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432 Genomics and Reproductive Biotechnology

1/estrogen concentration, and of the rate of matical relationship to be established. But
progesterone clearance in the liver. PGF2a in the absence of the latter, no true under-
concentration is a function of uterus PGF2a, standing has been made. The experiment is
and of luteal oxytoxin and perhaps of omega- not finished, even if we have constructed
6 fatty acid concentration. Luteinizing a large industry based on the empirical
hormone is a function of the concentration observations.
of gonadotropin-releasing hormone (GnRH),
low progesterone, and increased estrogen. Empirical approaches have been excellent
Follicle-stimulating hormone is a function of and have in fact made great strides in animal
the concentration of GnRH; of low progester- biology and production of food. But as bio-
one and of the concentration of estrogen and logical scientists, if we cannot provide direct
inhibin. Gonadotropin-releasing hormone chemical, and thus mathematical, evidence,
concentration is a function of the secretion of then we cannot truly move forward. The
GnRH by the hypothalamus, which is a func- exactitude required in gene transcription
tion of glucose concentration, the clearance control requires it. If as biochemists we are
of the GnRH by the liver, estrogen, low pro- so strict on showing a direct molecular
gesterone, and perhaps leptin concentration. mechanism to “prove a hypothesis”, why do
we shy away from a mathematical one as
From these theoretical equations and required in physics or chemistry? In biology,
functions, we see the connection of nutrient as in physics and chemistry, they are one
flux, primarily glucose, perhaps some spe- and the same.
cific fatty acids, perhaps NH3 in the uterus
(as a function of amino acid concentrations In no case does an equation stay in a model
and also increased temperature) to reproduc- unless there is a clear body of evidence to
tive physiology. The challenge, of course, is justify its inclusion. It is this author’s opinion
then to find sufficient data from the litera- that if even just a few reproductive and nutri-
ture to set parameters for these equations. If tional scientists made a fair effort, we could
none exists, specific experiments have to be have a working computer, dynamic, mecha-
designed to determine the parameters of the nistic model of nutrient use, and reproduc-
equation. If this is unsuccessful, then the tion in cattle and pigs within 2 years.
scientists involved need to judge whether
parameters cannot be obtained because the 18.6.4 One example of a transcriptomic
research tools are not there to measure approach to improve reproduction
them; there is some other reason for not
being able to measure parameters (measur- Now, finally, we turn our attention to the
ing the Vmax of acetyl CoA Carboxylase in title of the chapter. And with good reason,
adipose tissue of a live sow is fairly difficult as stated earlier, we cannot invoke “nutrig-
but can be done in vitro); or that in fact there enomics” of reproduction until we have laid
is no mechanistic relation, and adjust the the basis of nutrition, genetics, and repro-
model accordingly. This is a process that duction. Here we will describe a recent
scares many scientists, because it is much experiment that we have conducted in dairy
easier to say “glucose controls LH release” cattle, and refer to some other efforts that
or “prostaglandin F2A causes regression of promise to be a starting point for integration
the corpus luteum” than to actually obtain of transcriptomic data into dynamic models
data that allow a clear mechanistic, mathe- of nutrient use and reproduction, in this
case, of the dairy cow.

Nutrigenomics for Improved Reproduction 433

Adipose tissue has been discussed above. lipase was expressed at 4261 (SEM 509), the
Several metabolic regulators and cytokines most highly expressed gene-regulating nutri-
can be produced in and secreted from adipose ent flux. Leptin receptor was expressed at
tissue (Al-Hasani and Joost 2005). The objec- 734 (50) pre-partum and was only 12% less
tive of this study was to obtain a more in- at 14 DIM, thus leaving open the question
depth understanding of the transcriptomic if gene transcription is a mechanism for
adaptations in adipose tissue of Holstein changes in leptin concentration in lactation
heifers from the transition from pregnancy (which is still an open question).
to lactation, a key period in reproductive
success—the establishment of lactation, and Genes involved in cell synthesis, tran-
the “resetting” of the embryo and uterus for scriptional control, and inflammation
another ovulation and pregnancy. increased fivefold or more, including beta-
defensin, tenfold, cytokine inducible nuclear
We have conducted an initial analysis of protein, eightfold, chromosomal reading
the gene transcriptome in bovine adipose frame 4, sixfold, sarcoplasmic Ca ATP-ase,
tissue during the transition from pregnancy fourfold, leucine-rich repeat-containing 2,
to lactation (Sumner et al. 2009). We identi- 3.5-fold; voltage-dependent calcium channel
fied a set of heifers and first lactation animals subunit, 3.5-fold. Bos taurus uncoupling
that covered a range of genetic merits based protein 3 increased threefold, indicating
on sires milk production transmission possible proton uncoupling in white adipose
ability and the 305ME record of the first tissue. These data provide some initial
lactation animals. They were housed and fed insight into the global transcriptomic
similarly. We obtained adipose tissue by response of adipose tissue to lactation.
biopsy at 30 days pre-partum and 14 days
postpartum and extracted the RNA. This Anabolic pathway genes decreased (P <
was hybridized to the Affymetrix Genechip® 0.05), including (mean (% change), (SEM)):
Bovine Genome Array. Animals averaged SREBP, −25.1, (6.2); GLUT1, −57.3 (14.1);
29.8 (SEM = 1.3 kg/d of milk for the first 60 THRSP14, −30.8 (7.4); LPL, −48.4 (7.7), and
DIM (range 18.6 to 44.8 kg/d). They lost AcCoA Carboxylase, −60.6 (13.0). The regres-
42.6 kg of BW (SEM 8.4, range +9.1 to −113.6) sion of transcript change on milk production
and 0.38 BCS units (SEM 0.10, range 0 to was 0.18 for AcCoA carb and 0.26 for ATP-
−1.0) from 0 to 14 DIM. This is a normal CL (P < 0.05). Lipolytic control elements
range for dairy cattle, housed and fed alike increased, with much variation among
and gives a glimpse of the yet unknown animals, including Ca channel subunit
effects of genetic variance in a similar 338% (203); B2AR 52.0 (8.8); PKC receptor
population. 10.1 (2.6), and HSL mRNA 23.0 (17.9). The
regression of transcript change on milk was
There are about 24,000 gene products on 0.30 and 0.25 for B2AR and HSL mRNA.
these chips, with an admittedly low level of
confident annotation. Approximately 433 Regressions among variables in a multi-
genes increased 100% or more, 3406 variate system are often misunderstood.
increased 25% to 100%; 1951 decreased Some scientists think only “high regres-
25% to 50%, 337 decreased 75% or more. sions” are important, while a geneticist can
Genes expressed in greatest amounts prove that an “R Squared” of 0.05 can mean
included collagen and ribosomal proteins, millions of dollars when applied over many
and fatty acid binding protein. Lipoprotein animals for several generations. The reality
is, the regression is only what it is, and we

434 Genomics and Reproductive Biotechnology

can learn a fair bit from interpretation of not, we will have a more complete picture
linear, nonlinear, and multiple regressions. of the adaptive mechanisms of nutrient flux
to reproduction and vice versa. Changes in
We first need to understand the complex- lipogenesis and lipolysis are functions of
ity of the animal, and obtaining a “high changes in gene transcripts, with lipogenesis
regression value” among variables at the more related to changes in flux not directly
organ and metabolic level is neither likely related to mammary function, and lipolysis
nor the objective. We need to have an ordered more directly related. This result is com-
approach of both statistical and mechanis- pletely consistent with all the animal
tic, biomathematical research to identify the feeding, metabolic flux, enzyme activity,
key components of a system. If in fact, 18% and endocrine studies that have gone before,
to 30% of the change in transcript amount and has provided more knowledge of the
for key metabolic control proteins can be mechanisms of the partitioning of nutrients
related to milk production, that is a critical to support reproduction.
control point. If we categorize temporal
phases of research of metabolic control into Although direct studies of nutrigenomics
animal observations, empirical relation- of reproduction have been hard to find, we
ships, direct cause and effect studies, and should note at least two other ongoing
building of biochemical and mathematical studies that relate directly to this. This is
pathways, then we may say that we are pres- the effort of scientists at the University of
ently in the next phase: “transcriptomic Illinois to determine transcriptomic changes
studies,” both empirical and mechanistic. in the liver of pregnant and lactating cows
Upon reflection and interpretation, we can as affected by lactation and plane of nutri-
draw a direct line through every phase: tion (Loor et al. 2005, 2006). There are also
“animals that make more milk at the same other transcriptomic studies in specific
food intake lose more fat”; “increasing or reproductive organs, but as yet a true nutrig-
decreasing feed intake at the same milk pro- enomic approach has not been reported
duction alters body fat”; “animals with less (Rhoads et al. 2008a, b). It is only a matter
body fat, or greater rates of body fat loss have of time and will that such an effort will
decreased fertility”; “enzymes involved in expand.
fat synthesis and release vary with milk pro-
duction and feed intake”; and “transcripts 18.7 Future research directions
for enzymes involved in metabolic reactions
relate to changes in milk production.” With We have a long way to go. We need a rein-
the iterative, supportive evidence at hand, vigorated, multi-investigator, multidisci-
we can, with some confidence, identify plinary integrated approach to solve the
gene transcription of a few critical control present and future problems of reproduction,
proteins as a mechanism of the relationship and specific to the role of nutrigenetics
of nutrient flux in the adipose tissue and nutrigenomics for improved repro-
with reproductive processes (in this case duction, this research effort will require
lactation). construction and testing of mechanistic bio-
mathematical models. Finally, we need to
It remains to be mined from the data, if train students, scientists, and professionals
transcriptional regulation for proteins in the importance of using integrative
directly involved with ovarian function is
altered in early lactation. Even if they are

Nutrigenomics for Improved Reproduction 435

biology and biomathematical models to nal traits related to lactation efficiency
identify, solve, and prevent reproductive in sows. Journal of Animal Science 86:
problems. 1067–1080.
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Page numbers in italics refer to Figures; those in bold to Tables.

