations. In addition, the the real utility of genomics is in predicting
estimated effects of markers with associa- individual animal performance given the
tions at this signiﬁcance level may be biased genotype of the animal, and it is here that
upward because of the stringent criteria statistical analysis becomes even more
required to accept them (Bogdan and Doerge complicated. With the availability of dense
2005). In practice, a compromised statistical genome-wide genotyping in livestock, it
analysis strategy is typically adopted. The will become possible to know with relative
two or three QTL regions with the highest certainty how speciﬁc regions of the live-
signiﬁcance level for a particular phenotype stock genome or groups of haplotypes are
become targets for further research, keeping passed from parent to offspring. Simulation
in mind that one or more false positives may studies have been reported on the utility
be present, depending on the actual signiﬁ- of various methods to use this type of infor-
cance level of the locus. In this way, for a mation to predict breeding values by exam-
given population, the two or three genetic ining the effects of multiple markers across
loci with the greatest chance of being associ- the genome simultaneously. Methods that
ated with a trait of interest are identiﬁed for produce predicted breeding values from
further investigation using ﬁne-mapping marker combinations densely sampling the
techniques to obtain more evidence of true entire genome have been broadly termed
association. This same issue is a problem for “whole genome selection” or WGS methods.
experiments that investigate a list of candi- It is clear from these studies that use of ﬁxed
date genes for a particular phenotype. The least squares mean effects of statistically
more genes examined, the more false posi- signiﬁcant loci (selected using multiple
tives will be obtained. Acceptance of a can- regression model building methods) asso-
didate gene effect on a phenotype should ciated with a phenotype results in poor
prediction of breeding values (Meuwissen
Female Reproduction 37
et al. 2001). Statistical prediction of breeding Vallet et al. 2005b). Associated genomic
values incorporating genotype information regions resulting from reported genome
by ﬁtting the markers as random effects scans for QTL regions are typically very
with a common variance using a more quan- broad due to the small number of genera-
titative genetics approach (best linear unbi- tions examined in these experiments.
ased prediction [BLUP]) resulted in better Numerous potential genes fall within the
prediction of breeding values. However, the conﬁdence interval of these reported QTL.
best genotype-based prediction of breeding Because the regions are so broad, it has been
values was by using a Bayesian approach to very difﬁcult to identify causative genes and
ﬁtting the effects of genotypes at multiple variation in those genes to convert many of
loci where most of the markers were allowed the known QTL regions into genetic markers
to have no effect. The best way to predict that are useful in a variety of populations.
breeding values from genome-wide genotyp- Candidate gene approaches have also yielded
ing information is an area of ongoing intense genetic loci associated with a variety of
research. Nevertheless, WGS shows great reproductive traits. Thus, associations with
promise as a tool to use genomic data from reproductive traits run the gamut from
ﬁeld (e.g., dairy progeny tests) or research single SNP associations to huge genome
populations to predict breeding values of regions from linkage analysis. Rather than
industry animals. attempt to describe them all, we thought it
would be more useful to focus on a limited
2.5 Some illustrative examples of number of well-characterized associations
reproductive QTL with reproductive traits. These serve to illus-
trate the processes used and some of the
Numerous QTL for female reproductive limitations.
traits in livestock have been reported. A
couple of recent reviews are available for 2.5.1 QTL mapping for ovulation rate
swine (Buske et al. 2006; Rothschild et al. in sheep
2007). In addition, online resources are avail-
able. The AnimalQTLdb (Hu et al. 2005, 2007; A good example of the application of genom-
Hu and Reecy 2007; www.animalgenome. ics technology to reproductive traits is in the
org/QTLdb/) summarizes many QTL in application of this technology to loci affect-
swine and cattle, including their positions ing ovulation rate in sheep. Although ovula-
within the genome. The bovine QTL viewer tion rate represents a quantitative trait in all
(Polineni et al. 2006) is a website speciﬁc livestock species, several gene loci with
to cattle QTL (bovineqtlv2.tamu.edu/index. major effects on ovulation rate have been
html). Genomic regions associated with discovered in sheep. The ﬁrst of these loci
most of the easily measured traits have been was reported to be present on the X chromo-
reported, along with some subcomponent some (Davis et al. 1991) by virtue of its
traits that are more difﬁcult to measure such X-linked inheritance. This gene was named
as ovulation rate (Rathje et al. 1997; Rohrer FecX by virtue of the fact that it was a gene
et al. 1999; Wilkie et al. 1999; Kappes et al. affecting fecundity in sheep located on the X
2000; Cassady et al. 2001; Sato et al. 2006) chromosome. This gene had the curious pro-
and uterine capacity (Rohrer et al. 1999; perty that heterozygous animals displayed
increased ovulation rate, while homozygous
38 Quantitative Genomics of Reproduction
animals were sterile. A second Fec autosomal plete loss of gene function is associated with
gene, FecB, was localized to an ovine chro- sterility (Hanrahan et al. 2004). Curiously, in
mosomal region similar to human chromo- mice, knockout of the genes does not increase
some 4 (Montgomery et al. 1993), because ovulation rate in heterozygous mice (Yan
a genetic map for sheep at the time was et al. 2001), pointing out that it is sometimes
not available. Subsequent studies localized inappropriate to use results from other
the FecB gene to ovine chromosome 6 species to try to understand intricacies of
(Montgomery et al. 1994) based on detection control of reproductive traits in livestock.
of genes known to be within the human chro- These mutations display several curious
mosomal region in sheep/hamster somatic properties. Effects of BMP15 and GDF9 are
cell hybrid clones of an ovine chromosome 6 additive in that ovulation rates for doubly
translocation. Subsequent mapping con- heterozygous sheep are similar to the increase
ﬁrmed that this region of the ovine genome caused by each heterozygous genotype added
is syntenic (similar) to human chromosome together (McNatty et al. 2004). This result
4 (www.livestockgenomics.csiro.au/sheep/ occurs despite the fact that increased ovula-
mapcreator). The effect of the FecB gene dif- tion rate for each gene is associated with
fered from that of FecX in that it appeared to partial but not complete loss of function.
be an additive; heterozygous sheep had ovu- Failure of reproduction is likely associated
lation rates midway between the ovulation with very low expression of this pathway.
rates of homozygous sheep. Galloway et al. This result also illustrates the concept that
(2000) reported that the FecX gene was redundancy in gene function may inﬂuence
explained by mutations in the bone morpho- the success of a particular genetic associa-
genic protein (BMP) 15 gene. Simultaneous tion. The TGFβ family has many members
reports (Souza et al. 2001; Wilson et al. 2001) with potential to have redundant functions
indicated that the FecB gene was caused by a among the individual genes. BMPR-1B is one
mutation in the BMP-1B receptor. Finally, of seven type 1 receptors and is expressed in
other populations with phenotypic distribu- bone during skeletal development. Knockout
tions (increased ovulation rate of heterozy- studies in the mouse result in subtle changes
gous sheep, infertility of homozygous sheep) in skeletal development (Yi et al. 2000);
similar to FecX were explained by mutations however, changes in skeletal development
in the growth differentiation factor (GDF) 9 have never been reported in FecB homozy-
gene on sheep chromosome 5 (Hanrahan et gous sheep. What has been described are
al. 2004). Both GDF9 and BMP15 are members reductions in live weight (Walling et al.
of the transforming growth factor (TGF) β 2000), although this may be caused by a sepa-
superfamily, and BMP-1B is a member of the rate adjacent locus in FecB sheep. It seems
TGFβ type 1 receptors (McNatty et al. 2004; possible that subtle differences in weight
Souza et al. 2004). Despite knowledge that could be the result of BMPR-1B effects on
various mutations in these genes are respon- skeleton formation. Although these differ-
sible for changes in ovulation rate, the mech- ences are not sufﬁcient to outweigh the
anism whereby these changes result in advantage in fecundity, it illustrates the
differences in ovulation rate in sheep is still point that gene alterations can have unin-
not clear. In all cases, it appears that an tended effects, depending on the other
increase in ovulation rate is associated with pathways/functions in which that gene is
partial loss of gene function, although com- involved.
Female Reproduction 39
2.5.2 QTL mapping for lactation region to a small area of the chromosome
in cattle containing just a few genes (Olsen et al.
2005; Schnabel et al. 2005b). Subsequently,
There have been several QTL studies in polymorphisms in two different genes, osteo-
cattle for a variety of reproductive traits pontin (SPP1; Leonard et al. 2005; Schnabel
(Georges et al. 1995; Coppieters et al. 1998; et al. 2005b) and the ATP-binding cassette
Kappes et al. 2000; Ashwell et al. 2001, 2004; transporter G2 (ABCG2; Cohen-Zinder et al.
Boichard et al. 2003; Schrooten et al. 2004; 2005), were suggested to be responsible for
Schnabel et al. 2005a; Muncie et al. 2006; this QTL. This controversy (de Koning 2006)
Guillaume et al. 2007). Most of these studies points out the difﬁculty in identifying a
examine lactation performance in dairy polymorphism in a gene as the causative
cattle, taking advantage of national dairy polymorphism responsible for a QTL. The
herd record programs in various countries difﬁculty lies in the LD between polymor-
(i.e., known pedigree information), along phisms in nearby genes. In order to distin-
with the availability of sire performance guish the effects of one from the other, a
testing for dairy bulls (resulting in the accu- population must be found where the LD is
rate prediction of breeding values for dairy disrupted. In addition, to be convincing, a
traits), availability of semen for many of gene should have biological evidence sug-
these bulls (to obtain DNA), and relatively gesting that the gene is responsible for the
widespread use of individual bulls by artiﬁ- differences in a trait of interest (Ron and
cial insemination in the dairy industry. Weller 2007). However, in this case, the dis-
Thus, most cattle lactation QTL were dis- covered polymorphisms in both genes could
covered using high-accuracy, sire-predicted reasonably be expected to have an effect on
breeding values calculated from the evalua- milk traits. A more recent report seems to
tion of the lactation performance of result- suggest a resolution to the controversy, in
ing daughters. This once again reinforces the favor of the ABCG2 gene polymorphism
importance of pedigreed populations with (Olsen et al. 2007), since the previously
phenotypes in QTL analysis. Two of the best reported SPP1 polymorphism could be
characterized lactation QTL illustrate many excluded in their study. Similar to the Fec
of the issues involved in QTL analysis. genes in sheep, identiﬁcation of the poly-
morphism and gene responsible did not
Georges et al. (1995) was the ﬁrst to immediately suggest the physiological
describe a QTL for protein yield on bovine mechanism. The ABCG2 gene affects the
chromosome 6, located midway along the secretion of xenobiotics into milk (van
chromosome, a ﬁnding subsequently con- Herwaarden and Schinkel 2006) and excludes
ﬁrmed by numerous reports (Ashwell et al. xenobiotics from uptake from the gastroin-
2001, 2004; Boichard et al. 2003; Schrooten testinal (GI) tract and from cells elsewhere
et al. 2004). Likewise, a QTL for fat percent- in the body. It is difﬁcult to understand how
age in milk was reported at the top of bovine this function translates into changes in milk
chromosome 14 (Coppieters et al. 1998) and protein concentrations, and research to
was subsequently conﬁrmed by several answer this question is ongoing.
other reports (Boichard et al. 2003; Ashwell
et al. 2004; Schrooten et al. 2004). Turning to the fat percentage QTL on
chromosome 14, combined linkage–linkage
Combined linkage–linkage disequilibrium disequilibrium analysis was again used to
analysis reduced the chromosome 6 QTL
40 Quantitative Genomics of Reproduction
narrow this QTL to a small region near that explained by the K232A polymorphism
the centromere (Farnir et al. 2002). A subse- in DGAT1 (Gautier et al. 2007). This may
quent polymorphism that alters the coding be analogous to the different FecX gene
sequence of the acyl-CoA:diacylglycerol alleles in sheep, all resulting in the impair-
acyl transferase 1 (DGAT1) gene (substitutes ment of the BMP15 function. Thus, other
a lysine K for alanine A at amino acid 232 polymorphisms that alter the activity of
of the coding sequence) within the QTL DGAT1 in the mammary gland could have
region was reported to be the cause of the similar effects on fat percentage. These
QTL (Grisart et al. 2002; Winter et al. 2002; alterations could be increased transcription
Thaller et al. 2003). This gene codes for the of the gene or increased translation of the
enzyme responsible for the ﬁnal stage of tri- protein. Alternatively, another nearby gene
glyceride synthesis. It has been shown that could be responsible for the QTL effects not
the K allele of DGAT1 has greater triglycer- explained by the K232A polymorphism in
ide synthesizing activity than the A allele DGAT1.
