Reproductive Genomics in Domestic Animals is a thorough examination of genomics in the livestock industry, encompassing genome sciences, genome biotechnology, and reproduction. Recent developments in molecular genetics and genomics have enabled scientists to identify and characterize genes contributing to the complexity of reproduction in domestic animals, allowing scientists to improve reproductive traits. Providing the livestock industry with essential tools for enhancing reproductive efficiency, Reproductive Genomics in Domestic Animals surveys the current status of reproductive genomes and looks to the future direction of research.
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
Zhihua Jiang, Ph.D., is Associate Professor of Animal Genomics in the Department of Animal Sciences at Washington State University. Troy L. Ott, Ph.D., PAS, is Associate Professor of Reproductive Biology at Penn State University.