Aarskog syndrome, 82 anestrus, 72
abnormal offspring syndrome (AOS), 306 angiogenesis, in placental development, 309
abortion annexins, 344–345
anogenital distance, 399, 402
defined, 76 antigens
and leptospirosis, 109
acetyl CoA carboxylase, in adipose tissue of LHRH, 328–332
sperm, 323
dairy cattle, 425 zona pellucida, 326–328
acidic Seminal Fluid Protein (aSFP), 341 antiMüllerian hormone, 86
acrosin, 60 antiquitin, during meiotic maturation, 197
ACTB. See beta-actin gene AOS. See abnormal offspring syndrome
ACTG2. See gamma-actin 2 gene Apert–acrocephalosyndactyly, 82
adenine nucleotide translocator 2, in blastocyst apoptosis
and hernia development, 79
formation, 212 in preimplantation development, 218
adipose tissue AQN1 protein, 345
aquaporin gene family, in blastocyst formation,
in dairy cattle during lactation, 425
endocrine activity of, 415, 429 211
during lactation, 424 Arrhenius equation, 420
metabolic pathways in, 429–430 ART. See assisted reproductive technique
and reproduction, 416 artificial insemination (AI)
and reproductive success, 413, 415
transcriptomic adaptations in, 433 goal of, 61
adjuvants, in vaccine development, 320–322 preparation for, 348
Affymetrix® array, 193, 209, 272, 433 arylhydrocarbon receptor nuclear translocator
Affymetrix genotyping chips, 27
Affymetrix® rhesus macaque genome, 234 (ARNT) protein, 405
AF vaccines asexuality, 160
action of, 317 ASOs. See allele-specific oligonucleotides
antigens for, 322–323 assisted reproductive technique (ART)
commercially available, 332, 332
frequency of treatments with, 318–319 procedures, 306, 307
reversible, 318 association studies, with Y chromosome
route of administration for, 319
age at first service, genetic correlations with, polymorphisms, 143, 143
ATL. See average testicular length
25 ATP-binding cassette transporter G2 (ABCG2),
aging, reproductive, and mitochondria, 161–162
Agriculture, US Dept. of (USDA), AF vaccine 39
ATP citrate lyase, in adipose tissue of dairy
regulation of, 320
AKR1C gene, 70 cattle, 425
aldo-keto reductase 1C (AKR1C) gene, 70 atrazine, endocrine disruption caused by, 403
allele-specific amplification assay, 7 Atriodactyla order, 231
allele-specific oligonucleotides (ASOs), 7 Aujeszky’s disease, 99, 100
allele substitution effect, 33
amelogenesis imperfecta, 82 causative agent for, 110
amino acids, and fertility, 424 clinical presentation of, 110–111, 111
ampliconic sequence blocks, discovery of, 133 genetics of, 111
“amplicons,” 133 prevalence of, 110
anaphrodisia, 72 transmission of, 110
androgens, abortion induced by, 233 average daily gain (ADG), 330
average testicular length (ATL), 54
avians, toxicogenomics in, 407–408
5-azacytidine (5-AZA), 301


440 Index

azoospermia body fat
microdeletions observed with, 142 and fertility, 414–416
Y chromosome polymorphisms with, glucose conversion to, 429
145–146 and reproduction, 415

background exposure, 402 bone morphogenic protein (BMP15), 38, 70,
bacterial artificial chromosome (BAC) libraries, 380

12–13, 13 bovine brucellosis. See brucellosis
baculoviral inhibitor of apoptosis protein bovine herpesvirus type 1, 102, 103, 105
bovine mitochondrial transcription factor B1
repeat-containing 4 (BIRC4), 218
basic charge, Y-linked 2 (BPY2) gene, 141 (TFB1M), 163–165, 165
basic fibroblast growth factor (bFGF), and SSC bovine OTL viewer, 37
bovine paratuberculosis, 99
proliferation, 278
BAX, 218 causative agent for, 100
Beckwith-Wiedemann syndrome, 82 clinical presentation of, 101
beef bulls, reproductive deficiency in, 145. See genetics of, 101–102
heritability of, 102
also bull prevalence of, 100–101
benign prostatic hyperplasia, and LHRH transmission of, 101
bovine respiratory disease (BRD), 99
vaccines, 329 causative agent for, 102–104
best linear unbiased prediction (BLUP), 37 clinical presentation of, 105–106
beta-actin (ACTB)gene, 60 defined, 105
β-glucuronidase gene, 79 genetics of, 106
beta-catenin, in bovine preimplantation heritability of, 106
incidence rates for, 104
development, 211 prevalence of, 104
bFGF. See basic fibroblast growth factor transmission of, 104–105
binding properties, of homologous proteins, 341 bovine respiratory syncytial virus, 102, 105
bioinformatics, 262, 263 bovine viral diarrhea virus (BVDV), 102,
biology, integrative, 427–428
BIRC4. See baculoviral inhibitor of apoptosis 103–104, 105
BRD. See bovine respiratory disease
protein repeat-containing 4 breeding, animal, and toxicogenomics, 407
BIX-01294, 300, 301 breeding values
BLAST (basic local alignment search tool), 163
blastocyst development, and follistatin calculation of, 39
prediction of, 36–37, 41
supplementation, 194, 195 Brucella genus, taxonomy of, 106–107
blastocysts brucellosis, bovine
causative agent for, 106–107
formation of, 211–214 clinical presentation of, 107
IVF, 217 genetics of, 107–108
and onset of embryonic expression, 210 natural resistance to, 108
in preimplantation embryo, 205–206 prevalence of, 107
transcription in, 211 role of genetics in, 99
Blepharophimosis Ptosis Epicanthus inversus transmission of, 107
BSP. See bull seminal plasma proteins
Syndrome (BPES), 376 BTAY physical map, 144
blood sampling, in farm animals, 401 buck. See also deer
BLUP. See best linear unbiased prediction seminal plasma proteins of, 340
BMP15 (transforming growth factor), 38, 70, seminal plasma proteomics of, 350, 351
380 proteomic analysis of seminal plasma of,
boar. See also pig; swine
Meishan model, 279–280 QTL mapping for reproduction traits of,
neonatal, 282
QTL mapping for reproductive traits of, 58–59
reproductive deficiency in, 145
56–58, 57, 58 seminal plasma of, 339
reproductive genomics in, 279–283 seminal plasma proteins of, 340
seminal plasma of, 339
seminal plasma proteins of, 340, 343
seminal plasma proteomics of, 348, 349
testis development in, 279

seminal plasma proteomics of, 348, 349 Index 441
transcriptomics of testis in, 272–279
bull seminal plasma (BSP) proteins, 348 PRL genes in, 253
QTL for reproductive traits in, 56, 57
calf birth weights, 40 QTL mapping for lactation in, 39–41
callipyge mutation, 306 reproductive diseases in
calpastatin genes, 420
calving, difficulties with, 77 bovine paratuberculosis, 100
calving rate, defined, 161 BRD, 102–106
CAMKs, 232, 233 brucellosis, 106–108
candidate genes reproductive disorders in
abortion, 76
analysis of, 6 dystocia, 77
and association of phenotypes with freemartinism, 86, 87
prolonged gestation, 76–77
genotypes, 28 reproductive heritabilities in, 25, 25–26
for boar phenotypes, 280–282 uterine disease in, 73
causing embryonic and fetal death, 88 whole genome sequence in, 9, 9
choice of, 7–8 cattle feeding, biomathematical models for, 428
in CL of farm species, 233 causality, confirmation of, 402, 402
cryptorchidism associated with, 84, 84–85 cDNA libraries, 16, 16, 214–215
DigiCGA for, 90 cDNA microarray technologies, 263
DNA sequencing of, 29 cDNA sequences, large databases of, 262
during early pregnancy, 261 CDY gene family, 132, 138
for hernia development, 79 cell fate specification, 293
identification of for disease phenotypes, 89 cervicitis, 75
in IVP studies, 215 chemicals
positional, 8, 12 consumer, 402, 402
and reproductive traits in swine, 59, 59 endocrine-disrupting, 397, 398, 403, 404
selection of, 60 epigenetic effects of, 406–407
for spermatogenesis and male fertility international testing strategy for, 400
CDY gene family, 132, 138 endocrine disruption in, 408
DAZ gene family, 137–142 ovarian development in, 379
DDX3Y genes, 140–141 sex determination in, 381–382
HSFY gene family, 139–140 ChIP-chip methods, 296
PRY gene family, 132, 139 chorionic gonadotropin, in pregnancy, 422
RBMY gene family, 132, 139 chromatin accessibility, in SCNT, 307–308
USP9Y, 141–142 chromatin remodeling methods, and cloning
cannabinoid receptor 1 (CNR1), 167–168
capacitation, modulation of, 346 efficiencies, 308
capacitation rates, after ovulation, 344 chromodomain protein Y-linked (CDY) gene
cardiofaciocutaneous syndrome, 82
carrier proteins, in vaccine development, 320 family, 132, 138
catenins, in preimplantation embryo chromosomal abnormalities

development, 210, 211 and cryptorchidism, 84
cats, ZP vaccines for, 328 and XX/XY chimerism, 86
cattle. See also bull; cow; dairy cattle chromosome painting, 10–11
CL. See corpus luteum
age at puberty for, 54 claudins, in preimplantation embryo
follicular development in, 189–191
freemartinism in, 85 development, 210, 211
genomic information for, 8 cloning, of livestock animals though NT, 217
GH genes in, 255–256 c-Myc, 298–299, 299
heritability estimates for, 55, 56 CNR1, 167–168
high-density SNP chips in, 13 COD. See cystic ovarian disease
large insert libraries in, 13 coenzyme Q7 homolog, ubiquinone yeast
mapping of recessive disorders in, 14
persistently infected (BVD-PI), 106 (COQ7), and embryonic development,
pregnancy in, 237 171–172
collagen metabolism, and primary inguinal
hernia, 80–81
compaction, in preimplantation embryo
development, 210, 211

442 Index

complementary DNA (cDNA) CYP19 gene, 253, 367, 377
sequences, 5 cystic ovarian disease (COD), 70–72
synthesis and analysis of, 14
genetic background of, 71
conceptus pathogenesis of, 71
and global transcriptional profiling, 242 cytokines, immune response marked by, 326
horse, 241–242
and lifespan of CL, 235 dairy cattle. See also cattle
reproductive role of, 23–24 adipose tissue in, 424, 425
ruminant, 237–242, 238 with COD, 72
swine, 240–241 embryonic losses in, 420
and uterine PGF production, 231 increased milk production in, 40
linkage analysis of, 31
conceptus-endometrial interactions, 242 lipolysis in, 424, 426
connexin 31, in blastocysts, 215
consumer chemicals Dairy Cattle Reproductive Council Meeting,
Denver, 2006, 431
effects on reproductive system of, 402, 402
exposure to, 402 dairy industry, number of sires for, 53. See also
contigs, 13 milk production
contraceptive vaccines, antigens in, 323. See
databases, on nucleus-encoded mitochondrial
also AF vaccines genes/proteins, 162. See also specific
copper-zinc containing superoxide dismutase databases