(Grisart et al. 2004); thus, it makes sense
that a polymorphism that increases fat syn- Most of the original lactation QTL studies
thesis in the mammary gland would be asso- indicate interrelationships among various
ciated with an increase in milk fat percentage. milk traits. Although the two previously
Although there is a solid case for the effect described loci primarily affect protein (chro-
of this polymorphism on fat percentage, mosome 6) and fat (chromosome 14), these
it appears that it is not the only polymor- loci have effects on the measured milk traits.
phism segregating at this locus (Kuhn et al. In addition, Kaupe et al. (2007) reported a
2004). In this report, sires that are homozy- signiﬁcant negative effect of the DGAT1 K
gous for the A allele of the DGAT1 gene still allele on nonreturn rates, a measure of cow
segregate a QTL in this region for fat per- fertility. Allan et al. (2007) reported a signiﬁ-
centage in their descendants, and the authors cant association between polymorphisms in
present evidence that polymorphisms in the osteopontin gene with calf birth weights,
the promoter region of the DGAT1 gene suggesting possible correlations between the
may be responsible for the QTL in these chromosome 6 chromosomal region affect-
sires. They implicate a variable nucleotide ing milk protein with aspects of pregnancy.
repeat (VNTR) region in the promoter, with These are all examples of pleitropic effects
three to seven repeats of the sequence of speciﬁc genetic loci and support the
AGGCCCCGCCCTCCCCGG, as poten- concept that marker-assisted selection for
tially responsible for the additional QTL one trait may have consequences for other
effects in this region. This sequence con- traits. It seems very unlikely, given their
tains an SP1 transcription factor binding site expression and likely function in other
and increases transcription of a reporter gene tissues, that polymorphisms in genes like
in mammary gland epithelial cells (Furbass ABCG2 and DGAT1 will have effects solely
et al. 2006), although transcription of the on milk production. It is well established
reporter gene did not vary with the number that selection for increased milk production
of repeats. However, another report did not in dairy cattle has resulted in impaired fertil-
conﬁrm the effect of the VNTR region on ity (Lucy 2001). This is at least in part due
fat percentage, although the authors do indi- to antagonistic pleiotropy between genes
cate the presence of additional QTL beyond affecting both traits. Fortunately, loci are
likely to vary in the degree of multiple
Female Reproduction 41
effects, and the most efﬁcient use of whole 2.6 Future research directions
genome association technology will be its
ability to take these multiple effects of indi- As previously mentioned, two innovations
vidual loci into account. This will require will revolutionize genetic selection based
the collection of multiple phenotypes on the on genotyping of individual animals, the
same animals. routine availability of less expensive geno-
typing of sufﬁcient density to successfully
2.5.3 QTL mapping for litter size capture a large share of the genetic variation
in swine within each animal, and development of
statistical approaches that optimize the
Application of genomics to pig reproduction use of this information for prediction of
has been slower, due to lack of mutations individual animal breeding values. Dense
with large effects as in sheep, and the lack genotyping will be a natural by-product of
of availability of suitable populations with livestock genome sequencing efforts, com-
broad phenotypic collections as in cattle. bined with genome-wide SNP discovery
As previously indicated, genetic loci associ- research making use of new high-throughput
ated with reproduction in pigs (litter size) sequencing technologies. Because of the
have been reported using a candidate gene expense and complexity of this technology,
approach and signiﬁcant associations with it will initially be applied to research herds
litter size have been found for polymor- and elite livestock to improve the use of
phisms in the estrogen receptor (Rothschild these animals in genetic selection schemes,
et al. 1996; Short et al. 1997; Muñoz et al. and will therefore be the domain of scien-
2007), retinol-binding protein (Rothschild tists and livestock breeding companies.
et al. 2000), prolactin receptor (Drogemuller However, as more becomes known regarding
et al. 2001), and erythropoietin receptor regions associated with speciﬁc traits and as
(Vallet et al. 2005b). Genomic scans for genotyping technology becomes cheaper,
various reproductive traits in pigs have been subsets of markers for speciﬁc traits will
reported (Rohrer et al. 1999; Wilkie et al. become available to producers to help ﬁne-
1999; Cassady et al. 2001; Holl et al. 2004; tune livestock for speciﬁc environments or
Tribout et al. 2008). The early genome scans speciﬁc markets.
were performed in deﬁned populations that
were crosses of lines with divergent pheno- Comprehensive genotyping and WGS
types (e.g., Meishan and European crosses, studies on populations of animals for which
crosses between lines selected for ovulation a variety of traits have been measured will
rate, embryo survival, and a randomly provide needed information on the genetic
selected contemporary control line). Use of loci that explain various negative genetic
these populations maximized detection of correlations between traits and possibly
reproduction QTL, but because they were between the mother and offspring for the
done in lines that were not fully relevant to same trait. Information on the genetic archi-
production lines used in the swine industry, tecture of these correlated traits will provide
validation of the regions in industry relevant genetic loci that can be selected to manipu-
pigs is an extra step to utilization of results late these negatively correlated traits inde-
of these genomics experiments in swine pendently of each other, or at least allow
production. balanced selection procedures taking into
account effects of the various loci on traits.
42 Quantitative Genomics of Reproduction
Selection for negatively correlated traits is trait, it seems likely that there may be fetal
now typically done using an index, to balance genes that only affect pregnancy outcome
selection for the traits. Index selection puts given an appropriate maternal environment,
selection pressure on all loci affecting both which would be controlled by genes of the
traits, both those with multiple antagonistic dam. Analysis for epistatic, environmental,
effects and those that independently affect and multiple genome interactions will be a
each trait. The net effect of this selection is future direction of QTL analysis of reproduc-
slower progress in changing the independent tive traits.
loci. Determination of the effects of loci
inﬂuencing various traits will allow a more Perhaps the brightest future for the genom-
direct and controllable approach to selection ics of female reproductive traits will be the
for correlated traits. information derived from the identiﬁcation
of the genes and the genetic variation within
Much of genomic analysis currently deals genes that are responsible for differences in
with independent additive effects of loci on reproductive traits. While not essential for
associated traits. Dominance and imprinting the primary utility of the technology, eluci-
effects at loci could also be incorporated dation of genes and polymorphisms respon-
into selection schemes as these effects can sible for differences in performance will
be readily detected in association studies. almost certainly follow from the identiﬁca-
Imprinting is deﬁned as differences in the tion of QTL affecting these traits, once the
expression of an allele depending on its regions are sufﬁciently narrowed to enable
parental origin. More difﬁcult are epistatic utility among livestock populations at large.
interactions between loci and environment However, using the milk production QTL on
by genetic locus interactions. A special case chromosome 6 as an example, proving that
that is similar to these effects but speciﬁc to a speciﬁc polymorphism within a speciﬁc
pregnancy associated traits is the interac- gene is actually responsible for the QTL can
tions between maternal, paternal, and fetal be difﬁcult. Any polymorphism will have
genetic inﬂuences on a trait. Epistatic gene nearby DNA variation more or less associ-
interaction occurs when the inﬂuence of a ated with it. Proof that a speciﬁc polymor-
genetic locus on a trait is dependent on the phism is responsible for the difference in the
presence or absence of alleles at other loci. trait will require elimination of the contri-
A useful reproductive example might be loci bution of other linked loci and/or corrobo-
inﬂuencing ovulation rate, loci inﬂuencing rating physiological studies that support the
uterine capacity, and their combined inﬂu- effect of a speciﬁc polymorphism. This could
ence on litter size. Because of the sequential take the form of transgenic incorporation of
nature of expression of ovulation rate and the polymorphism into unaffected individu-
uterine capacity, the inﬂuence of genes asso- als, but such experiments in livestock are
ciated with differences in uterine capacity currently very difﬁcult. In addition, the
will only be observed if the alleles needed lesson from sheep ovulation rate QTL and
for high ovulation rate are present. Similarly, dairy cattle milk production QTL on chro-
given the existence of environment by geno- mosome 6 suggest that establishing the
type interactions, some gene allele effects identity of the gene and the polymorphism
may only be observed under the appropriate does not necessarily immediately lead to an
environmental conditions. Finally, in the understanding of the role of that gene in the
case of multiple genotype interactions on a trait. Nevertheless, identiﬁcation of genes
Female Reproduction 43
responsible and elucidation of the physiolog- Ashwell, M.S., Heyen, D.W., Sonstegard,
ical mechanisms could lead to other nonge- T.S., Van Tassell, C.P., Da, Y., VanRaden,
netic means of improving reproductive and P.M., Ron, M., Weller, J.I., and Lewin,
other traits. This represents the overlap H.A. 2004. Detection of quantitative
between QTL genomics and so-called func- trait loci affecting milk production,
tional genomics, or the elucidation of how health, and reproductive traits in Holstein
gene function translates into differences cattle. Journal of Dairy Science 87(2):
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the greatest beneﬁt that may arise from QTL
studies, information about the genes, and Ashwell, M.S., Van Tassell, C.P., and
gene mechanisms that affect reproductive Sonstegard, T.S. 2001. A genome scan to
traits, leading to a variety of strategies to identify quantitative trait loci affecting
improve those traits. economically important traits in a US
Holstein population. Journal of Dairy
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Quantitative Genomics of Male Reproduction
Eduardo Casas, J. Joe Ford, and Gary A. Rohrer
3.1 Introduction the study of the genome. This term, pro-
posed by Thomas R. Roderick in 1986
An individual male that is selected as a sire (Editorial Perspective 1997), is used to iden-
impacts the output of a livestock enterprise tify the location of underlying genetic varia-
proportionately to a much greater extent tion. Limited studies have been focused on
than a single female. Adoption of artiﬁcial male reproduction in livestock species.
insemination combined with improved Thus, the objective of this chapter will be to
methods to estimate genetic merit narrowed establish the current status of quantitative
the number of sires that provide semen for genomics for male reproduction.
the dairy industry (Funk 2006). Similarly,
incorporation of marker-assisted selection 3.2 Male reproduction phenotypes
by beef, sheep, and swine producers will lead
to greater use of fewer sires with the most 3.2.1 Testes
desirable genetic worth, thereby magnifying
the impact of the fertility of these selected The testes are the primary organ of male
individuals upon productivity. In spite of reproduction, responsible for producing
these obvious changes in animal production, male gametes (spermatozoa) and hormones
investment of research into male reproduc- (steroids and proteins). Within the testes,
tion has diminished steadily during the past Sertoli cells provide support to germ cells as
decade. they mature into spermatozoa, while Leydig
cells are responsible for a wide range of ste-
Genome is understood as all the genetic roidal hormones (Reeves 1987). Production
material contained within the chromo- of spermatozoa is the primary function of
somes. The term was used by H. Winkler for males in most stud farms; it is desirable for
the ﬁrst time in 1920, when “gene” and males to produce spermatozoa as young and
“chromosome” were fused in a single word.
