Reproductive Genomics in Domestic Animals

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
Valéria 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