(CU/ZN-SOD), 219 data mining approaches, 198
copy number variant (CNV), detection of DAZ gene family, 135–138
DCN. See decorin
differences in, 7 Ddx20 gene, 170
COQ7 gene, 171–172 DDX3Y genes, 140–141
corpus luteum (CL) DEAD (Asp-Glu-Ala-Asp) box polypeptide 20

function of, 183 (DDX20), 170
and global transcriptional profiling, 242 DEAD box polypeptide 3, Y-linked (DDX3Y)
and PGF function, 232
regression of, 192–193, 231, 432 gene, 140–141
retained, 72–73 death
corpus luteum (CL) rescue, in horse, 241–242
Costello syndrome, 82 embryonic, 88
cow. See also cattle fetal, 88
oviductal reservoir in, 344 decorin (DCN), 232
PL in, 256–257 deer. See also buck
PLPs of, 259 linkage maps for, 10
“CpG deserts,” 294 ZP immunization in, 327
“CpG islands,” 294, 296 deletion analysis, in infertile men, 136
CRABP1 gene, 209 “depot” effect, of antigen entrapment, 321
CREB (cyclic AMP responsive element-binding Desert hedgehog (Dhh) protein, 371
desmosomes, in blastocyst formation, 211,
protein-1) regulated transcription
coactivator 1 (CRTC1), 170 213
Crohn’s disease, 100 DGAT1 gene, 40
cryptorchidism dibuthyl phthalate, reproductive effects of, 403
clinical syndromes associated with, 81, 82 diet, and genetic control, 424. See also
genes tested for association with, 83–84, 84
in humans, 84 nutrition
and mouse gene knockout models, 83, 83–84 diethylstibestrol, endocrine disruption caused
transgenic models related to, 83, 83
CUL7 gene, 171, 172 by, 398–399, 403
cullin 7 (CUL7), and embryonic development, digital candidate gene approach (DigiCGA), 90
171, 172 dilution theory, mtDNA, 158
cumulus cell, bovine, 197 dioxins, antiestrogenic effects of, 405
cumulus cell markers, poor quality oocytes disease resistance, and profitability, 113
associated with, 195–196 disomies, uniparental, 302
CU/ZN-SOD. See copper-zinc containing distal arthrogryposis, 82
superoxide dismutase DLK1 protein, 306
DMRT1bY, 381, 382
DNA ligases, and embryonic development, 172

Index 443

DNA methylation, 294. See methylation, DNA role of insulin-like growth factors in,
alterations in, 406–407 259–260
and endocrine disruption, 404
in epigenetic change, 300 schematic, 206
testis during, 270
DNA vaccines, for immunocontraception, transcription of DNA methyltransferases in,
DNMT3a, 217 in vivo development, 214–215
DNMT3b, 217 embryonic genome activation (EGA)
DSC2 gene, 209 and first cell differentiation processes, 210
dystocia, defined, 77 timing of, 209
embryonic loss, and nutritional status, 420
E-cadherin endocrine disruption
in bovine preimplantation development, complexity of, 404–405
211 concept of, 398
in preimplantation embryo development, in domestic animals, 399–401, 401
210, 211 epigenetics of, 406–407
experimental evidence of, 399
E-cadherin-catenin cell adhesion family, in explained, 398
blastocyst formation, 211 in humans, 398–399
irreversible effects of, 403
ecotoxicogenomics, 397–398 models for studying, 401, 401
EGA. See embryonic genome activation phenomenon of, 397
EGF. See epidermal growth factor research on, 408
egg incubation, temperature of, 367 species differentiation in, 404
Ehlers-Danlos syndrome, 78 timing aspect of, 403
ejaculate volume, genetic parameters for, 55 toxicogenomics of, 404–408
electrophoresis in vivo and in vitro data on, 401, 401
endocrine disruptors
of oocyte proteome, 196 chemicals of concern, 401–402, 402
for protein analysis, 16 definition of, 404–405
elongation factor 1 alpha, in blastocyst mechanisms of action for, 403–404
transgenerational effects of, 404
formation, 212 vulnerable windows and late effects,
death of, 87–88 endocrine-exocrine theory, for CL rescue in
effect of JY-1 siRNA species on, 187, 188
freemartinism in, 85–87 swine, 236
parthenogenetic, 302 ENDOG, 171, 172
stillbirth of, 88 endometritis, 75
in vivo-derived vs. in vitro-produced,
in cattle, 73, 73–74
215–216 transient, 75
embryogenesis endometrium
and global transcriptional profiling, 242
EST sequencing project for pig, 188 and luteolytic mechanism, 236
and oocyte regulation of follicular porcine, 240
sheep, 239
development, 186–188, 187–189 temporal gene expression changes in, 405
Sox9 in, 370 endonuclease G (ENDOG), and embryonic
embryonic development
blastocyst formation, 211–214 development, 171, 172
compaction, 210, 211 energy balance, and reproductive success, 415
effect of culture medium on early, 218–219 enzyme inhibitors, seminal plasma proteins as,
effect of in vitro production on, 215
epigenetic modifications, 216–218 344, 347
and first cleavage division, 206–209 enzymes
functional genomics of, 219–220
hatching, 214 anabolic control, mRNA sequences for, 424,
nucleus-encoded mitochondrial genes and, 426

171–174 genetic regulation of, 427–428
onset of embryonic expression, 209–210 epidermal growth factor (EGF), and SSC
oxygen radicals in, 208
physiological genomics of, 205–206 proliferation, 278

444 Index Fanconi anemia, 82
farm animals. See also livestock species;
epigenetic reprogramming
and chemical inhibitors, 301 specific animals
methods for, 297 endocrine disruption in, 400–401
molecular changes during, 299–300 Y chromosome of, 144
by retroviral transduction, 298–299, 299 farrowing survival, genetic correlations with, 24
SCNT, 297–298 fat, and fertility, 414–416. See also adipose
Yamanaka four-factor experiment, 298–299
tissue; body fat
epigenetics fat percentage, for lactating cattle, 40
abnormalities in, 307, 308 fatty acids
chromatin marks and developmental
potential, 296–297 during pregnancy, 423
chromatin modifications, 295, 295–296 and reproductive process, 419–420
and controversy over active DNA Fec genes, in sheep, 39
demethylation, 294–495 FecX gene, 38
defined, 293 feral cat population, control of, 332
and DNA methylation, 294 feral populations, sperm antigens for control of,
of endocrine disruption, 406–407
and nutrient flux, 423 325–326. See also wildlife populations
fertility, 161
epigenome, defined, 293
erythropoietin receptor, genetic variation in, and adipose tissue, 429
and mitochondrial genetics, 158–162
29 nuclear mitochondrial genomes in, 162–174
ES (embryonic stem) cell, 298 nutritional development of, 419
Escherichia coli, in endometrium, 74 and nutritional status, 414, 415
ESR1. See estrogen receptor alpha and polymorphisms on Y chromosome, 142
EST. See expressed sequence tag (EST) role of fatty acids in, 420
estradiol fertility, female
and mitochondria, 161
effect of recombinant JY-1 protein on, 187, nucleus-encoded mitochondrial genes and,
in follicular growth, 190, 191 fertility, male
estrogen, 432
candidate genes for, 137–142
and conceptus signaling, 236 nucleus-encoded mitochondrial genes and,
in gonad differentiation, 374
from male pig fetuses, 283 167–170
estrogen production, and FOXL2, 377 and polymorphisms of Y chromosome, 142–145
estrogen receptor, and genetic variation, 29 fertility control, of wild or feral populations,
estrogen receptor alpha (ESR1) expression, 237
estrogen receptor gene (ESR1), 59, 60 318. See also AF vaccines
estrus, silent, 72 fertility selection, Y chromosome gene-based
ESTs. See expressed sequence tags
ethinyl estradiol, effects of, 406, 408 MAS strategy for, 146
eukaryotic translation initiation factor 1A, fertilization

Y-linked (EIFIAY), 141 gamete interaction in, 346–347
ewe. See also ram; sheep mammalian, 339
sperm oviductal reservoir in, 344
PL in, 256–257 fertilization experiments, in vitro, 160
ZP immunization in, 327 fetal death, use of term, 87
ewe oviduct, as surrogate in vivo system, 215 fetal membrane, dropsy of, 77
expressed sequence tag (EST) sequencing, 183 fetal-placental unit, and nutrient flux, 422
gene discovery from, 197–198 fetus
of JY-1 gene, 186–188, 187–189 immunotolerance developed by, 105–106
of oocyte in swine, 188 PRRS in, 112
of ovarian tissues reproductive disorders associated with

follicular and luteal transcriptomes, death, 87–88
184–185 freemartinism, 85–87
role of insulin-like growth factors in
oocyte, 184–186
expressed sequence tags (ESTs), 16, 163, development of, 259–260
stillbirth of, 88
211–212 FGF. See fibroblast growth factor
expression profiling, of ovarian functions, 184 FIBP protein, 190