Genomics is the discipline that focuses on
54 Quantitative Genomics of Reproduction
as much as possible. Semen collection in the number of Sertoli cells in the testis.
livestock production systems (dairy and beef Similarly, the number of Sertoli cells in the
cattle, and swine industries) is an expensive testis is directly proportional with testicular
process. Therefore, it is necessary to identify size (Huang and Johnson 1996; Lunstra et al.
males with larger testis to increase the 2003; Ford et al. 2006). Lunstra et al. (1988)
number of doses per ejaculate and to reduce proposed a simple method to estimate testis
costs (Ford et al. 2006). volume, scrotal circumference (SC) that rep-
resents the connected circumference of two
3.2.2 Puberty apposed circles of equal radius (r), using the
The age at which males reach puberty is less
well deﬁned than in females. Puberty is the SC = 4r + 2πr.
age at which fertile spermatozoa are present
in the ejaculate. However, spermatozoa are 3.2.4 Average testicular length (ATL)
formed in seminiferous tubules prior to
being observed in the ejaculate. In bulls, ATL is the mean length of both testicles.
spermatozoa are present in seminiferous Then, assuming each testicle is a prolate
tubules at least 10 weeks prior to being spheroid, paired testicular volume (PTV)
observed in an ejaculate (Bearden et al. 2004). may be calculated as follows:
Lunstra et al. (1978) deﬁned puberty in bulls
as the age at which the male produces an PTV = 0.0396(ATL)(SC)2.
ejaculate containing at least 50 × 106 sper-
matozoa with more than 10% progressive 3.2.5 Semen evaluation
motility observed in an ejaculate. Genetic
variation exists for age at puberty, given that Physical and physiological characteristics of
diverse cattle breeds reach puberty at differ- semen that are considered as important
ent ages. Lunstra and Cundiff (2003) and traits in semen evaluation include total
Casas et al. (2007) estimated age at puberty sperm production, sperm motility, sperm
for crossbred animals derived from different viability, and percentage of abnormal sper-
cattle breeds. The Angus breed reaches matozoa (Hafez 1987). A male is considered
puberty at an earlier age (238 day of age), fertile at puberty when important traits in
while Brahman reach puberty later in life semen evaluation achieve thresholds for
(320 day of age). Thus, age at puberty is an these characteristics. However, in intensive
important component of a livestock produc- production systems (such as dairy), where
tion system that can be modiﬁed through there is a constant need for artiﬁcial insemi-
use of appropriate breeds. nation, males are considered fertile when
sperm characteristics reach the age at freez-
3.2.3 Testicular volume able semen. This is the age when the bull
produces an ejaculate containing at least
Testicular volume is a desirable characteris- 500 million sperm with more than 50% pro-
tic in males. Large testes are associated with gressive motility. The age at freezable semen
increased sperm production in bovine and represents a threshold after which freezing
swine (Lunstra et al. 1988; Ford et al. 2006). of semen becomes economically feasible
Sperm production is directly associated with (Hafez 1987; Lunstra et al. 1993).
Male Reproduction 55
3.3 Genetics, genomics, and for total sperm production ranges between
quantitative trait loci (QTL) 0.37 and 0.40, and Oh et al. (2006) estimated
the heritability for this trait between 0.27
3.3.1 Genetic variation of and 0.48 in swine. Lunstra et al. (1988)
male reproduction and Kealey et al. (2006) reported heritabili-
ties of moderate magnitude for % motility
Selection programs directed toward improv- in cattle (Table 3.1), indicating that semen-
ing male reproduction are lacking in all live- related traits have an underlying genetic
stock species of economic importance. component.
Limited attempts have been made to estab-
lish the genetic variation underlying male Genetic components also contribute to
reproduction. Toelle et al. (1984) reported the expression of testicular physical attri-
moderate heritability estimates for testes butes. Young et al. (1986) indicated that tes-
traits in Duroc and Yorkshire boars (Table ticular volume has a heritability ranging
3.1). Repeatability is the upper limit of the between 0.12 and 0.55 in swine. In cattle,
heritability, given that it includes the total the heritability for the same trait has been
genetic variance and the proportion of the estimated to be 0.37 (Lunstra et al. 1988).
environmental variance unique to the indi- The magnitude of the heritability estimates
vidual. Huang and Johnson (1996) and Smital indicates that inclusion of testicular physi-
et al. (2005) estimated that repeatability for cal attributes in selection programs would
semen traits ranged between 0.16 and 0.74 be effective.
in pigs. If the environmental variance was to
be negligible, the heritability of semen traits 3.3.2 Genomics approaches
would range between the values indicated
by Huang and Johnson (1996). Huang and An important component of genomics is the
Johnson (1996) indicated that repeatability development of genomic maps. The ﬁrst
Table 3.1 Genetic parameters for male reproductive traits in swine and cattle.
Species Trait H2 ± SE Reference
Swine Testicular volume (140 d) 0.21 ± 0.11 Toelle et al. (1984)
Cattle Testicular volume (168 d) 0.30 ± 0.12 Toelle et al. (1984)
Testicular volume (98 d) 0.12 ± 0.14 Young et al. (1986)
Testicular volume (154 d) 0.55 ± 0.12 Young et al. (1986)
% spermatogenesis 0.22 ± 0.22 Young et al. (1986)
Tubular diameter 0.50 ± 0.25 Young et al. (1986)
Total sperm cells/ejaculate 0.27–0.48 Oh et al. (2006)
Testis length (cm) 0.34 ± 0.06 Lunstra et al. (1988)
Paired testis volume (cm3) 0.37 ± 0.06 Lunstra et al. (1988)
Motility (%) 0.41 ± 0.06 Lunstra et al. (1988)
Motility (%) 0.22 ± 0.09 Kealey et al. (2006)
Scrotal circumference (cm) 0.57 ± 0.09 Kealey et al. (2006)
Scrotal circumference (cm) 0.31 ± 0.10 Quirino et al. (2004)
Concentration 0.16 ± 0.08 Kealey et al. (2006)
Ejaculate volume (mL) 0.09 ± 0.08 Kealey et al. (2006)
Ejaculate concentration 0.23–0.36 Carabano et al. (2007)
56 Quantitative Genomics of Reproduction
developed maps, known as linkage maps, QTL for production traits has been done in
consisted mostly of microsatellites. Linkage most livestock species producing a wealth of
maps have been developed for most econom- information regarding searches for QTL for
ically relevant species: porcine (Rohrer et al. growth traits like birth weight, weaning
1994, 1996; Archibald et al. 1995), bovine weight, ﬁnal weight, and growth rate. There
(Barendse et al. 1994, 1997; Bishop et al. have also been searches for QTL for milk
1994; Kappes et al. 1997), ovine (Crawford production and its components (Georges
et al. 1995; De Gortari et al. 1998), equine et al. 1995; Zhang et al. 1998; Rodriguez-Zas
(Penedo et al. 2005), and caprine (Vaiman et al. 2002; Ashwell et al. 2004) and for carcass
et al. 1996). The current effort is to produce traits that are economically important and
the complete sequence of the genome for expensive to measure (Rohrer and Keele
most economically relevant species and to 1998a,b; Casas et al. 2001, 2003, 2004a;
develop single nucleotide polymorphism Rohrer et al. 2001; Li et al. 2004; Mizoshita
(SNP) maps (Snelling et al. 2007; Li et al. et al. 2004; Walling et al. 2004). Detection of
2008). These maps have been used to iden- informative QTL for these traits allows pro-
tify markers associated with, and to assess ducers to identify animals with the most
the existence of genes involved in the expres- genetic potential at an earlier age than in
sion of economically important traits in traditional selection schemes.
3.3.3 QTL basics 3.4 QTL identiﬁed for male
Economically important traits in livestock
are considered quantitative traits because Male reproductive traits in livestock have
they are controlled by several genes. been infrequently studied. Several studies
Although quantitative traits are regulated by have established the existence of genetic
several genes (Geldermann 1975), it has been variation for male reproductive traits in live-
postulated that not all genes have similar stock (Table 3.1). However, a limited number
inﬂuence in their expression, and that few of studies identiﬁed chromosomal regions
genes contribute to a greater extent to the where genes associated with male reproduc-
expression of genetic variation (Lande 1981). tive traits reside. Table 3.2 lists the chromo-
We now have the technology to identify the somes in which QTL for male reproductive
regions where genes inﬂuencing economi- traits have been detected.
cally important traits reside in the genome;
however, this is not a new concept (Smith 3.4.1 QTL mapping for boar
1967). These approaches require phenotypic reproduction traits
information on large populations of animals
with known parentage. In boars, several chromosomal regions likely
contain genes associated with male repro-
The genomic regions where genes inﬂuenc- ductive traits. Evidence suggests the pres-
ing the expression of economically impor- ence of QTL for these traits on swine
tant traits reside are known as QTL. Given chromosomes X, 3, and 8 that harbor genes
that multiple genes inﬂuence quantitative associated with plasma follicle-stimulating
traits, several chromosomal regions will hormone (FSH), and testicular weight in
inﬂuence a speciﬁc trait. Identiﬁcation of
Table 3.2 Quantitative trait loci for male reproductive traits in livestock. Male Reproduction 57
Species Chromosome Trait Reference
Swine SSC3 Plasma FSH Rohrer et al. (2001)
Cattle SSC3 Testicular weight Sato et al. (2003)
SSC8 Plasma FSH Rohrer et al. (2001)
SSC10 Plasma FSH Rohrer et al. (2001)
SSCX Plasma FSH Rohrer et al. (2001)
SSCX Testicular weight Sato et al. (2003)
SSCX Testicular weight Ford et al. (2001)
Casas et al. (2004b)
BTA5 Plasma FSH Casas et al. (2004b)
BTA29 Paired testis weight Casas et al. (2004b)
BTA29 Paired testis volume Casas et al. (2004b)
BTA29 Age at puberty Casas et al. (2004b)
BTA29 Body weight at castration
FSH, follicle-stimulating hormone.
males. In sows, similar chromosomal regions the family structure of the population
have been associated with ovulation rate studied. No additional studies have been
(Rohrer et al. 1999), but it remains to be conducted in other livestock species showing
determined if the same genes are involved evidence of a QTL on chromosome X for
in both traits in both sexes. male reproduction traits.
