Contributors xi
Preface xv
Part I Quantitative Genomics of Reproduction 3
1 Reproductive Genomics: Genome, Transcriptome, and Proteome Resources 5
Noelle E. Cockett
1.1 Introduction 5
1.2 Discovery of underlying genetic influences 5
1.3 Characterization of gene expression 14
1.4 Resources for protein analysis 16
1.5 Future research directions 17
References 17
2 Quantitative Genomics of Female Reproduction 23
Jeffrey L. Vallet, Dan J. Nonneman, and Larry A. Kuehn
2.1 Introduction 23
2.2 Female reproductive phenotypes 23
2.3 Genetic markers and genotyping methods 26
2.4 Association of phenotypes with genotypes 28
2.5 Some illustrative examples of reproductive QTL 37
2.6 Future research directions 41
References 43
3 Quantitative Genomics of Male Reproduction 53
Eduardo Casas, J. Joe Ford, and Gary A. Rohrer
3.1 Introduction 53
3.2 Male reproduction phenotypes 53
3.3 Genetics, genomics, and quantitative trait loci (QTL) 55
3.4 QTL identified for male reproduction traits 56
3.5 Future research directions 60
References 61
4 Genetics and Genomics of Reproductive Disorders 67
Peter Dovc, Tanja Kunej, and Galen A. Williams
4.1 Introduction 67
4.2 Reproductive disorders associated with the ovary 68
4.3 Reproductive disorders associated with the vagina and uterus 73
4.4 Reproductive disorders associated with pregnancy and placenta 76
4.5 Reproductive disorders associated with male reproductive organs 78
4.6 Reproductive disorders associated with embryos and fetuses 85
4.7 Future research directions 89
References 90
5 Genomics of Reproductive Diseases in Cattle and Swine 99
Holly Neibergs and Ricardo Zanella
5.1 Introduction 99
5.2 Bovine paratuberculosis 100
5.3 BRD 102
5.4 Brucellosis in cattle 106
5.5 Leptospirosis in swine 108
5.6 Aujeszky’s disease (pseudorabies) 110
5.7 PRRS 111
5.8 Future research directions 113
References 113
6 Comparative Genomics of the Y Chromosome and Male Fertility 129
Wansheng Liu
6.1 Introduction 129
6.2 Characteristics of the mammalian Y chromosome 129
6.3 Sequence and gene content of the Y chromosome 131
6.4 Function of Y chromosome genes in spermatogenesis and male fertility 136
6.5 Polymorphisms of the Y chromosome and male fertility 142
6.6 Future research directions 145
References 146
7 Mitochondriomics of Reproduction and Fertility 157
Zhihua Jiang, Galen A. Williams, Jie Chen, and Jennifer J. Michal
7.1 Introduction 157
7.2 Cytoplasm mitochondrial genomes in fertility and reproduction 158
7.3 Nuclear mitochondrial genomes in fertility and reproduction 162
7.4 Future research directions 174
References 174
Part II Physiological Genomics of Reproduction 181
8 Functional Genomics Studies of Ovarian Function in Livestock: Physiological Insight Gained and Perspective for the Future 183
Beau Schilling and George W. Smith
8.1 Introduction 183
8.2 Transcriptomics of ovarian tissues: EST sequencing 184
8.3 Transcriptomics of ovarian tissues: Microarray studies 189
8.4 Proteomics of ovarian tissues 196
8.5 Future research directions 197
References 199
9 Physiological Genomics of Preimplantation Embryo Development in Production Animals 205
Luc J. Peelman
9.1 Introduction 205
9.2 Preimplantation developmental stages and transcriptomics 206
9.3 Preimplantation developmental systems and transcriptomics 214
9.4 Future research directions 219
References 220
10 Physiological Genomics of Conceptus–Endometrial Interactions Mediating Corpus Luteum Rescue 231
Troy L. Ott and Thomas E. Spencer
10.1 Introduction 231
10.2 Physiological genomics of luteal regression 232
10.3 Physiological genomics of blocking luteal regression 235
10.4 Future research directions 242
References 243
11 Physiological Genomics of Placental Growth and Development 251
Sukanta Mondal
11.1 Introduction 251
11.2 Placental development: Basics 252
11.3 Placental hormones and peptides 253
11.4 Transcriptomics of placental development 261
11.5 Future research directions 263
References 263
12 Cellular, Molecular, and Genomic Mechanisms Regulating Testis Function in Livestock 269
Kyle Caires, Jon Oatley, and Derek McLean
12.1 Introduction 269
12.2 Spermatogenesis 270
12.3 Transcriptomics of testis in bulls 272
12.4 Reproductive genomics in boars 279
12.5 Future research directions 283
References 284
Part III Genomics and Reproductive Biotechnology 291
13 The Epigenome and Its Relevance to Somatic Cell Nuclear Transfer and Nuclear Reprogramming 293
Jorge A. Piedrahita, Steve Bischoff, and Shengdar Tsai
13.1 Introduction 293
13.2 The epigenome 293
13.3 Epigenetic reprogramming 297
13.4 Genomic imprinting 301
13.5 SCNT and epigenetic abnormalities 307
13.6 Future research directions 310
References 310
14 Biotechnology and Fertility Regulation 317
Valeria Conforti
14.1 Introduction 317
14.2 Basic aspects in vaccine development 318
14.3 Specific aspects in vaccine development 320
14.4 Sperm antigens 323
14.5 Zona pellucida antigens 326
14.6 LHRH antigens 328
14.7 Future research directions 332
References 333
15 Proteomics of Male Seminal Plasma 339
Vera Jonakova, Jiri Jonak, and Marie Ticha
15.1 Introduction 339
15.2 Proteins of seminal plasma 340
15.3 Function of seminal plasma proteins 343
15.4 In vitro effects of seminal plasma proteins 347
15.5 Properties of major proteins of seminal plasma of domestic animals 348
15.6 Future research directions 352
References 352
16 Evolutionary Genomics of Sex Determination in Domestic Animals 367
Eric Pailhoux and Corinne Cotinot
16.1 Introduction 367
16.2 State of knowledge of sex differentiation 369
16.3 Sex differentiation in domestic mammals 374
16.4 Sex determination in nonmammal domestic species 380
16.5 Future research directions 382
References 383
17 Toxicogenomics of Reproductive Endocrine Disruption 397
Ulf Magnusson and Lennart Dencker
17.1 Introduction 397
17.2 Reproductive endocrine disruption 398
17.3 Reproductive endocrine disruptors 401
17.4 Toxicogenomics 404
17.5 Future research directions 408
References 408
18 Nutrigenomics for Improved Reproduction 413
John P. McNamara
18.1 Introduction 413
18.2 Nutritional physiology of reproduction: A brief view 414
18.3 Mechanistic connections between nutrient flux and reproductive processes 417
18.4 History of integration of physiological state, nutrient flux, and reproduction 421
18.5 Nutritional physiology of pregnancy and lactation 422
18.6 Nutrigenetics and nutrigenomics approaches for improved fertility, pregnancy, and lactation 427
18.7 Future research directions 434
References 435
Index 439