Index 445

fibroblast growth factor (FGF), 252 gene expression
fibronectin (FN1), in blastocyst formation, 212 and cDNA libraries, 15–16, 16
fibronectin type II, in seminal plasma, 340, 340, characterization of, 14
analysis of gene expression, 14–15
349, 350 synthesis and analysis of cDNA, 14
filamin A, 216 “global,” 15
fluorescent in situ hybridization (FISH), 10
flux control models, 429 Gene Expression Omnibus (GEO) database, 272
flux diagram, 418, 418 gene expression profiling, 308
FN1, 213, 216. See also fibronectin gene function
folate-binding protein, genetic variation in, 29
follicle, ovarian and differences between animals, 43
technologies for testing, 198
EST sequence analysis of, 184 gene ontology analysis, of ovarian follicle, 185
luteinization of, 191–192 genes. See also candidate genes
follicle-stimulating hormone (FSH), 329, 432 associated with ovarian cysts, 71–72
molecular mechanisms controlling, 191 in gonad differentiation in mammals, 373,
and Sertoli cell regulation, 282, 283
and testis development, 269–270 374
follicular development, oocyte regulation of, during lactation, 433
nucleus-encoded mitochondrial
185–188, 187–189
follicular growth, in cattle, 189–191 protein-coding, 163
folliculogenesis, in sex differentiation, 380 pro-apoptotic, 218
Food and Drug Administration (FDA), AF sex-detemining, 382
Genetically Modified Organism (GMO), 382
vaccine regulation of, 320 genetic fragments, analysis of, 12–13, 13
fosmid vectors, 12 genetic maps, in livestock species, 10, 10
founder, heterogametic, creation of, 382–383 genetic markers
founder animal, in genotype association studies, in candidate gene selection, 6
coinheritance of, 8
35 in genome scan, 9
FOXL2 gene and genotyping methods, 26–28
genetic profiling, 251
as female steroidogenic factor, 377 genetics, mitochondrial, 158
in nonmammal domestic species, 380–381 genetic variation
and ovarian pathway, 377 analysis of, 8–9
PIS-regulated, 376–377 analysis of genetic fragments, 12–13, 13
in sex determination, 372, 373 and candidate gene associations, 6–8, 8
fragile Xq chromosome, 87 characterization of, 5–6
F-ratio profiles, on swine chromosome X, 57, 58 linkage maps for, 10
freemartinism, 85 physical maps in, 10, 10–12, 11
detection of, 86 position candidate genes in, 12
genetic background of, 87 in reproductive traits, 42
Freund’s adjuvants, 321, 328 role of SNPs in, 33, 34
frogs, atrazine in, 403–404 search for, 30
FSH. See follicle-stimulating hormone and whole genome association, 13, 13–14
whole genome sequence in, 9–10, 10
galectin-1, 216 gene transcription
gamete interaction, 346–347 effect of dietary nutrients on, 414
gamma-actin 2 (ACTG2) gene, 59 in metabolic regulation, 427
GAMT, 167, 168 genital infections, in cows, 105
GATM. See glycine amidinotransferase genome, use of term, 53
GDF9, 380 genome projects, 427
GDF9 (transforming growth factor), 38. See also genome scans, 9
and association of phenotypes with
growth and differentiation factor
GenBank database, 163, 186 genotypes, 28
gene alterations, unintended effects of, 38 LD (linkage disequilibrium) analysis, 30–32,
gene chip, 193. See also microarray studies
gene copy numbers 33, 34, 34–35
by linkage analysis, 30–31
differences in, 28 methods for, 30
on Y chromosome, 142, 143

446 Index

genome-side scanning experiments, 89 GH. See growth hormone
genome-wide association (GWA) mapping, 13, glucose

13–14 in bovine embryos, 213
genomic analysis during pregnancy, 423
in reproductive process, 416, 419
of independent additive effects of loci on glucose flux, and reproductive success, 416
associated traits, 42 glucose transporter 1, in adipose tissue of dairy

of in vivo preimplantation embryo cattle, 425
development, 214 GLUT (glucose transporter) genes, 213–214, 215
glycine amidinotransferase (GATM), 262
genomic associations, statistical analysis of, glycosylation, and PRL family genes, 254
35–37 GMO. See Genetically Modified Organism
GnRH. See gonadotropin-releasing hormone
genomic equivalence, on sequence level, 294 GnRH-L, 329
genomic imprinting, 261–262, 301 goat

evolutionary context, 303, 304 cryptorchidism in, 84
and fetal placental function, 304, 305, 306–307 early ovarian organization in, 377
and localized imprinting control regions, 303 freemartinism in, 87
nonequivalence, 302 genomic information for, 8
and parental conflict hypothesis, 303–304 GH genes in, 255–256
uniparental models, 302–303 large insert libraries in, 13
genomic markers, for female reproductive traits, linkage maps in, 10
ovarian development in, 378, 378
23 ovarian differentiation in, 375–376, 378–380
Genomic Research Porcine Gene Index, 185 PL in, 256
genomic resources, for livestock species, 5, 17 sex differentiation in, 379
genomics SRY expression in, 375
studying endocrine disruption in, 401, 401
comparative, 89–90 testis development in, 378, 378
functional, 263 gonadal differentiation
real utility of, 36 genes in, 373, 374
use of term, 53 in mammals, 369
genomics information, websites containing, 8 in reptiles, 367
genotype association studies gonadal regression, and LHRH immunization,
populations in, 35–37
problem of multiple tests in, 36 330
genotypes, and phenotypes, 28–29 gonadotropin-inhibiting hormone related
candidate gene approach, 29–30
genome scans in, 30 peptide 2 (GNIH-RP2), 408
LD, 31–32, 33, 34, 34–35 gonadotropin-releasing hormone (GnRH),
and statistical analysis of genomic
associations, 35–37 and luteinizing hormone, 432
genotyping, 41–42 and testis development, 269–270
availability of, 41 and germ cell differentiation, 271–272
goal of, 26 in Meishan boars, 280
genotyping methods, 26 Gorlin syndrome, 82
gene copy number and, 28 granulosa cell gene expression, and oocyte
indels/microsatellites, 27–28
SNPs, 26–27 competence, 196
GEO. See Gene Expression Omnibus growth and differentiation factor 9B (GDF9B),
germ cell differentiation, 270
in different species, 274–275 70
initiation of, 277 growth hormone (GH), 251
regulation of, 271–272 growth hormone (GH) gene, and placental
steps of, 271
timing of, 270–272 development, 255–256
germ cells growth rate, 419
in gonad differentiation, 374 guanidinoacetate N-methyltranferase (GAMT),
sexual dimorphism, 373
gestation 167, 168
and nutrient flux, 413 GUSB gene. See β-glucuronidase gene
prolonged, 76–77 GWA. See genome-wide association mapping

Index 447

Hammond, Sir John, 421–422 HSFY gene family, 132, 139–140
Hampshire-Duroc (HD) cross animals, exposed HSP-7 (seminal plasma protein), 343
HSP70.1, 219
to PRRSV, 113 HSP70.2, 218
Hand1 mRNA, expression of, 253 Human 2-D PAGE Databases, 162
“haplotype blocks,” 32, 34 Human Mitochondrial Genome Database
Hardy-Weinberg equilibrium, 29
heat shock transcription factor, Y-linked gene (mtDB), 162
Human Mitochondrial Protein Database
(HSFY), 132, 139–140
heat stress, and uterine environment, 420 (HMPDb), 162
HEG. See highly expressed genes humans
GH genes in, 256
adipose tissue in, 433 PRL genes in, 253
AF methods for, 329–330 SRY expression in, 375
hemicastration, 280 Human Sperm Antigen, 80kDa (80kDaHSA),
heparin-binding proteins, of boar seminal
plasma, 345 Huntingtin interacting protein 1 (HIP1), 167,
hernias, classification of, 78. See also inguinal
hernia hybridoma technology, 323, 324
herpesviruses, antibodies against, 111 hydatidiform moles, 302
high-density SNP chips, in livestock species, 13, hydrometra, 75
highly expressed genes (HEG), in placenta, 263 growth rate and, 419
high-throughput analysis, 5 and testis development, 269–270
hypothyroidism, postnatal, 279
in identification of SNPs, 6–7
of proteins, 16 ICRs. See imprinting regional control centers
HINTW gene, 382 ICSI. See intracytoplasmic sperm injection
HIP1, 167, 168 IFN-τ1 (interferon tau) in blastocysts, 215
histone acetylation, 296–297 IGF-binding proteins (IGF-BPs), 260
histone code, 295 IGF receptors, 260
histone deacetylase (HDAC) inhibition, 405 IGFs. See insulin-like growth factors
histone deacetylation, 300, 300 IGF2 transcripts, placental-specific, 306
histone proteins, modifications of, 295, 295 IGR2R, 218
Histophilus somni, 103 ILF3. See interleukin enhancer binding factor 3
H3K4me3, 296 Illumina BovineSNP50 BeadChip, 102
HMT1. See hnRNP methyltransferase-like 1 Illumina genotyping, 27
hnRNP methyltransferase-like 1 (HMT1), 217 IMMP2L, 167, 168, 171
homeorhesis immune system, direct activation of, 321
concept of, 422 immunocontraception, 317
in pregnancy, 422 immunogenicity, improving, 332
homeostasis, and nutrient flux, 421–422 immunosterilization, 317, 330
homozygote, misclassification as, 6 imposex, in marine animals, 398
hormones imprinting regional control centers (ICRs), 303
genetic regulation of, 427–428 indels. See insertions/deletions
during lactation, 423–424 infection. See also specific infection
modeling of, 431–432
of pregnancy, 423 bovine paratuberculosis, 100–102
reproductive, 416 role for genetics in, 99
horse transplacental, 105
genomic information for, 8 infertility
high-density SNP chips in, 13 in farm animals, 145
large insert libraries in, 13 and gene copy number, 143
luteal maintenance in, 236 in large animals, 145
physiological responses to conceptus signaling and leptospirosis, 109
infertility in men, Y chromosome deletion and,
in, 241–242
whole genome sequence in, 9, 9 136–137
ZP immunization in, 327 informatics techniques, 262, 263
house-keeping gene, 15

448 Index

inguinal hernia keyhole limpet hemocyanin (KLH), 320
and collagen metabolism, 81 kinetic flux, 429
defined, 78 KIT expression, 273
genetic factors in development of, 79 Klf4, 298–299, 299
QTL for, 79–80, 80 KLH. See keyhole limpet hemocyanin
recurrent, 79, 81 Klinefelter’s syndrome, 369
risk factors for, 78 knockout studies

inhibin co-receptor betaglycan (TGFBR3), 190, in cryptorchidism, 83, 83–84
191 in embryonic development, 173
of endocrine disruption, 403
inner membrane peptidase (IMP) complex, 168 of ovarian function, 380
inner mitochondrial membrane peptidase 2-like Kozak consensus sequence, 166–167, 167
KRT8. See keratin 8
(IMMP2L), 167, 168 KRT18. See keratin 18
insertions/deletions (indels), detection of, 26, 27
in silico SNP detection, 7 lactation
in situ hybridization tchniques, 10, 10 and adipose tissue, 415
Institute of Biomedical Technologies, CNR, in cattle, QTL mapping for, 39–41
and nutrient flux, 413, 421
Italy, 163 nutritional physiology of, 423–426, 425
insulin, in glucose conversion to body fat, transition from pregnancy to, 433