There is evidence that a gene or cluster of Swine chromosome 3 harbors genes asso-
genes, residing on swine chromosome X, is ciated with male reproduction (Table 3.2).
involved in the expression of male reproduc- Sato et al. (2003) identiﬁed a chromosomal
tive traits (Figure 3.1; Nonneman et al. region associated with testes weight span-
2005). Lunstra et al. (1997) indicated that ning the interval between marker SWR1637
Meishan sires exhibited smaller testes when and S0094. These markers are located in
compared with conventional swine breeds. centimorgans 28 and 58 of the swine linkage
Ford et al. (2001) and Rohrer et al. (2001), map, respectively (Rohrer et al. 1996). The
using a population derived from Meishan maximum evidence for the presence of the
and White Composite, determined that QTL for testes weight was at centimorgan
animals inheriting this speciﬁc region of the 47. In the same chromosomal region, Rohrer
X chromosome from the Meishan breed had et al. (2001) identiﬁed a QTL associated with
smaller testicles and greater plasma FSH plasma FSH in males. The location of the
concentrations identiﬁed when compared QTL from Rohrer et al. (2001) resided
with the White Composite. Sato et al. (2003), between markers SW2527 and SW2618.
using a crossbred population from Meishan These markers are located at centimorgan
and Duroc, conﬁrmed these ﬁndings. A QTL 42 and 51 of the linkage map, respectively
for testicular weight has also been detected (Rohrer et al. 1996). For this region of chro-
in the X chromosome in mice (Le Roy et al. mosome 3, Sato et al. (2003) indicated that
2001). In cattle, Casas et al. (2004a) evalu- animals inheriting the Meishan allele had
ated a paternal half-sib family obtained from heavier testes weight, while Rohrer et al.
an F1 sire (Brahman × Hereford) but were (2001) found that in this region, animals
unable to analyze the X chromosome due to with the Meishan allele had less plasma FSH
58 Quantitative Genomics of Reproduction
Figure 3.1 F-ratio proﬁles on swine chromosome X indicating evidence of QTL for plasma follicle-
stimulating hormone (FS), testicular weight (TW), and backfat (B). Genetic markers are aligned in their rela-
tive position on the porcine cytogenetic, genetic, and physical maps and compared with the human physical
sequence map. Units are in centimorgans (cM), centirays (cR), and megabases (Mb). Figure was repro-
duced from Nonneman et al. (2005).
concentration. It is possible that a gene in established whether similar genes may be
this chromosomal region has an antagonis- inﬂuencing the same trait in males and
tic effect. That is, for this chromosomal females.
region, animals with the Meishan allele
exhibit lower plasma FSH and lighter testes 3.4.2 QTL mapping for bull
as opposed to what has been observed on reproduction traits
swine chromosome X (Ford et al. 2001;
Rohrer et al. 2001; Sato et al. 2003) and what In cattle, a QTL for plasma FSH was identi-
has been observed in the Meishan breed ﬁed on chromosome 5 (Casas et al. 2004b).
(Lunstra et al. 1997). This QTL resides between centimorgans 47
and 82 of the bovine chromosome 5 linkage
Regions of swine chromosome 3, 8, and X, map (Kappes et al. 1997). Several studies
where QTL for plasma FSH have been iden- have detected QTL for ovulation rate or
tiﬁed, reside in similar locations where QTL twinning rate in cattle in this chromosome.
for ovulation rate have been detected. Rohrer Lien et al. (2000) and Cruickshank et al.
et al. (2001) indicated that it remains to be
Male Reproduction 59
(2004) detected a QTL for twinning rate in a the genome (candidate genes under a QTL),
similar region of bovine chromosome 5. based on their putative role in the expression
Similarly, Kappes et al. (2000) identiﬁed a of male reproductive traits, or at random.
QTL for ovulation rate on a similar region
of the chromosome. The position of the QTL Wimmers et al. (2005) provided some evi-
in the three studies is similar to the position dence for the effect of a marker at the gamma-
where the QTL for plasma FSH was identi- actin 2 (ACTG2) gene for sperm volume in
ﬁed by Casas et al. (2004b). If the QTL for boars (Table 3.3). This gene resides on swine
ovulation rate in females and the QTL for chromosome 3, making it a potential candi-
plasma FSH in males are caused by a single date associated with male fertility traits. Lin
gene, then the mechanism behind the QTL et al. (2006b) evaluated markers at the gonad-
for ovulation rate is possibly related to regu- otropin-releasing hormone receptor gene and
lation of FSH in the female with a similar reported an SNP in this gene that associates
effect on FSH expression in males. with % motility and abnormal sperm rate
(Table 3.3). This gene could be considered a
3.4.3 Candidate genes associated with putative candidate gene for the QTL detected
male reproduction in this chromosome. Rohrer et al. (2001) pos-
tulated a candidate gene for the QTL detected
Several studies have attempted to establish on swine chromosome X. They indicated
association between molecular markers and that androgen receptor (AR) is one potential
male reproductive traits. Table 3.3 shows a candidate for this QTL. Lin et al. (2006c)
summary of these associations. Markers evaluated a marker developed in this gene
have been developed and evaluated in diverse and found it to be unassociated with any
populations for their association with the male reproductive trait. However, Nonneman
expression of male reproductive traits based et al. (2005) postulated that a marker in the
on the gene in which they reside. These genes thyroxine-binding globulin (TBG) could be
have been selected based on their location on used in marker-assisted selection. Differ-
ences in plasma FSH concentration and
Table 3.3 Candidate genes associated with male reproductive traits in swine.
Chromosome Gene Trait Reference
1 ESR1 Sperm volume Terman et al. (2006)
Sperm concentration Terman et al. (2006)
3 ACTG2 % sperm alive Terman et al. (2006)
7 PGK2 Sperm volume Wimmers et al. (2005)
Sperm concentration Lin et al. (2006c)
Semen volume Chen et al. (2004)
% motility Lin et al. (2006b)
Abnormal sperm rate Lin et al. (2006b)
Testis weight Nonneman et al. (2005)
FSH concentration Nonneman et al. (2005)
% motility Lin et al. (2006a)
Abnormal sperm rate Lin et al. (2006a)
ESR1, estrogen receptor; ACTG2, gamma-actin 2; ACR, acrosin; PGK2, phosphoglycerate kinase 2; GNRHR, gonadotropin-releasing
hormone receptor; TBG, thyroxine-binding globulin; ACTB, beta-actin.
60 Quantitative Genomics of Reproduction
testis weight were observed when comparing Thurston et al. (2002), using ampliﬁed frag-
alternative alleles in this gene. The TBG ment length polymorphisms, found 16 can-
gene resides in the same region where the didate genetic markers associated with
QTL for plasma FSH was detected (Figure differences in semen freezability within a
3.1), making TBG a likely candidate gene for small population of boars previously classi-
this QTL. ﬁed as good and poor freezers. Thurston
et al. (2002) proposed that these ﬁndings
Terman et al. (2006) evaluated a marker demonstrate the existence of a genetic basis
for estrogen receptor gene (ESR1) and found to this variation. No indication is given to
an association with male fertility traits the location in the genome where these
(Table 3.3). Interest in ESR1 was stimulated markers reside. Therefore, the information
by the report of Rothschild et al. (1996) presented by Thurston et al. (2002) is of
implicating an association of allelic variants limited use in genomic studies.
for this gene with litter size. Acrosin is a
trypsin-like serine proteinase extrinsically Chanock et al. (2007) indicated that it is
associated with membranes of the mamma- unlikely that a single study may establish a
lian sperm acrosome (Straus and Polakoski genotype–phenotype association without
1982). Acrosin is required during the acro- the need for replication. This is the case for
some reaction, to facilitate sperm penetra- studies where candidate genes are selected
tion to the oocyte (Westbrook-Case et al. based on their location in the genome (under
1994) and acrosin activity has been associ- QTL) and followed by the selection of can-
ated with infertility in humans (Nakagawa didate genes. The QTL scan is presented as
et al. 1997). Lin et al. (2006c) evaluated a initial evidence of the presence of a gene in
signiﬁcant marker near this gene on swine a speciﬁc chromosomal region, and evalua-
chromosome 5 and observed a signiﬁcant tion of markers in genes under this QTL in
allele substitution effect for sperm concen- additional populations is a replicate of the
tration (Table 3.3). Phosphoglycerate kinase study. Conclusions drawn from these studies
2 (PGK2) is an enzyme that modulates sperm are useful and productive in the implemen-
metabolism during epididymal transport tation of programs where this information is
(Salisbury et al. 1977). Chen et al. (2004) to be used. Results from candidate genes
evaluated an SNP in this gene on swine based on their putative role in the expres-
chromosome 8 (Table 3.3) and observed that sion of traits studied, imply the existence of
homozygous animals for one allele had the genetic variation for male reproductive
tendency to produce a smaller sperm volume traits; however, most studies showed weak
than homozygous animals with the alterna- association between markers and traits, and
tive genotype. Additionally, Lin et al. (2006a) no replication was pursued. This may lead
evaluated haplotypes developed from SNPs to incorrect conclusions about the role of
in the beta-actin (ACTB) gene (Table 3.3) and selected genes based exclusively on their
observed that different haplotypes affected role in the expression of a trait.
the variation of % motility and abnormal
sperm rate in populations of Pietrain and 3.5 Future research directions
Pietrain × Hampshire boars.
The objective of improvement programs is
Markers throughout the genome have to identify those individuals with the best
been used to detect chromosomal regions
associated with boar sperm viability.
Male Reproduction 61
genetics, to become the founders of the fol- Nicholson, D., Coppieters, W., Van de
lowing generation. Artiﬁcial insemination Weghe, A., Stratil, A., Wintero, A.K.,
is the most used tool to disseminate the Fredholm, M., Larsen, N.J., Nielsen, V.H.,
improvement in a species or population. Milan, D., Woloszyn, N., Robic, A.,
Male reproduction is one of the most impor- Dalens, M., Riquet, J., Gellin, J., Caritez,
tant components in this process. A single J.-C., Buraud, G., Ollivier, L., Bidanel, J.-
male will have a greater impact in the P., Vaiman, M., Renard, C., Geldermann,
improvement of a trait than any female. H., Davoli, R., Ruyter, D., Verstege,
Despite this fact, insufﬁcient emphasis is E.J.M., Groenen, M.A.M., Davies, W.,
placed on the study of male reproduction. Hoyheim, B., Kieserud, A., Andersson, L.,
Few studies have focused on the study of Ellegren, H., Johansson, M., Marklund, L.,
genetic variation behind the expression of Miller, J.R., Anderson Dear, D.V., Signer,
male reproductive traits. This variation can E., Jeffreys, A.J., Moran, C., Le Tissier
be exploited to improve reproduction in Muldano, P., Rothschild, M.F., Tuggle,
males through breeding programs. However, C.K., Vaske, D., Helm, J., Liu, H.-C.,
the cost and time required to obtain appro- Rahman, A., Yu, T.-P., Larson, R.G., and
priate phenotypic data from large popula- Schmitz, C.B. 1995. The PiGMaP consor-
tions of males hamper this research. tium linkage map of the pig (Sus scrofa).
Mammalian Genome 6: 157–175.
Genomics is a thriving area of research Ashwell, M.S., Heyen, D.W., Sonstegard,
that will assist in understanding the genetic T.S., Van Tassell, C.P., Da, Y., VanRaden,
basis of physiological mechanisms. Of the P.M., Ron, M., Weller, J.I., and Lewin,
limited number of studies where genomics H.A. 2004. Detection of quantitative trait
of male reproductive traits are analyzed, loci affecting milk production, health,
most have shown weak associations between and reproductive traits in Holstein cattle.