429–430 lactide:glycolide ratio, 319
insulin-dependent glucose transporter, 430 lactoferrin, endometrial, 74
insulin-like growth factors (IGFs), 251, 415–416 lactogen, placental, 422
laminin, 277
and folliculogenesis, 72 large offspring syndrome (LOS), 219, 303–304,
genetic variation in, 29
in placental development, 259–260 306
and SSC proliferation, 278 Large White Landrace, exposure to PRRSV of,
integrin beta 1 (ITGB1), 218
interleukin enhancer binding factor 3 (ILF3), 113
LD. See linkage disequilibrium
217 Lelystad-like virus, 111
intracytoplasmic sperm injection (ICSI), 273 LEPR. See leptin receptor
intrauterine growth restriction (IUGR), 303–304 leptin
in vitro culture systems, and gene-expression in
and adipose tissue, 415–416
preimplantation embryos, 216–218 in lactation, 433
in vitro fertilization (IVF), and mtDNA defects, leptin receptor (LEPR), 218
Leptospira, 108
161 leptospirosis
ITGB1. See integrin beta 1 causative agent for, 108
IUGR. See intrauterine growth restriction clinical presentation of, 109
IVF. See in vitro fertilization genetics of, 109
incidence of, 108
JAM. See junction adhesion molecule porcine, 100
Johne’s disease, 100 prevalence of, 108
jumonji, AT-rich interactive domain ID transmission of, 108–109
leukemia inhibitory factor (LIF), and SSC
(JARIDID), 141
junction adhesion molecule (JAM), in proliferation, 279
Leydig cells
preimplantation embryo development,
210, 211 in Meishan boars, 280
JY-1 gene in testis, 279
expression of, 186–187 LHRH. See luteinizing hormone-releasing
regulatory role for, 187–188, 188
species specificity of, 187–188, 189 hormone
JY-1 protein recombinant (rJY-1), biologic LHRH vaccines
actions of, 187, 187
applications of, 329
Kallman syndrome, 82 longevity of, 331
keratin 8 (KRT8), in blastocyst formation, 212 LIF. See leukemia inhibitory factor
keratin 18 (KRT18), in blastocyst formation, 212

Index 449

lifetime productivity, genetic correlations with, luteinizing hormone-releasing hormone (LHRH).
25 See also LHRH vaccines

ligand-receptor interaction, species differences antigens
in, 254–255 need for purification of recombinant,
linkage analysis recombinant, 330–331
on animal populations, 30
disadvantages of, 31 immunization
and genome scan, 28–29 and cross-reactivity with isoforms, 329
for positional candidate genes, 12 and gonadal regression, 330
in males and females, 329
linkage disequilibrium (LD) and pregnancy, 331
and arrangement of haplotypes, 34
defined, 31 physiology of, 328
determination of degree of, 32 luteolysis, PGF-induced, 233
measure of, 34
naturally occurring, 34 major histocompatibility complex (MHC)
genes related to, 77
linkage disequilibrium (LD) analysis, 13 and resistance to leptospirosis, 109
compared with linkage analysis, 35
and genome scan, 28–29 malathion, and mitochondrial electron
with unrelated animals, 34 transport, 219

linkage-linkage disequilibrium analysis, 39 MALDI. See matrix-assisted laser desorption/
linkage maps, 8–9 ionization

development of, 56 male-specific region (MSY) genes. See MSY
in livestock species, 10, 10 genes
lipase, in dairy cattle during lactation, 425
lipid synthesis, in bovine adipose tissue during malignant melanoma metastasis suppressor, 262
“mammalian Y gene catalog,” 146
lactation, 424, 425 mammals, sex determination in, 129
lipogenesis, modeling of, 429 mammary development, at lactation, 423. See
lipolysis, modeling of, 429
lipolysis control proteins, mRNA sequences for, also lactation
mammary gland, and nutrient flux, 422
424, 426 Mannheimia haemolytica, 102–103, 105
lipopolysaccharide (LPS), in vaccine preparation, MAP. See Mycobacterium avium subspecies

322 paratuberculosis
litter size mapping, 251
MARC. See Meat Animal Research Center
genetic contribution to, 24 Marfan syndrome, 78
genetic correlations with, 24 marker-assisted selection (MAS), of fertility-
in swine, QTL mapping for, 41
livestock species related traits, 145
genome-wide maps in, 9 mass spectrometric (MS) techniques, 352
genomic resources in, 5, 17 matrix-assisted laser desorption/ionization
large insert libraries in, 12–13, 13
physical map for, 10, 10–12 (MALDI), of oocyte proteome, 196
long interspersed nuclear elements (LINEs), 142 Meat Animal Research Center (MARC), Swine
luteal function, ESTs generated for, 185
luteal regression Resource Population of, 280
PGF mediated, 231 medaka fish, 381
physiological genomics of, 232–235 meiosis, 269
physiological genomics of blocking Meishan breed, 57

conceptus signals, 235–237 reproductive phenotypes in, 280–282
uterine responses to conceptus signals, spermatogenesis in, 279–280
meningoencephalitis, in Aujeszky’s disease, 111
237–242, 238 metabolic flux, summary integration of, 430
luteinization metabolic reaction, genetic elements of, 429
changes in gene expression associated with, and genetic control, 424
192 Pettigrew’s model of, 429
role of glucose in, 419
of ovarian follicle, 191–192 methoxychlor, endocrine disruption caused by,
luteinizing hormone (LH), 329, 432
molecular mechanisms controlling, 191
and testis development, 269–270

450 Index

methylation, DNA cytoplasm, 158
abnormal, 309 in nucleus, 162–164
controversy over, 294–295 sequencing of, 158
defined, 294 mitochondrial transcription factor A (mtTFA),
and histone acetylation, 296–297
in regulation of transcription, 299 219
transcriptional control by, 295–296 MITOMAP, 162
and transcriptional repression, 297 MitoP2 database, 163
MitoRes, 163
methylation analysis, 308 mitosis, 269
methylation/demethylation, of DNA, 216 MnSOD, in blastocysts, 215
metritis, puerperal, 73, 73–75 molecular technologies, and role of placenta,
MGI genes, and prolonged gestation, 77
MHC. See major histocompatibility complex 251–252
mice. See also knockout studies; mouse monkeys, CL regression in, 234
monophosphoryl lipid A (MPL), in vaccine
poly-ovulatory nature of, 380
PRL genes in, 253 preparation, 322
Michaelis-Menten parameters, 429 morbidity, due to BRD, 106
microarray studies morula, 205
of ovarian tissue mouse, PLPs of, 259. See also mice
Mouse Genome Informatics (MGI) database, 68
CL regression, 192–193 mRNA, synthesizing cDNA from, 14
follicular growth and development, 189–191 MSY (male-specific region) genes, 129, 130–131
luteinization of dominant follicle, 191–192
oocyte competence, 193–196, 195 comparative map of, 135, 135
oocyte maturation, 193 palindromes in, 133
physiological significance of, 199 protein-coding genes in, 134
of testis tissue grafts, 272–273 mtDNA (mitochondrial DNA)
microdeletions, Y chromosome, 136, 142 and fertility status, 161
microsatellites inheritance of, 158–160
defined, 27 mutation rate of, 160
in linkage analysis, 30 polyploid nature of, 160
in QTL analyses, 27–28 sequencing of, 158
milk production somatic mutations in, 161
and COD, 71 mtTFA. See mitochondrial transcription factor
and fertility, 417
and impaired fertility, 40 A
QTL analysis of, 42 MUC1 gene, and pyometra, 74
misclassification, problem of, 6 muramyl dipeptide (MDP), in vaccine
mitochondria. See also mtDNA
defined, 157 preparation, 322
and female fertility, 161 mutations
function of, 157
genome size of, 157 cryptorchidism associated with, 84–85
and male fertility, 161 USP9Y, 143
and reproductive aging, 161–162 Mycobacterium avium subspecies
mitochondrial biogenesis, 174
mitochondrial chromosomes, transmission of, paratuberculosis (MAP), 100
chromosomal regions associated with, 102
158 resistance to, 101–102
mitochondrial disease, clinical expression of, shedding of, 101
Mycoplasma bovis, associated with BRD, 102,
mitochondrial genes 103, 105
MYL6 gene, in blastocysts, 213
calculation of density of, 164 myostatin genes, 420
functions of nucleus-encoded, 174
overlapping genes associated with, 166 Na/K-ATPase gene family, in blastocyst
mitochondrial genetics, special features of, formation, 211, 212

158–161 Nanog, 298, 300
mitochondrial genomes National Center for Biotechnology Information

characterization of, 158, 159 (NCBI), Human Genome Resources at, 163
natural resistant associated macrophage protein