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tility rate in females. Genomic regions in Teale, A.J., Fries, R., McGraw, R.A.,
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Identiﬁcation of ampliﬁed restriction
fragment length polymorphism markers
Genetics and Genomics of Reproductive Disorders
Peter Dovc, Tanja Kunej, and Galen A. Williams
4.1 Introduction mutations for reproductive disorders a dif-
ﬁcult task. In addition, the frequency of the
Genetics of reproductive traits in farm majority of reproductive disorders is rather
animals is becoming an increasingly impor- low, thus making acquisition of appropriate
tant ﬁeld of research of late and certainly has material quite often problematic. Some
been signiﬁcantly propelled by the advances reproductive disorders are caused by complex
in genomic research. The literature describ- developmental mechanisms, which are dif-
ing reproductive disorders in farm animals ﬁcult to explain by simple genetic means.
is densest during two periods of time. The An example for such a disorder is cross-
ﬁrst period (late 1970s, early 1980s) described contamination of fetal bloodstream with
mostly anatomical and pathophysiological cell populations and sex hormones through
characteristics of disorders without refer- placental anastomoses causing formation of
encing possible causal mutations in the can- XX/XY chimeras in the case of dizygotic
didate genes. Publications from the second pregnancies with fetuses of different sex.
period (late 1990s through the present) XX/XY chimeras appear in many species
attempted to either conﬁrm the role of can- with rather different frequencies with
didate genes by identifying causal mutations equally varied effects. The clinical conse-
or apply genomic approaches in order to quences are by far the most severe in cattle,
identify quantitative trait loci (QTL) regions, less so in sheep and pigs, and virtually no
associated markers, or homologous regions negative effects in horses. From this example,
across the species barrier, which could be it is obvious that the same phenomenon
involved in the genesis of reproductive (bloodstream communication among fetuses
disorders. However, the traditional assump- of different sex) can result in completely
tion of the polygenic nature of reproductive different clinical consequences. Apparently,
traits, in addition to likely environmental the frequency and extent of hormone and
effects, makes the identiﬁcation of causal blood cell exchange between feti is a result
68 Quantitative Genomics of Reproduction
of species speciﬁc architecture of placental In mouse, Simon et al. (1997) described the
circulation in cattle; however, the real cause crucial role of connexin 37 in oogenesis and
for the formation of anastomoses remains ovulation. Connexin 37 is a member of the
unclear. family of gap junction proteins, which are
structurally related transmembrane proteins
In this chapter, we will review relevant that assemble to form vertebrate gap junc-
literature and present the current status of tions. Connexin 37 is present in gap junc-
relevant information related to reproductive tions between oocyte and granulosa cells and
disorders in farm animals. In some cases, we is involved in cell–cell signaling, which criti-
will refer to similar disorders in man or in cally regulates complex cellular interactions
model organisms (mainly mouse) in order that are required for oogenesis and ovulation.
to give some hints for necessary further Mice lacking connexin 37 lack graaﬁan fol-
research in this important but difﬁcult licles, resulting in arrested oocyte develop-
ﬁeld. ment before achieving meiotic competence.
These mice then fail to ovulate and develop
4.2 Reproductive disorders numerous corpora lutea.
associated with the ovary
In the Mouse Genome Informatics (MGI)
4.2.1 Ovarian subfunction database, 11 genes associated with the gene
ontology term “ovulation from ovarian
Ovarian subfunction can result in several follicle” were found, including Adamts1,
undesired phenotypic traits that affect repro- a disintegrin-like and metallopeptidase (rep-
ductive capacity in virtually all species. The rolysin type) with thrombospondin type 1
most frequently studied traits relating to motif, 1; Afp, alpha fetoprotein; Agt, angio-
this disorder are ovulation rate, silent heat, tensinogen (serpin peptidase inhibitor, clade
and litter size. Therefore, selection strate- A, member 8); Bfo, bell ﬂash ovulation;
gies and different methods of genetic screen- Foxo3, forkhead box O3; Nos2, nitric oxide
ing have been applied to identify the major synthase 2, inducible, macrophage; Nos3,
genetic causes underlying ovarian subfunc- nitric oxide synthase 3, endothelial cell;
tion. Due to the economic importance of Nrip1, nuclear receptor interacting protein
ovulation rate, this is the most systemati- 1; Oas1d, 2′-5′ oligoadenylate synthetase 1D;
cally studied trait related to ovarian func- Pgr, progesterone receptor; and Sirt1, sirtuin
tion in farm animals. Certainly, for selection 1 (silent mating type information regulation
purposes, genes enhancing ovulation rate are 2, homolog) 1 (Saccharomyces cerevisiae).
of central interest; however, allelic counter- These candidate genes may be associated
parts of positive alleles could be considered with ovarian subfunction due to their pleio-
as alleles that have negative effect on the tropic mode of action in different tissues.
A comparative mapping approach based
Ovulation is the ﬁnal event in the process on 11 genes from human chromosome
of ovarian follicle maturation and describes 4p16-p15 and exploitation of porcine large-
the discharge of the ovum from the graaﬁan insert genomic libraries revealed 11 poten-
follicle. Conversely, ovulation failure is a tial candidate genes for the ovulation rate
situation when the ripe follicle does not in the porcine homologous region at SSC8
rupture and discharge its ovum. (Campbell et al. 2003). Seven genes (GNRHR,
IDUA, MAN2B2, MSX1, PDE6B, PPP2R2C,
Genetics and Genomics of Reproductive Disorders 69
and RGS12) were mapped using informative mannosidase 2B2 (MAN2B2) for ovulation
microsatellite markers, three genes (LRPAP1, rate within the targeted QTL region on the
GPRK2L, and FLJ20425) were mapped using p-terminal end of pig chromosome 8 (Figure
single nucleotide polymorphisms (SNPs), 4.1) in a Meishan-cross resource population.
and two genes were identiﬁed using marker Eleven nonsynonymous mutations in the
information in selected genomic clones coding region for mannosidase 2B2 were
assigned since they were present in clones identiﬁed and tested for statistical asso-
that contained mapped markers (HGFAC ciations with ovulation rate in a resource
and HMX1). The resulting linkage map con- population over three generations. The most
tains markers associated with 14 genes in signiﬁcant effect was associated with a
the ﬁrst 27 cM of the porcine chromosome polymorphism located at position 1574 of
8. In the region with the highest F-ratio the mRNA (1574A>G) where the additive
were markers closest to the MAN2B2 effect of the 1574A allele was estimated
gene. In a later study, Campbell et al. (2008) to be −0.89 ova. Due to the fact that this
identiﬁed positional candidate gene, coding polymorphism was not associated with
OVRATE OVRATE OVRATE OVRATE
SSC 2 SSC 3 SSC 4 SSC 8 SSC 10
SSC 1 SSC 5 SSC 9
OVRATE SSC 6
OVRATE SSC 18 SSC Y
SSC 11 SSC 14 SSC 16 SSC 17
SSC 12 SSC 15
QTL Mapper v. 1.643 SSC X
Figure 4.1 Genomic distribution of QTL for the ovulation rate in pigs (AnimalQTL database; www.
animalgenome.org/QTLdb/). Courtesy of the NAGRP Bioinformatics Project Team.
70 Quantitative Genomics of Reproduction
ovulation rate in the occidental population, or GDF9 mutations were anovulatory,
the authors concluded that MAN2B2 whereas animals heterozygous for BMP15 or
has either a unique epistatic interaction GDF9 or heterozygous or homozygous for
within the Meishan-cross population or the ALK6 had elevated ovulation rates (Notter
1574A>G SNP is in linkage disequilibrium 2008). The authors were able to show by
with the causative genetic variant in the immunizing ewes against BMP15 or GDF9
Meishan-cross population. that both proteins are essential for follicular
development and control of ovulation rate.
Further studies revealed a number of can- Several point mutations in two growth
didate genes possibly associated with ovula- factor genes (BMP15 and GDF9) and a related
tion rate in pigs. Among them were the most receptor (ALK6) have been found to be
promising gene for the aldo-keto reductase associated with ovulation rate in different
1C (AKR1C) gene, which was also associated sheep breeds (McNatty et al. 2005a). As well,
with age at puberty and nipple number heterozygotes for mutations in BMP15 or
(Nonneman et al. 2006). Four candidate GDF9 or homozygotes for the ALK6 muta-
genes (PIP5K2A, ITIH2, GAD2, and AKR1C2) tion had higher ovulation rates (i.e., +0.6–10)
were identiﬁed in the vicinity of the QTL than their wild-type contemporaries. The
region at SSC10 (Nonneman and Rohrer expression of BMP15 and GDF9, which is
2003). A physiological candidate gene, SPP1, restricted to the oocyte, supports a new para-
was found in the QTL region on the short digm in reproductive biology, presenting the
arm of the SSC8 (King et al. 2003). oocyte as a major player in the regulation of
Galloway et al. (2002) found an interesting
effect of the bone morphogenic protein 4.2.2 Ovarian cyst
(BMP15) locus in sheep. BMP15, also known
as growth and differentiation factor 9B Cystic ovarian disease (COD) is a common
(GDF9B), is a member of the transforming disease in cattle, particularly in dairy breeds
growth factor beta superfamily (TGFbeta), and less common in sows, mares, dogs, and
which is, in humans, rodents, and sheep, cats. The disease is characterized by gross
expressed only in the oocyte. Inactivation of estrus abnormalities, either anestrus or more
the BMP15 gene in mice has only minor frequent and prolonged estrus. COD includes
effects on fertility, whereas in sheep hetero- the formation of the cystic follicle (CF),
zygous for a BMP15 mutation, an increase luteal cyst (LC), and cystic corpus luteum
in ovulation rate has been observed, but (CCL). Mature follicle ovulation failure is
homozygote animals are infertile. However, a result of exogenous or endogenous dis-
the discovery that a point mutation in the ruption of the hypothalamo-hypophyseal-
BMP1B receptor in Booroola sheep is respon- ovarian axis. The anovulatory follicular
sible for increased ovulation rate conﬁrms structure can regress or persist as a follicular
the importance of the TGFbeta signaling cyst or LC. CFs do not rupture, are signiﬁ-
molecules in early folliculogenesis. cantly enlarged, and may appear as multiple
CFs on both ovaries. They are usually
McNatty et al. (2005b) conﬁrmed the caused by insufﬁcient level of luteinizing
involvement of BMP15, GDF9, and activin hormone. The two pathological forms of
receptor-like kinase 6 (ALK6), otherwise bovine COD, follicular cysts, and LCs are
known as the BMP receptor type IB (BMPRIB),
on the ovulation rate in sheep. As previously
shown, animals homozygous for the BMP15
Genetics and Genomics of Reproductive Disorders 71
etiologically and pathogenetically related At the ovarian level, cellular and molecu-
but differ clinically. lar changes in the growing follicle may con-
tribute to anovulation and cyst formation.
It is a common belief that COD is caused Differences in receptor expression between
by high milk production. However, this cystic ovarian follicles and dominant folli-
observation is biased since higher-producing cles may be an indication of the pathways
cows are more likely to be examined, more involved in cyst formation (Vanholder et al.
likely to be treated if found to have COD, 2006).
and more likely to remain in the herd despite
some decrease in reproductive performance. Although the genetic background of COD
Multiple evidences suggest that COD etiology is unclear, there are several reports
increases milk production, rather than high in the literature revealing the association of
production causing cows to develop COD. different loci with the appearance of COD.