1 (NRAMP1), 107

Index 451

NE Index Line (NEI) animals, exposure to of reproduction, 427, 428, 434
PRRSV in, 113 research in, 434–435
nutrition, and reproductive functions, 431–432
neonatal tolerization, 323, 324
NIMAs. See noninherited maternal antigens occludin (OCLN), in preimplantation embryo
nitric oxide (NO) synthase 3 (NOS3), 171, 172 development, 210, 211
noninherited maternal antigens (NIMAs),
Oct-3/4, 298–299, 299, 300, 300
induction of tolerance against, 78 OCT-4 gene, 214
non-recombining region (NRY), on Y oligodeoxynucleotides (ODNs), synthetic CpG,

chromosome, 130 322
Noonan syndrome, 82 oligonucleotides, in expression arrays, 15
Northern blot analysis, 14 oligozoospermia, 142, 145–146
Online Mendelian Inheritance in Animals
to compare expression of in vivo and in vitro
porcine embryos, 215 (OMIA), 8
Online Mendelian Inheritance in Man (OMIM),
of estrous cycle, 185
of pig embryogenesis, 188 81, 162
NRF1 gene, 172 oocyte
NT. See nuclear transfer
nuclear genes, overlapping genes associated bovine, 197
competence of, 193–196, 195, 206
with, 166 EST sequencing analysis of, 184–186
nuclear genome, human, nucleus-encoded maturation of, 193
and onset of embryonic expression, 210
mitochondrial genes in, 165 posttranscriptional regulatory mechanism of,
nuclear receptor coactivator 3 (NCOA3),
170–171 prepubertal, 207
nuclear reprogramming regulatory role of, 186
role of glucose in development of, 419
and chromatin state, 301 OPA1 gene, 172–173
during SCNT, 293 optic atrophy 1 (OPA1) gene, 172–173
nuclear respiratory factor 1 (NRF1), and osteopontin (SPP1) gene, 39, 40
OT. See oxytocin
embryonic development, 172 ovalbumin (OVA), 320
nuclear transfer (NT), cloning of livestock ova-LHRH (recombinant antigen), 332
ova-LHRH vaccine, 330
animals through, 217 ovarian cycle
nucleus regulation of, 183
uterine-dependent, 231
gene transfer from mitochondria to, 162, 164 ovarian differentiation, in goat, 375–376, 377,
mitochondrial genome in, 164–167, 165–167
transfer of mitochondrial genes into, 166 378–380
“null” allele, 6 ovarian failure, syndromic form of premature,
nutrient flux
and cattle feeding, 428 372
models of, 428 ovarian pathway, in sex determination,
and reproductive process, 413, 417–419, 418
early embryonic losses, 420–421 ovarian tissues
homeorhesis in, 422
homeostasis in, 421–422 proteome composition of, 199
integration of physiological state into, proteomics of, 196–197
transcriptomics of
role of fatty acids in, 419–420 EST sequencing, 184–188, 187–189
role of glucose in, 419 microarray studies, 189–196, 195
theoretical equations for, 432 ovary
nutrient-reproduction model, basis for, 428–431 cystic disease of, 70–72
nutrient status, and reproductive physiology, 427 disorders of
nutrigenetics retained corpurs luteum, 72–73
defined, 414 silent heat, 72
in pregnancy, 422 growth rate and, 419
of reproduction, 427 subfunction of, 68–70, 69
research in, 434–435
defined, 414
in pregnancy, 422

452 Index

oviductal reservoir, establishment of, 344–345 genome scans in, 30–31
ovulation LD, 31–32, 33, 34, 34–35
and statistical analysis of genomic
capacitation rates after, 344
defined, 68 associations, 35–37
genomic distribution of QTL for, 69, 69 identification of genes influencing, 5
mathematical model for, 431 phenotypes, female reproduction
and nutrient flux, 413 complex, 24, 25
in sheep, QTL mapping for, 37–38 and complexity of reproduction, 23–24
silent, 72 pleiotropy, 24–25
ovulation failure, defined, 68 and trait measurement, 25–26
ovulation rate, in swine, 191 phenotypes, male reproduction
oxidative damage theory, 160 average testicular length, 54
OXTR. See oxytocin receptor puberty, 54
oxytocin (OT), and uterine PGF production, semen evaluation, 54
testes, 53–54
241 testicular volume, 54
oxytocin receptor (OXTR), 237 “phenotypic anchoring,” 405–406, 408
phosphoglycerate kinase 1 (PGK1), 218
PAG-1. See pregnancy-associated glycoprotein-1 phosphoglycerate kinase 2 (PGK2), 60
palindromes, in MSY, 133 phosphoproteome, oocyte, 197
PANK2, 167, 171 physical map assignments, 10, 10–12, 11
pantothenate kinase 2 (PANK2), 167, 171 phytoestrogens, 397, 401
paratuberculosis. See bovine paratuberculosis adverse effects of, 398
parental conflict theory, 303, 304, 306 effects on reproductive system of, 402,
parthenogenesis, 302, 304, 304
Pasteurella multocida, 103, 105 402
paternally expressed gene (PEG10), 262 endocrine disruption caused by, 399
pathogen-associated molecular patterns Piau boars, 281
pig. See also boar; sow; swine
(PAMPs), 321 developing of ovaries in, 379–380
PCR. See polymerase chain reaction endocrine disruption in, 403
PCR-RFLP. See polymerase chain genomic information for, 8
hernia in, 78, 79
reaction–restriction fragment length high-density SNP chips in, 13
polymorphisms immunized against LHRH, 331
PDGF. See placenta-derived growth factor inguinal hernia in, 79–80, 80
Ped. See preimplantation embryo development large insert libraries in, 13
Ped gene, 207 litter size in, 24
PEG. See preferentially expressed genes luteal maintenance in, 236
PEG10. See paternally expressed gene as model for human oral exposure, 400
peptidomics, and endocrine disruption, 407 ovulation rate in, 69, 69
perilipin, in dairy cattle during lactation, 425 reproductive disorders in
Perissodactyla (equidae) order, 231
pesticides. See also chemicals freemartinism, 87
effects on reproductive system of, 402, 402 prolonged gestation, 77
and endocrine disruption, 397 research on nutrition and reproduction in,
“pests,” AF vaccines for, 319
PGCs. See primordial germ cells 429
PGDF. See platelet-derived growth factor sex differentiation in, 379
PGE:PGF ratio, 235–236 spermadhesin genes of, 342
PGF. See prostaglandin F2α SRY expression in, 375
PGK1. See phosphoglycerate kinase 1 studying endocrine disruption in, 401, 401
PGK2. See phosphoglycerate kinase 2 whole genome sequence in, 9, 9
pharmaceuticals. See also chemicals piglet
effects on reproductive system of, 402, 402 with Aujeszky’s disease, 110, 111, 111
and endocrine disruption, 402 spermatogenesis in, 282–283
phenotypes stillborn, 89
and genotypes, 28–29 PIS regulated transcript number 1 (PISRT1),
candidate gene approach, 29–30
PISRT1, 114

Index 453

pituitary gland polymerase chain reaction–restriction
growth rate and, 419 fragment length polymorphisms
and testis development, 269–270 (PCR-RFLP), 6

PL. See placental lactogen polymorphisms, genetic, effects on gene
PLAC-1. See placenta specific-1 function of, 30
polymorphisms of Y chromosome, and male
effects of imprinted gene expression on, 305 fertility, 142–145
as endocrine organ, 252–253
and genomic imprinting, 301 porcine leptospirosis, 100
hormones and peptides porcine respiratory and reproductive syndrome

GH, 255–256 (PRRS), 100
IGFs, 259–260 causative agent for, 111–112
PL, 256–257 clinical presentation of, 112–113
PLPs, 259 genetics of, 113
PRL, 253 prevalence of, 112
PRPs, 257–259 transmission of, 112
origin of, 252 poultry, seminal plasma proteomics of, 351,
physiology of, 305
primary cell types of, 252 351. See also chicken
retained, 77–78 PPP1CC, 167, 168
role of, 251 Prader-Willi syndrome, 82
SCNT (somatic cell nuclear transfer)-derived, preferentially expressed genes (PEGs), in

308, 309 placenta, 263
transcriptomics of pregnancy

genomic imprinting, 261–262 BRD during, 105
microarray assessment, 261 BVDV during, 104
tracking gene expression signatures, 262–263 in cattle, 237
placenta-derived growth factor (PDGF), 252 disorders of
placental anastomoses, reproductive disorders
abortion, 76
associated with, 67 dropsy of fetal membrane, 77
placental lactogen gene family, 422 dystocia, 77
placental lactogen (PL), 251, 256–257 prolonged gestation, 76–77
retained placenta, 77–78
ovine, 257 effects of LHRH immunization on,
ruminants, 257
placenta specific glycoprotein 10 (PSG-10), 262 331
placenta specific-1 (PLAC-1), 262 nutrient flux during, 421
plastic softeners nutritional physiology of, 422–423
endocrine-disrupting, 400 PRRS infection during, 112
exposure of pigs to, 403 SCNT, 308
fetal exposure to, 399 ZP immunization during, 328
platelet-derived growth factor (PDGF) family, pregnancy-associated glycoprotein-1 (PAG-1),

371 261
platyfish, sex-determining gene of, 382 pregnancy recognition signaling, in swine,
platypus, sex determination in, 381
pleiotropy 240–241
pregnancy specific beta 1 glycoprotein
defined, 24
examples of, 40 (PSG-beta 1), 263
PLPs. See prolactin-like proteins preimplantation embryo development (Ped)
Polled Intersex Syndrome (PIS) mutation, 114
poly(A) polymerase (PAP) mRNA, 208 gene, 207
polychlorinated biphenyls (PCBs), and uterine preweaning survival, genetic correlations with,

occlusion in seals, 398 24
polymerase chain reaction (PCR) primates

allele-specific, 7 GH genes in, 256
quantitative real-time reverse transcription placenta of, 252
primordial germ cells (PGCs)
(qRT-PCR), 14–15 DAZ genes in, 137
real-time, 14 and formation of sex cords, 271
PRL. See prolactin
Prl3d1 gene, 253
PRL-like hormones, 255

454 Index

progesterone and ovarian function, 183, 199
effect of recombinant JY-1 protein on, 187, 187 and ovarian tissues, 196–197
in follicular growth, 190, 191 of seminal plasma, 352
in late pregnancy, 423 technology, 242
in luteal regression, 185 proteomic studies
metabolized by estrogenic preovulatory of horse conceptus, 241
follicles, 192 on seminal plasma proteins, 352
modeling of role in reproduction of, 431–432 PRPs, 257. See prolactin-related proteins
and nutritional physiology of pregnancy, 422 PRRS. See porcine respiratory and reproductive

prolactin-like proteins (PLPs), 251, 259 syndrome
prolactin (PRL), 251 PRY gene family, 132, 139
pseudoautosomal regions (PARs), genes residing
auto-paracrine effects of, 255
mating-induced surges in, 233 on, 129
in placental development, 253–255 pseudorabies, 110
in pregnancy, 422 PSG-10. See placenta specific glycoprotein 10
prolactin receptor, genetic variation in, 29 PSG-beta 1. See pregnancy specific beta 1
prolactin-related proteins (PRPs), 251
bovine, 258 glycoprotein
ovine, 258–259 PTGS2. See prostaglandin-endoperoxide
in placental development, 257–259
proliferation inhibitors, in testis development, synthase 2
PTPBL-related gene on Y (PRY), 132, 139
370 puberty, male, 54
pronuclei microsurgery experiments, 302 puerperal metritis, 73, 73–75
prostaglandin-endoperoxide synthase 2 (PTGS2), pyometra, 73, 73–75

239 qPCR. See quantitative polymerase chain
prostaglandin F2α (PGF), for mediating luteal reaction

regression, 231 qRT-PCR. See quantitative real-time reverse
prostaglandin F receptor (Ptgfr), and fetal death, transcription