The incidence of COD increases with age Sharif et al. (1998) reported the association
with the reported herd incidence of 5–25% of bovine leukocyte antigen (BoLA) alleles
per lactation. (BoLA-DRB3.2*22, *2, and*16) with a lower
risk of COD in Holstein cattle. Increased
The pathogenesis of ovarian cyst develop- expression of LH receptor and 3b-hydroxys-
ment is still poorly understood, but the teroid dehydrogenase mRNAs in granulosa
general hypothesis is that COD results cells and increased follicular estradiol-17b
from an imbalance of neuroendocrine hor- concentrations were associated with domi-
mones involving the hypothalamic-pituitary- nant cysts compared with normal follicles
gonadal axis, by endogenous or exogenous (Calder et al. 2001). In transgenic female
factors. The lack of the preovulatory surge of mice overexpressing plasminogen activator
luteinizing hormone (LH) in cystic cows inhibitor-1, increased incidence of polycys-
seems to be associated with a lowered gonad- tic ovarian changes was found (Devin et al.
otropin-releasing hormone (GnRH) content 2007).
in the hypothalamic area (Hooijer et al. 2003).
Secretion of GnRH/LH from the hypothala- In the MGI database, 22 genes associated
mus-pituitary is aberrant, which is caused by with the GO term “ovary cysts” were
insensitivity of the hypothalamus-pituitary found: Amhr2, anti-Müllerian hormone type
to the positive feedback effect of estrogens. 2 receptor; Bmp15, bone morphogenetic
Cysts occurring within the ovary include fol- protein 15; Brca1, breast cancer 1; Cyp19a1,
licular cysts, LCs (luteinized follicular cyst), cytochrome P450, family 19, subfamily a,
cystic corpora lutea, cystic rete ovarii, inclu- polypeptide 1; Esr1, estrogen receptor 1
sion cysts derived from the surface epithe- (alpha); Fanca, Fanconi anemia, complemen-
lium, and cysts of the subsurface epithelial tation group A; Fancl, Fanconi anemia,
structures. Luteal and follicular cysts are complementation group L; Foxc1, forkhead
derived from anovulatory graaﬁan follicles box C1; Fshr, follicle-stimulating hormone
and most likely represent different manifes- receptor; Gdf9, growth differentiation factor
tations of the same condition. In cattle, fol- 9; Gja1, gap junction protein, alpha 1; Kiss1,
licular cysts develop most commonly in KiSS-1 metastasis suppressor; Kit, kit onco-
heavily producing animals during the winter gene; Lhb, luteinizing hormone beta; Mos,
period. In some cases of cystic ovarian degen- Moloney sarcoma oncogene; Nobox, NOBOX
eration, mucometra, a uterus distended with oogenesis homeobox; Ots1, ovarian tera-
a ﬂuid containing much mucin, can occur. toma susceptibility 1; Pdcd4, programmed
72 Quantitative Genomics of Reproduction
cell death 4; repro46, reproductive mutant characteristic is that female animals do not
46, JAX Reproductive Mutagenesis Program; give any behavioral signal that an ovarian
Rspo2, R-spondin 2 homolog (Xenopus follicle is maturing and rupturing although
laevis); Tom1l2, target of myb1-like 2 the follicle maturation and ovulation
(chicken); and Ybx2, Y box protein 2. occurred normally. In the case of silent heat,
ovulation can be detected by palpation or by
The increased permeability of microves- measuring estrogen levels in the blood. The
sels, causing the accumulation of follicular frequency of silent heat decreases with the
ﬂuid in CFs may be caused by expression of progress of lactation, so that incidence is
vascular endothelial growth factor (VEGF) relatively low by 4 months postpartum.
receptors in the granulosa and theca interna Palpation and measuring of estrogen in milk
layers (Isobe et al. 2008). Ortega et al. (2008) or in plasma are the only methods allowing
suggested an important role for the insulin- detection of cows with true silent heat.
like growth factor (IGF)-I in the regulation of Analysis of the most common factors
folliculogenesis and also its involvement in involved in silent heat syndrome revealed a
the pathogenesis of COD in cattle. However, number of possible causes including negative
in the rat model, considerable changes in energy balance postpartum, high milk yield,
the ovarian expression of IGF-I, ﬁbroblast age, breed, season, stress, and other diseases,
growth factor (FGF)-2, and VEGF were and also the quality of estrus detection and
detected in induced COD (Ortega et al. 2007). housing (Hoedemaker 2008), placing the inci-
dence of silent heat between 10% and 40%
In high-yielding dairy cows with COD, a in different herds (Zdunczyk et al. 2005). The
signiﬁcantly lower insulin response to a fact that there were observed differences in
standard glucose load was observed (Opsomer silent heat frequency among breeds and that
et al. 1999), and therefore, insulin was con- disturbance of the hypothalamo-hypophysial
sidered as a factor in the pathogenesis of ovarian system, which is under genetic as
COD. In animals with COD, the follicular well as environmental control, supports the
cysts synthesized a signiﬁcantly higher assumption that a genetic component is also
amount of estrogen receptor alpha in all fol- involved in the silent heat syndrome.
licular layers than secondary, tertiary, and
atretic follicles in healthy animals (Salvetti 4.2.4 Retained corpus luteum
et al. 2007). Ovaries of animals with COD
exhibited altered estrogen receptor expres- Retained corpus luteum is characterized by
sion compared with that in normal animals. the failure of corpus luteum resorption at
Dissen et al. (2000) reported that an abnor- the appropriate time in the reproductive
mally elevated production of nerve growth cycle. As a consequence, the animal remains
factor (NGF) within the ovary sufﬁces to anestral. Abnormal persistence of the corpus
initiate several structural and functional luteum occurs in several species. In the
alterations associated with the development bitch, the corpus luteum is normally retained
of follicular cysts in the rat ovary. for a prolonged period after ovulation, but in
other species, retention of the corpus luteum
4.2.3 Silent heat in undesirable, because it frequently pre-
vents normal cycling. Corpus luteum reten-
In the literature, silent heat is frequently tion in cattle usually occurs postpartum,
referred to as silent estrus, silent ovulation,
anaphrodisia, or anestrus. The prevailing
Genetics and Genomics of Reproductive Disorders 73
frequently in association with disorders metrial hyperplasia with secondary bacterial
such as fetal mummiﬁcation, endometritis, infection (Figure 4.2). Typical is the accumu-
pyometra, or hydrometra. These disorders lation of purulent or mucopurulent material
often disrupt normal cyclic luteolysis, most within the uterine lumen, persistent corpus
likely because of impaired transfer of pros- luteum is present, and the cervix is closed
taglandin F2α from the uterus to the ovary. (Sheldon et al. 2006). Pyometra is frequent
In the mare, retention of the corpus luteum in older bitches, 4–6 weeks after estrus, in
can occur spontaneously, in the absence of cows; it is invariably accompanied by the
uterine disorders and affected mares cease persistence of an active corpus luteum and
cycling. In some species, the corpus luteum interruption of the estrous cycle. In affected
may persist in the absence of pregnancy, mares, the cervix is often ﬁbrotic, inelastic,
which causes “pseudopregnancy” with clin- or otherwise impaired. Mares may continue
ical signs of pregnancy. to cycle normally, or the cycle may be inter-
rupted. Discharge from the genital tract may
4.3 Reproductive disorders be absent or intermittent. As a rule, affected
associated with the vagina animals do not exhibit any systemic signs of
and uterus illness, but affected mares may be in poor
condition. Metritis is an inﬂammation of
4.3.1 Pyometra and puerperal metritis the uterus, while puerperal metritis is an
infection of the pregnant uterus. Cows
Pyometra is a hormonally mediated dies- failing to eliminate infection more than 21
trual disorder characterized by cystic endo- days after calving develop endometritis,
Cow and Dirty cow Vet visit Sick cow Vet visit Repeat breeder
Apparently Normal cow Normal cow
Clinical Fetid red/brown, Fever normal cow
exam watery diarrhea Dehydration Subclinical Pyometra
Dull Clinical endometritis
Inappetance endometritis Normal
yield Fluid in uterus
Puerperal metritis Clinical Uterine distension
Vaginal Discharge Discharge Discharge Normal
Rectal Enlarged uterus Fluid in uterus Fluid in uterus Fluid in uterus
palpation Fluid in uterus
00 14 21 28 35 42 60
Figure 4.2 Classiﬁcation and diagnosis of uterine disease in postpartum cows. Metritis develops between
1 and 21 days after calving, endometritis between 22 and 42 days. Pyometra occurs 43 days onward after
calving in cows with an active corpus luteum (CL) and closed cervix (Chapwanya 2008). Reprinted with
permission from IFP Media, Irish Veterinary Journal.
74 Quantitative Genomics of Reproduction
which is either a clinical or a subclinical reduction in lactoferrin observed in early
inﬂammation of the uterine endometrium diestrus may impair antimicrobial defense.
characterized by a purulent vulval discharge Also, enhanced expression of lactoferrin
up to 42 days postpartum with no signs of mRNA in the endometrium with pyometra
systemic illness. Unresolved endometritis may be associated with neutrophil invasion
often progresses to pyometra. into the uterus to combat the infection.
Acute puerperal metritis occurs in all Ishiguro et al. (2007) studied the relation-
species within the ﬁrst postpartum week. ship between adherence of Escherichia coli
It results from the infection of the repro- and expression of mucin-1 mRNA in the
ductive tract at parturition and often endometrium of beagle bitches at different
follows complicated parturition. The caus- stages of the estrous cycle and in those with
ative organisms in cattle are most frequently cystic endometrial hyperplasia/pyometra
Arcanobacterium pyogenes in association complex. Bitches with pyometra had a lower
with gram-negative anaerobic bacteria such level of expression of the MUC1 gene, and
as Fusobacterium necrophorum. The condi- the number of E. coli adhering to the endo-
tion is acute in onset. Affected cows, mares, metrial epithelial cells was inversely corre-
ewes, does, or sows are depressed and may lated with the level of MUC1 transcription.
be febrile without appetite. A fetid, watery Sugiura et al. (2004) demonstrated suppressed
uterine discharge is characteristic for cows activity of cellular immunity in the ﬁrst half
but may not be present in other species. of the diestrous stage, characterized by sig-
Puerperal metritis is often associated with niﬁcantly decreased response of peripheral
retained placenta, dystocia, and stillbirth, blood mononuclear cells (PBMNCs) to infec-
and usually occurs toward the end of the tion, but increased in proestrus/estrus. This
ﬁrst week postpartum. is probably the consequence of increased pro-
gesterone concentration and minimal estro-
Expression of lactoferrin in canine uterus gen release. This marked decrease of immune
has been investigated during the estrous resistance allows the expansion of E. coli,
cycle in normal bitches and bitches exhibit- which enters the uterine cavity through the
ing pyometra (Kida et al. 2006). Lactoferrin loosened cervical canal during estrus, leading
is a nonspeciﬁc antimicrobial agent, synthe- to pyometra onset. In some rat strains,
sized in the canine uterus during the normal chronic administration of exogenous estro-
estrous cycle. Real-time reverse transcrip- gens induces pyometritis, suggesting that
tion polymerase chain reaction (RT-PCR) there is genetic variation in susceptibility to
analysis revealed the presence of lactoferrin estrogen-induced inﬂammation and pyome-
gene transcripts in the endometrium at all tritis. Using two inbred rat strains, Pandey
stages of the estrous cycle, reaching the et al. (2005) demonstrated signiﬁcant strain-
highest levels in estrus. In normal bitches, speciﬁc differences in the incidence of
endometrial lactoferrin mRNA increased pyometra after 10 weeks of treatment with
from proestrus to estrus followed by dra- synthetic estrogen diethylstilbestrol (DES).