88 QTL. See quantitative trait loci
prostate cancer, and LHRH vaccines, 329 QTL regions, in genotype association studies,
proteasomal degradation, of receptor complexes,
405 QTN. See quantitative trait nucleotide
protein analysis, resources for, 16–17 quail, endocrine disruption in, 407–408
proteinase inhibitors quantitative polymerase chain reaction (qPCR),

and pyometra in mare, 75 28, 234, 273
in seminal plasma, 349, 350 quantitative real-time reverse transcription PCR
protein expression, research on, 220
protein metabolism, in fertility, 424 (qRT-PCR), 14–15
protein phosphatase 1, catalytic subunit, quantitative trait

gamma isoform (PPP1CC), 167 defined, 23
proteins mapping, 14
quantitative trait loci (QTL), 6
associated with testis development, 272 for boar phenotypes, 280–282
produced by conceptus, 235 generated by genome scans, 31
seminal plasma, 339 and genetic imprinting, 307
on genome scan, 12
bull, 348 milk production, 43
as enzyme inhibitors, 347 with pleiotropic effects, 25
function of, 343–347, 352 reproductive, 37
game interaction and, 346–347
localization and expression, 342–343 mapping for lactation in cattle, 39
modulation of capacitation, 345–346 mapping for litter size in swine, 41
properties of, 348, 349–351, 351–352 mapping ovulation rate in sheep, 37–38
structure and properties, 340, 340–342 utility of, 23
in vitro effects of, 347–348 quantitative trait loci (QTL) analysis
transcriptional regulation for, 434 of embryonic and fetal death, 88
proteomics, 16 genetic effects attributed to dam in, 24
of bull seminal plasma, 341–342 for inguinal and scrotal hernias, 79–80
and endocrine disruption, 407

in male reproduction, 56 Index 455
boar, 56–58, 57, 58
bull, 58–59 reproduction process, phases of, 339
reproductive diseases and disorders
for maternal effect on dystocia, 77
of ovulation rate in swine, 191 BRD, 102–106
populations in, 39 in cattle
of reproductive traits, 42
quantitative trait nucleotide (QTN), 33 bovine paratuberculosis, 100
brucellosis, 106–108
rabbit ZP2 (rZP2), 327 causal mutations for inherited, 89
radiation hybrid (RH) mapping, 10, 11, 11–12 caused by cross-contamination of fetal
RAF1 protein kinase, 173
ram. See also sheep bloodstream, 67
economic loss attributed to, 99
cryptorchidism in, 84 of embryos and fetuses
seminal plasma proteins of, 340
seminal plasma proteomics of, 350, 351 death in utero, 87–88
rat Freemartin syndrome, 85–87
PLPs of, 259 stillbirth, 88–89
PRL genes in, 253 endocrine-disrupting chemicals and, 398
RBMY gene family, 132, 139 in farm animals, 68
Rcho-I trophoblast cell line, 254 male
real-time PCR, quantitative (Q-RT-PCR), 190, cryptorchidism, 81–85, 82, 84
hernia inguinalis, 78–81, 80
191, 198 of ovary
recessive disorders, in cattle, 14 cystic ovarian disease, 70–72
recombinant technology, for LHRH antigens, ovarian subfunction, 68–70, 69
retained corpus luteum, 72–73
330–331 silent heat, 72
reproduction pregnancy-associated
abortion, 76
cytoplasm mitochondrial genomes in, dropsy of fetal membrane, 77
158–162 dystocia, 77
prolonged gestation, 76–77
effects of nutrients on, 416 retained placenta, 77–78
and mitochondrial genetics, 158–161 in swine
nuclear mitochondrial genomes in, 162–174 Aujeszky’s disease, 110–111
nutrient flux in, 413 leptospirosis, 108–109
nutrigenetics of, 427 PRRS, 111–113
nutrigenomics of, 427, 434 of uterus
nutritional physiology of, 431–432 cervicitis, 75
endometritis, 75
body fat and reproduction, 414–416 hydrometra, 75
metabolic flux in, 416 pyometra and puerperal metritis, 73, 73–75
nutrigenomics and nutrigenetics, 414 uterine torsion, 75
nutrigenomics for improved reproduction, of vagina
prolapse, 76
417 vaginitis, 75
transcriptomic approach to improve, reproductive efficiency
and advanced biotechnological approaches, 252
432–434 ovarian cycle in, 183
reproduction, female reproductive system, effect of chemicals on,

complexity of, 23–24 402, 402
complex phenotypes in, 24, 25 reproductive tissues/organs, EST sequences for,
pleiotropy in, 24–25
quantitative genomics of, 23 16, 16
trait measurement in, 25–26 reproductive traits
reproduction, male
and artificial insemination, 61 genetic locus effects on, 32, 33
candidate genes associated with, 59, 59–60 and genetic selection, 26
genetic variation of, 55, 55 genetics of, 67
genomics approaches to, 55–56 heritabilities for, 24, 25, 417
QTL basics for, 56 QTL analysis of, 42
quantitative genomics of, 53 reproductive traits, female, QTL for, 37–41

456 Index

reproductive traits, male Sertoli cell differentiation, in sex determination,
genetic parameters for, 55, 55 370
genomics and, 61
QTL identified for, 55, 56, 57 Sertoli cells
boar, 56–58, 57, 58 in Meishan boars, 280
bull, 58–59 in testis, 279
thyroid hormone regulation of, 281
descriptive discovery, 184 sex- and reproduction-related (SRR) genes, 134
empirical approaches in, 432 sex chromosomes
modeling approach to, 427
human, 130, 130
restriction fragment length polymorphism of major vertebrate groups, 367–368, 368
(RFLP) analysis, 26–27 mammalian, 131, 133–134
sex cords, in undifferentiated gonads, 378–379
retinol-binding protein, genetic variation in, 29 sex determination, 369
RNA-binding motif protein, Y-linked (RBMY) in mammals, 369

gene, 132, 139 cascade after switch, 370–371
Robertsonian translocations, 76 critical balance, 373–374, 374
rodents. See also mice; mouse; rat ovarian pathway, 371–373
role of SRY in, 369
estrous cycles of, 233 and sexual dimorphism of germ cells, 373
placenta of, 252 in nonmammal domestic species, 380–382
PL in, 256 in vertebrates, 367, 368
R-Spondin 1 (RSPO1) gene sex differentiation, in domestic animals,
and ovarian pathway, 377
in sex determination, 372, 373 374–375
RT-PCR analysis, of follistatin mRNA early ovarian differentiation, 375–376
early ovarian organization in goat, 377–378, 378
abundance, 194, 195 FOXL2 gene in, 376–377
ruminants in goat, 379
goat ovarian differentiation, 378–379
physiological responses to conceptus signaling mono-ovulatory/poly-ovulatory
in, 237–240, 238
folliculogenesis, 380
placenta of, 252 pig species, 379–380
PL in, 256 SRY conservation across species, 375
sexual dimorphisms, diversity of, 368–369
saccharide-based interactions, of seminal sheep. See also ewe; ram
plasma, 351 establishment of pregnancy in, 237, 238
genomic information for, 8
SAGE. See serial analysis of gene expression GH genes in, 255–256
sarcosine (SOX), in blastocysts, 215 high-density SNP chips in, 13
SCNT. See somatic cell nuclear transfer hormone replacement studies in, 239–240
scrotum large insert libraries in, 13
linkage maps in, 10
genetic parameters for, 55 mixed-sex fetuses in, 86
hernia of, 78–81 QTL mapping for ovulation in, 37–38
SDHD gene, 173 reproductive heritabilities in, 25–26
semen collection, 54, 401 SRY expression in, 375
semen evaluation, 54 studying endocrine disruption in, 401, 401
seminal fluid, antimicrobial activity of, 344 shipping fever, 102
seminal plasma short interspersed nuclear elements (SINEs), 142
mammalian, 339, 352 signal transducer and activator of transcription
proteonomics of, 339, 348, 349–351, 351–352
3 (STAT3), 218
localization and expression, 342–343 silent heat syndrome, 72
physiology, 343–347 simulation studies, 36
structure and properties, 340, 340–342 SINES. See short interspersed nuclear elements
in vitro effects, 347–348 single base insertions/deletions (indels), on Y
separation procedures, 1099
sequencing technologies, high-throughput, 41. chromosome, 142
single nucleotide polymorphism (SNP) arrays,
See also high-throughput analysis
Sequenom genotyping technology, 27 high-density, 6
serial analysis of gene expression (SAGE), 14, 15
serine palmitoyl transferase (SPT), 263

Index 457

single nucleotide polymorphisms (SNPs) sperm antigens, 323–324
detection of, 26 in DNA vaccines, 326
and genotyping, 26–27 epididymis-specific, 324
identification of, 6–7 female infertility and, 325
on Y chromosome, 142 for human contraception, 324
vasectomized model for indentification of,
SIRT1, 167, 169 324–325
sirtuin (silent mating type information for wildlife population control, 325

regulation 2 homolog) 1 (SIRT1), 167, spermatids, 271, 272
169 spermatogenesis, 269, 283
SLC25A19, 171, 174
SMCP, 167, 169 candidate genes for, 137–142
SNP chips, in livestock species, 13, 13–14 donor-derived, 277
SNPs. See single nucleotide polymorphisms genetic parameters for, 55
SOD. See superoxide dismutase germ cell differentiation in, 270–272
SOF. See synthetic oviductal fluid in Meishan boars, 280
Solexa, 296 nucleus-encoded mitochondrial genes
solute carrier family 25, member 19
(SLC25A19), 171, 174 affecting, 167
solute carrier family 11 member 1 gene in piglets, 282–283
(Slc11A1), 107 process of, 276
soma, 294 and subcutaneous testicular grafting, 273
somatic cell hybrid analysis, 10, 11 in swine, 279–280
somatic cell nuclear transfer (SCNT) spermatogenic failure
and epigenetic abnormalities, 307, 308 with Y chromosome polymorphisms, 143,
angiogenesis, 309
chemical methods to improve efficiency of 143
SCNT, 307–308 and Y haplogroups, 142–143
placental abnormalities, 308–309 spermatogonia, 271
mammalian cloning by, 297 spermatogonial stem cells (SSCs)
nuclear reprogramming after, 296 functional assay for, 276–277
nuclear reprogramming during, 293 self-renewing proliferation of, 278–279
placental anomalies associated with, 310 transplantation experiments, 276
process of, 307 in vitro maintenance of, 278
somatic cell nuclear transfer (SCNT) embryos, spermatozoa
214 production of, 53–54
somatic cell nuclear transfer (SCNT) in vitro handling of, 348
procedures, and gene-expression in sperm capacitation, seminal plasma proteins in,
preimplantation embryos, 216–218
Sotos syndrome, 82 345–346
Southern blot analysis, 299–300 sperm dysfunction, and mitochondria, 161
sow. See also pig sperm mitochondria-associated cysteine-rich
endocrine disruption in, 399––400
nutrient use in, 429 protein (SMCP), 167, 169
SOX. See sarcosine sperm-ovum interaction, 346–347
Sox2, 298–299, 299, 301 SPT. See serine palmitoyl transferase
SOX9 gene SRR. See sex- and reproduction-related genes
in nonmammal domestic species, 380–381 SRY gene, 270, 369, 371, 375
in sex determination, 370 SSCs. See spermatogonial stem cells
sperm SSH. See suppression subtractive hybridization
preservation of, 348 stallion. See also horse
production of, 269
spermadhesins seminal plasma proteins in, 340, 341,
amplification of, 342 342–343
boar, 340
cDNA sequences of, 342 seminal plasma proteomics of, 350
detection of, 343 STAT3. See signal transducer and activator of
in seminal plasma, 340, 340, 349, 350
transcription 3
statistical approaches, development of, 41
sterility, of freemartins, 85
steroid 5 alpha reductase 1 (Srd5a1 ), and fetal

death, 88
steroid-dependent diseases, and LHRH vaccines,


458 Index

steroid hormone treatments, in sex testes
differentiation, 367 average length for, 54
biology of, 284
steroid receptors, proteosome-mediated development of, 269, 279, 283, 378, 378
degradation of, 404 physiology of, 53
structural organization of, 269
sterol regulatory element binding protein transcriptomics of
(SREBP), in adipose tissue of dairy cattle, ectopic testis xenografting, 273–275
425 manipulation of testis tissue before
xenografting, 275–276
stillbirth microarray analysis on testis tissue grafts,
causes of, 88 272–273
QTL analysis in, 89 SSC transplantation, 276–279
volume of, 54
subclinical infections, with PRRSV, 112
subfertility testes genes, 133
testicular descent, 78
in farm animals, 145
in large animals, 145 and hernia development, 79
and leptospirosis, 109 phases of, 81
and mitochondria, 161 testicular dysgenesis syndrome, 399
sulfotransferase family member estrogen testicular volume
genetic parameters for, 55
preferring member I (SULT1EI), 261 in Meishan boars, 280
SULT1EI. See sulfotransferase family member testiculopathies, 136
testis differentiation, in nonmammal domestic
estrogen preferring member I
superoxide dismutase (SOD) family, and luteal species, 381
testis genes, 145
function, 233–234 testis organogenesis, critical event in, 371
SuperSAGE, 15 Testis Specific Auto-antigen70 (TSA70), 325
suppression subtractive hybridization (SSH) testis tissue grafting bioassay, 282–283
testis xenografting
experiment, 207
surfeit 1 (SURF1), 171, 173–174 ectopic, 273–275
survivin, in blastocysts, 215 manipulation of testis tissue before,
sweet clover disease, 399
swine. See also boar; pig 275–276
candidate genes associated with male
reproductive traits in, 59, 59 and germ cell differentiation, 271–272
in Meishan boars, 280
heritability estimates for, 55, 56 and Sertoli cells regulation, 282
litter size in, 41 2,3,7,8-tetrachlorodibenso-p-dioxin (TCDD),
ovulation rate in, 191
physiological response to conceptus signaling 405
TETY genes, 135, 136
in, 240–241 TFAP2A. See transcription factor AP-2 alpha
QTL analysis in, 31, 41, 56, 57 thyroid hormones
reproductive diseases in
regulated by, 283
Aujeszky’s disease, 110–111 and testis development, 279
leptospirosis, 108–109 thyroid stimulating hormone (TSH), in adipose
PRRS, 111–113
reproductive heritabilities in, 25, 25–26 tissue of dairy cattle, 425
reproductive traits in, 56, 57 tight junction (TJ), in preimplantation embryo
SCNT in, 309
swine chromosome 3, 57, 58 development, 210, 211
synthetic oviductal fluid (SOF) medium, 218 tight junction (TJ) gene family, in blastocyst

TAF7L, 167, 169 formation, 211
tamar, SRY expression in, 375 TNAIP3 gene, 84
target cells/tissues, effects of LHRH tolerization

immunization on, 331 neonatal, 323, 324
TATA box binding protein (TBP)-associated of testicular antigens, 324
tolerogen, 323
factor (TAF7L), 167, 169 Toll-like receptors (TLRs), 321
TCA. See tricarboxylic acid TONDU, 263
Temperature-dependent Sex Determination

(TSD), 367, 368

Index 459

toxicogenomics, 397–398 uterine torsion, 75
advantage of domestic animal genetics, 407 uteroferrin, 236
in avians, 407–408 uterus
and complexity of endocrine disruption,
404–405 disorders of
defined, 405 cervicitis, 75
epigenetics, 406–407 endotrimitis, 75
gene expression analysis, 405–406 hydrometra, 75
phenotypic anchoring, 405–406, 408 uterine torsion, 75

toxicological studies, on endocrine disruption, and heat stress, 420
402 pyometra of, 73, 73–75

transcripotomics experiments, 405 vaccination, with pseudorabies vaccine, 111
transcriptional activator, SRY as, 369 vaccine development
transcriptional profiling, global, 242
transcription factor AP-2 alpha (TFAP2A), 261 adjuvants in, 320–322
transcription factors, in epigenetic antigens, 322–323
carrier proteins in, 320
reprogramming, 301. See also specific longevity in, 318
factors production costs, 319
transcriptome analyses, of genes in testicular regulatory requirements for, 319–320
and ovarian differentiation, 373 reversibility in, 318
transcriptomes, reproductive, 16 safety in, 318
transcriptomics and sperm antigens, 323–326
and endocrine disruption, 407 vaccines. See also AF vaccines
for ovarian function, 183–199, 187–189, 195 antifertility, 317
of placental development, 261–263 immunocontraceptive, 317
transcriptomic studies, 433–434 veterinary, 332, 333
transforming growth factor (TGF), 38 vagina, disorders of, 75, 76
transforming growth factor beta superfamily vaginal prolapse, 76
(TGFbeta), 70 vaginitis, 75
transgene expression, in ectopic tissue grafting, variable nucleotide repeat (VNTR) region, 40
276 vascular endothelial growth factor (VEGF), 72,
triacylglycerol, breakdown to free fatty acids of,
430 252, 406
tributylin, in anti-fouling paints, 398 causes of disregulation of, 309
tricarboxylic acid (TCA) cycle, 208 testis tissue treated with, 275–276
trophectoderm cells VDAC3, 167, 169–170
cell-cell junctions in, 210, 211 VEGF. See vascular endothelial growth factor
differentiation of, 211 vertebrates, sex determination in, 367, 368
trophoblast cells, in placenta, 252, 253 veterinary vaccines, against reproductive
trophoblastic tissue, PL in, 256
TSD. See Temperature-dependent Sex antigens, 332, 333
Determination vinclozolin, endocrine disruption caused by, 407
Turner’s syndrome, 369 viruses

ubiquitin C-terminal hyhydrolase-L1 (UCHL1), associated with BRD, 102
197 PRRS, 111
pseudorabies, 110
ubiquitin-specific peptidase 9, Y-linked VNTR. See variable nucleotide repeat region
(USP9Y), 700 voltage-dependent anion channel 3 (VDAC3),

UCHL1. See ubiquitin C-terminal hydydrolase-L1 167, 169–170
uniparental models, 302–303
urogenital tract, disorders of female, 75 W chromosome, in chicken, 381–382
USP9Y, 141 Weaver syndrome, 82
USP9Y mutation, 143 Western blot analysis, 342
uterine capacity, genes associated with whole genome associations, 6
whole genome selection (WGS), 36, 41–42
differences in, 42 whole genome sequence assemblies, in
uterine prolapse, 399
livestock species, 9, 9

460 Index mammalian, 129–131, 130, 145
in sex determination, 129
wildlife populations and spermatogenic failure, 136
endocrine disruption in, 398 types of polymorphisms on, 142
fertility control for, 318 YEAF1 gene, 208
sperm antigens for control of, 325–326 yeast artificial chromosome (YAC) libraries, 12,
ZP vaccines for, 328
Wnt4, in sex determination, 372, 373 Y haplogroups, and sperm counts, 142–143
Y-linked markers, for male fertility selection,
X chromosome
G-banded ideogram of, 130, 130 144–145
human, 134
in sex determination, 129 ZA. See zonula adherens
Z chromosome, in chicken, 381–382
X-degenerate sequences, 131 zearalenon, effect on pigs of, 399–400
xenobiotics, hormone-like activity of, 397 Z factors, in fetal ovaries, 373
xenografting, of ectopic testis tissue, 273–275 ZO-1. See zonula occludens protein 1
XK, Kell blood group complex subunit-related zona pellucida (ZP), 211, 214. See also ZP

Y-linked (XKRY) gene, 141 immunization; ZP vaccines
XX/XY mosaicism, diagnosis of, 85 characteristics of, 326
glycoprotein components of, 346
Yamanaka four-factor experiment, 298–299 in reproduction process, 339
Y chromosome vaccines for female contraception, 326–327
zonula adherens (ZA), in preimplantation
ancestral, 135
BAC-based physical map of equine, 144 embryo development, 210, 211
chimpanzee, 131 zonula occludens protein 1 (ZO-1), 212–213
compared with X chromosome, 134 ZP. See zona pellucida
in fertility/infertility, 142 ZP immunization
functionally clustered genes on, 133–134
G-banded ideogram of, 130, 130 and ovarian histopathology, 327–328
genes on, 134–136, 135 during pregnancy, 328
human, 131 ZP vaccines
for cats, 328
gene content of, 132, 133 for female contraception, 326–327
sequencing of, 131–133, 132, 145 for wildlife population control, 328
structure of, 132, 133

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