matic reduction from estrus to day 10 of In addition, they could also show that a con-
diestrus. Levels of lactoferrin mRNA were genic rat strain carrying the RNO5 segment
higher in bitches with pyometra than in from a susceptible line in the genetic back-
healthy animals. In the canine uterus, lacto- ground of the pyometra resistant line consis-
ferrin expression is related to the blood tently developed pyometra, supporting the
concentration of estrogen and a dramatic
Genetics and Genomics of Reproductive Disorders 75
assumption that a strong candidate gene cervix uteri), and endometritis (inﬂam-
for pyometra susceptibility is located mation of the endometrium) represent the
within this region. The susceptibility to 17β- most common forms of inﬂammation of
estradiol induced pyometritis appears to seg- the female urogenital tract. In mare,
regate as a recessive trait in crosses between Troedsson (1999) reported an interesting
rat strains, supporting evidence for a major ﬁnding that spermatozoa trigger peripheral
genetic determinant of susceptibility to 17β- mononuclear cell chemotaxis into the
estradiol induced pyometritis on rat chromo- uterine lumen, which would suggest that
some 5 (Gould et al. 2005). The presence of transient endometritis is a normal physio-
potent proteinase inhibitors has also been logical response to breeding. In mares with
associated with the incidence of pyometra in impaired uterine defense mechanisms, the
mare. Pemberton et al. (1994) investigated condition may develop into persistent endo-
the possibility that the severity of endome- metritis and subsequently lead to reduced
tritis in thoroughbred mares correlates with fertility.
the haplotypes of plasma alpha 1-proteinase
inhibitor (alpha 1-PI). The frequency of the 4.3.4 Uterine torsion
N haplotype was much higher in mares with
pyometra compared with the rest of the pop- Uterine torsion is torsion of the body and
ulation. This ﬁnding supports the hypothe- uterus in cows and mares and of a horn of
sis that other two haplotypes (S and T), in the uterus in the sow. It causes dystocia
contrast to haplotype N, may have protec- characterized by the nonappearance of
tive function. any part of the fetus in the vulva. Uterine
torsion has been deﬁned as a rotation of
4.3.2 Hydrometra more than 45 degrees of the uterus around
its long axis that occurs at the junction
Hydrometra is a collection of watery or between the cervix and the corpus. The
mucoid ﬂuid in the uterus. Postmating non- extent of the rotation is usually 180 degrees,
infectious hydrometra and hydrovagina of although cases with torsion from 60 to
unknown etiology, leading to a scrotum-like 720 degrees have been reported. Heifers
swelling of the perineum, were observed in and cows bearing twins have lower risk of
mice (Kunstýr et al. 1982). The mice were uterine torsion. In cattle, most uterine tor-
otherwise clinically healthy, and the disease sions are to the left (counterclockwise), and
could not be transmitted to other females. with the severe torsion, circulatory embar-
Hydrometra was observed also in goats rassment occurs (Drost 2007). In heifers, the
where the diagnosis can be easily made by odds of a uterine torsion are higher in
ultrasound. The incidence in older goats is animals that receive calcium in order to
normally signiﬁcantly higher than in year- prevent milk fever than in nontreated
lings (Hesselink 1993). animals. However, there is no association
between milk fever and uterine torsion in
4.3.3 Vaginitis, cervicitis, multiparous animals. Very little is known
and endometritis about the genetic background for uterine
torsion, but it appears that large term fetuses
Vaginitis (inﬂammation of the vagina, predispose a cow to uterine torsion (Frazer
colpitis), cervicitis (inﬂammation of the et al. 1996).
76 Quantitative Genomics of Reproduction
4.3.5 Vaginal prolapse tion rate, compared with 1/29 translocation
(Schmutz et al. 1997).
Vaginal prolapse (estral eversion, vaginal
hyperplasia) is an edematous enlargement of 4.4.2 Prolonged gestation
vaginal tissue during estrus. Usually, the
prolapse contains only the mucosa of the Prolonged gestation is most frequently a
ventral ﬂoor, but it may also contain the result of defective function of fetal hypotha-
urinary bladder or the cervix. In mouse, lamic-pituitary-adrenal axis, which is no
Connell et al. (2008) found that Hoxa11-null longer able to initiate parturition. The
mice had no detectable uterosacral liga- absence or developmental abnormality of
ments. Nikolova et al. (2007) suggested the fetal adrenal or pituitary glands is char-
linkage of familial pelvic organ prolapse in acteristic for all forms of prolonged gestation
human to HSA1q31 and identiﬁed an SNP (Graves et al. 1991). The prolonged gestation
in the LAMC1 promoter region for which may be caused by genetic as well as other
the rare T variant segregated with the phe- factors.
notype. This SNP affected the binding site
for NFIL3, a transcription factor coexpressed In cattle, the inherited form of prolonged
with LAMC1 in the vaginal tissue. gestation is characterized by pregnancy, pro-
longed for 3 weeks to 3 months. The pheno-
4.4 Reproductive disorders type of the calf can be normal except for the
associated with pregnancy great size, which requires cesarean section
and placenta (fetal giantism). It has been reported in
Holstein, Ayrshire, and Swedish breeds of
4.4.1 Abortion cattle. The calf weighs 48–80 kg at birth and
shows signs of postmaturity. Breathing is
Abortion is a premature expulsion from the difﬁcult as a result of failure of surfactant
uterus of the products of conception; termi- release, and the calf may die from hypogly-
nation of the pregnancy before fetus is viable cemia. At necropsy, hypoplasia of the ante-
(Blood et al. 2007). In cattle, cytogenetic rior pituitary and adrenal glands is seen. In
abnormalities were found in aborted calves. another type, it is characteristic that the
Hanada and Geshi (1995) reported abnormal fetus does not develop beyond the 6-month
60, XX, rob(7;12) karyotype in aborted stage, is much smaller than normal, and
Japanese black cattle fetuses. The deleteri- has severe developmental abnormalities,
ous effect of the Robertsonian translocation like Cyclops calves with only one eye. Such
7/21 was conﬁrmed cytogenetically in cases have been reported in Ayrshire,
unbalanced embryos (Hanada et al. 1995). Guernsey, and Jersey breeds. The pedigree
Schmutz et al. (1996) performed cytogenetic data suggest that this type of defect is caused
analysis in aborted and stillborn calves by a recessive gene. Calves are usually dead
and found association between spontaneous when delivered; however, there is no spon-
abortions and neonatal losses with chromo- taneous parturition in affected Guernsey
somal aneuploidy. The deleterious effect of animals due to nonfunctional pituitary gland
the 14/20 Robertsonian translocation was in the fetus. The third type is characterized
conﬁrmed in cattle, having stronger effect by multiple skeletal deformities and cleft
on embryo mortality than a lowered concep- palate and has most frequently been reported
in Hereford cattle. Affected calves show
Genetics and Genomics of Reproductive Disorders 77
evidence of pituitary aplasia or hypoplasia, tabilities for dystocia were 0.13 and 0.09,
arthrogryposis, torticollis, kyphosis, and respectively. The genetic correlation between
scoliosis. direct and maternal effects were close to zero,
and during the last 20 years, only slight
In pigs, Wilkie et al. (1999) suggested QTL genetic improvement of calving difﬁculty
for gestation length on SSC9, SSC15, and was detected. Kühn et al. (2003) found signiﬁ-
SSC1, which are associated with the number cant maternal effect on calving difﬁculty in
of corpora lutea. In the MGI database, there the central part of the BTA8 chromosome in
were seven genes associated with the term German Holstein cows. In addition, a QTL
abnormal gestational length; six associated for maternal effect on dystocia was found in
with long and one with short gestational the middle part of BTA18, whereas direct
period. effects on dystocia were found on BTA6
at 44 cM. QTL on BTA18 were also detected
MGI genes associated to the term “abnor- in Swedish dairy cattle (Holmberg and
mal gestational length” include Akp5, Andersson-Eklund 2006) as were QTL on
long gestation period; Akr1c18, long gesta- BTA6. In Danish Holstein cattle, four signiﬁ-
tion period; B4galt1, long gestation period; cant QTL were found for calving difﬁculty on
Cdkn1c, short gestation period; Cenpb, chromosomes 8, 18, 25, and 28. Analysis of
abnormal gestational length; Inhbb, long the family material in Holstein Frisian cattle
gestation period; and Lpar3, long gestation identiﬁed three signiﬁcant QTL inﬂuencing
period. calving ease (Ashwell et al. 2005) on chromo-
somes 8, 17, and 27.
4.4.3 Dropsy of fetal membrane
In general, all studies support the ﬁnding
Dropsy of fetal membrane is characterized that there is little correlation between direct
by abnormal accumulation of serous ﬂuid in and maternal effect; however, there is a
the allantoic sac. It occurs in cows, rarely in slight correlation between dystocia and still-
mares, and is often associated with dystocia, birth. Probably due to low heritability, there
uterine inertia, and death or abortion of the was little selection progress in calving dif-
fetus (Blood et al. 2007). It has been fre- ﬁculties over the last few decades.
quently observed in cattle–bison hybrids.
Genetic background is not clear. 4.4.5 Retained placenta
4.4.4 Dystocia Retained placenta is failure to pass the pla-
centa within 24 h postpartum (Kelton et al.
Dystocia is deﬁned as calving difﬁculty 1998). Retained placenta affects 5–10% of
resulting from prolonged spontaneous calv- calvings and greatly increases the risk of
ing or prolonged or severe assisted extraction metritis and endometritis. Due to the physi-
(Mee 2008). Calving difﬁculties are often cat- ological basis of placenta expulsion, the
egorized in three categories: easy calving, genes related to major histocompatibility
slight problems, and difﬁcult calving. The complex (MHC) were suggested as possible
overall frequency of difﬁcult calvings in candidate genes involved in retained pla-
Norwegian red cattle was estimated to be centa. Sharif et al. (1998) found the associa-
2–3% in heifers and 1% in cows at second or tion of the bovine MHC DRB3 (BoLA-DRB3)
later calvings (Heringstad et al. 2007). allele *3 with a lower risk of retained
Posterior means of direct and maternal heri-
78 Quantitative Genomics of Reproduction
placenta. In the study of Joosten et al. (1991), abdominal cavity, mainly fat tissue and
the MHC class I compatibility between dam intestines are present in the inguinal canal,
and calf increased the risk of retained pla- whereas scrotal hernia refers to a situation
centa. They suggested that compatibility of where hernial contents are present in the
MHC products between dam and calf might scrotum. As a consequence of hernia, the
negatively inﬂuence placental maturation surrounding connective tissue can exert
and expulsion, and therefore increase the strong pressure on the soft hernial material,
risk of retained placenta. Induction of toler- reducing the blood ﬂow due to the strong
ance against noninherited maternal antigens pressure on the veins, which may develop
(NIMAs) might be implicated in the occur- into gangrena and sepsis. Because of familial
rence of the disorder, suggesting a tolerance- incidence, hernias are considered a heredi-
inducing effect of NIMA in cattle in relation tary disease of the connective tissue in man
to retained placenta. In addition to genetic and animals (Smith and Sparkes 1968).
factors, circulating PgF2alpha and nutri- Hernias also often occur in patients with
tional parameters at parturition in dairy Marfan or Ehlers–Danlos syndrome. The
cows were associated with retained pla- most frequently affected species in farm
centa. In horses, Sevinga et al. (2004) sug- animals is pig, where hernia inguinalis and
gested, based on MHC data, a negative effect hernia scrotalis occur, depending on popula-
of inbreeding on the incidence of retained tion, at frequencies from 1.7% to 6.7%
placenta in Friesian horses. (Thaller et al. 1996). Scrotal hernia espe-
cially is believed to be a genetic disorder
4.5 Reproductive disorders with recessive inheritance (Jubb et al. 2007).
associated with male
reproductive organs Several anatomical characteristics such as
abnormally wide inguinal canal and not
4.5.1 Hernia inguinalis and scrotalis obliterated processus vaginalis are consid-
ered as risk factors in the development of
Inguinal and scrotal hernias are caused by inguinal and scrotal hernia. Most frequently,
the weakness of the inguinal canal that the distal jejunum and ileum slide through
embraces different organs and acts as a the vaginal ring and enter the inguinal canal.
natural corset. Due to the pressure in the Herniation of the small colon and omentum
abdominal cavity, a rupture in the inguinal are less common. In addition, abnormalities
canal can develop, and internal organs, most during the process of testicular descent may
commonly intestines, can be pushed through also contribute to the predisposition for the
the rupture. Hernias are considered to be development of inguinal and scrotal hernia
congenital defects, which are caused by in male pigs. Testicular migration is charac-
connective tissue weakness. Depending on terized by rapid development of the guber-
location, hernias can be classiﬁed as dia- naculum, which is the key anatomical
phragmatic, scrotal (inguinal), or umbilical structure controlling descent of testes from
(abdominal). In the context of reproduction, the abdomen, where it develops into the
two types of hernias are of relevance: ingui- scrotum. Swelling of the gubernaculum,
nal and scrotal hernia. By deﬁnition, in the caused by deposition of hyaluronan, extends
case of inguinal hernia, the contents of the the inguinal canal. Testicular descent occurs
after biodegradation of this structure by pro-
Genetics and Genomics of Reproductive Disorders 79
The involvement of genetic factors in the Therefore, GUSB became a positional candi-
development of inguinal and scrotal hernias date for inguinal and scrotal hernia. In order
has been demonstrated in several studies to test the association between GUSB poly-
(Cook et al. 2000; Koskimies et al. 2003); morphisms and incidence of inguinal/scrotal
however, the mode of inheritance has not hernia, extensive sequence analysis of the
been clariﬁed. In humans, an autosomal porcine GUSB gene and SNP-based associa-
dominant inheritance with incomplete pen- tion analysis were conducted. However, due
etrance and involvement of genomic imprint- to the polygenic character of the trait and
ing has been proposed (Gong et al. 1994). only one candidate gene from the targeted
Collagen matrix has also been studied as genomic region in this analysis, no associa-
a target in recurrent inguinal hernia in tion could be conﬁrmed (Beck et al. 2006).
man (Zheng et al. 2002). In this context,
expression of procollagen type I/III, matrix Following the physiology of testicular
metalloproteinases (MMPs) 1 and 13 were descent in humans, extensive apoptosis has
investigated. Zheng et al. (2002) found in been proposed in the smooth muscles around
patients with recurrent inguinal hernia the processus vaginalis after testicular
decreased ratio of collagen types I to III and descent. In pigs, a genome scan has revealed
increased expression of MMP-1 and MMP- ﬁve chromosomal regions associated with
13, suggesting that recurrent inguinal hernias hernia inguinalis/scrotalis (Knorr et al. 2006).
should be considered as a disease of the col- In order to determine whether a disturbed
lagen matrix due to the involvement of con- apoptosis might be responsible for hernia
nective tissue. The estimated h2 values for development in pig, Germerodt et al. (2008)
inguinal and scrotal hernias range from 0.20 determined chromosomal positions of genes
to 0.86 (Mikami and Fredeen 1979). Several involved in apoptosis, isolated sequence
candidate genes coding for proteins involved tagged site (STS) markers speciﬁc for the
in the gubernacular growth such as insulin- disorder-associated chromosomal regions,
like receptor 3, Müllerian inhibiting sub- and evaluated the role of apoptosis in the
stance (MIS), and relaxin, as well as calcitonin inguinal occlusion and testicular descent.
gene-related peptide released from genito- Interestingly, all identiﬁed porcine apoptotic
femoral nerve, have been considered as pos- genes have been mapped to genomic regions
sible candidates for hernia development. associated with porcine inguinal/scrotal
hernia. Physiological data based on signiﬁ-
Taking into account the physiology of cant decrease of Ca2+ concentration in pigs
testicular descent, it has been hypothesized with hernia, which might be a consequence
that mutations affecting genes coding for the of perturbed apoptosis in affected pigs, as
hyaluronan degrading enzymes (hyaluroni- well as the assignment of apoptotic genes to
dase, β-hexosaminidase, and β-glucuronidase) chromosomal regions associated with the
could prevent obliteration of the processus disorder, support the involvement of apop-
vaginalis and so indirectly increase the totic genes in hernia development in pigs.
chance for hernia formation (Beck et al. 2006).
Using a genome-wide linkage scan, the β- Based on a whole genome scan (Figure 4.3),
glucuronidase gene (GUSB) was mapped Grindﬂek et al. (2006) identiﬁed suggestive
within the genomic region on porcine chro- QTL for inguinal and scrotal hernias. Several
mosome 3 (SSC3) associated with congenital promising candidate genes are located within
inguinal and scrotal hernia (Beck et al., 2006). these regions: collagen type IXα (COL9A1),
estrogen receptor 1 (ESR1), calcitonin gene-
80 Quantitative Genomics of Reproduction
SSC 2 SSC 3 SSC 4 SSC 8 SSC 10
SSC 1 SSC 5 SSC 7 SSC 9
IHERN IHERN IHERN IHERN IHERN
IHERN IHERN IHERN
SSC 18IHERN SSC Y
SSC 11 SSC 16
SSC 12 SSC 14 SSC 15
Figure 4.3 QTL for inguinal hernia in pigs (AnimalQTL database; www.animalgenome.org/QTLdb/).
Courtesy of the NAGRP Bioinformatics Project Team.
related peptide (CGRP), insulin-like hormone map chromosomal regions associated with
3 (INSL3), MIS, collagen type II (COL2A1), hernia inguinalis/scrotalis. However, further
insulin-like hormone 5 (INSL5), and cyto- studies are required in order to further
chrome P450 family19A1 (CYP19A1). Some narrow down the suggestive QTL regions,
of these candidate genes (MIS, INSL3, relaxin, to investigate the candidate genes, and to
and CGRP) were already identiﬁed in other conﬁrm the suggestive QTL in other popula-
studies (Clarnette and Hutson 1997; Kubota tions. Similarly, as with other complex
et al. 2002). Grindﬂek et al. (2006) revealed traits, the identiﬁcation of haplotypes asso-
signiﬁcant QTL for inguinal and scrotal ciated with inguinal and scrotal hernias may
hernia on 8 out of 19 porcine chromosomes, be helpful in selection programs against the
the most promising being located on SSC1, disorder.
SSC2, SSC5, SSC6, SSC15, SSC17, and SSCX.
One haplotype on SSC5 has been found to Abnormal collagen metabolism is thought
be transmitted to hernia pigs with four times to play an important role in the development
higher frequency than to healthy pigs. of primary inguinal hernia (Rosch et al. 2002).
The altered ratio of the collagen subtypes
In a recent study, Germerodt et al. (2008) can result either by a modiﬁed synthesis or
applied 15 porcine STS markers to ﬁne- by an imbalanced breakdown. The cleavage
Genetics and Genomics of Reproductive Disorders 81
is regulated by the activity of the MMPs, spermatic cord, together with the testicular
proteins of a family of zinc-dependent endo- artery and vein, is a complex series of events,
peptidases. Among them, MMP-1 and MMP- which require concerted action of hormones,
13 are the principal matrix enzymes cleaving constitutive mechanisms, and the nervous
ﬁbrillar types I, II, and III collagen. A defec- system. The complete descent of the testis
tive collagen metabolism contributes to occurs in most species prenatally with the
decreased tensile strength and mechanical exception of the dog, where it occurs post-
stability of both the connective tissues and natally. Defects in the testis descent cause
the induced scar tissue. Therefore, these several problems ranging from impaired
alterations in collagen formation should be spermatogenesis and reduced fertility to
of central relevance in the pathophysiology increased rate of testicular neoplasia and tes-
of hernias (Rosch et al. 2002). ticular torsion. It is widely accepted that
cryptorchidism can be caused by genetic
Knowledge of the transcriptional regula- or environmental factors, but the genetic
tion of collagen in patients with primary component seems to prevail, and therefore,
inguinal hernia may help to elucidate the breeding from affected individuals is not rec-
pathogenesis of primary inguinal hernia. In ommended. However, when outbreaks of
normal skin, types I and III collagen are cryptorchidism occur, the genetic compo-
known to exist in a ratio of up to 4:1. The nent seems to be less likely; therefore, in
results indicated that the ratio of type I to such cases, hormonal and environmental
type III procollagen mRNA was decreased in factors (endocrine disruptors) should be con-
patients with primary hernia. This decrease sidered as possible causes.
was mainly due to the increase of type III
procollagen mRNA. They concluded that Testicular descent is divided in three
abnormal change of type I and type III colla- phases: relative transabdominal migration
gen mRNAs contributes to the development phase, the intra-inguinal migration and
of primary inguinal hernia (Rosch et al. 2002). extra-inguinal migration. From studies of
hernia cases, there is strong evidence that
It has been shown that recurrent inguinal MIS is involved in the regulation of the ﬁrst
hernias are a disease of the collagen matrix. phase of migration, the second phase requires
An increase of MMPs MMP-1 and MMP-13 increased intra-abdominal pressure, and
mRNAs and proteins was observed in the ﬁnally, the extra-inguinal migration is con-
recurrent hernia group and showed signiﬁ- trolled by androgenic hormones, calcitonin
cant differences compared with the control gene-related protein, genitofemoral nerve,
group (Zheng et al. 2002). and other factors.
4.5.2 Cryptorchidism In the literature, cryptorchidism has been
associated with at least 393 different syn-
Cryptorchidism is deﬁned as the incomplete dromes, and the list of clinical syndromes
descent of the testis and associated struc- with known genetic mutations that feature
tures from the abdomen through the ingui- cryptorchidism, published by Barthold (2008),
nal canal into the scrotum. It is common was expanded for the purpose of this review
in humans, pigs, horses, and companion with additional clinical syndromes extracted
animals (2–12%) but rare in cattle, sheep, from the Online Mendelian Inheritance
and goats (≤1%) (Amann and Veeramachaneni in Man (OMIM) and Disease databases
2007). Descent of the testis, epididymis, and (Table 4.1). The location of loci in cattle was