Reproductive Genomics in Domestic Animals

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.

• Contributors xiPreface xvPart I Quantitative Genomics of Reproduction 31 Reproductive Genomics: Genome, Transcriptome, and Proteome Resources 5Noelle E. Cockett1.1 Introduction 51.2 Discovery of underlying genetic influences 51.3 Characterization of gene expression 141.4 Resources for protein analysis 161.5 Future research directions 17References 172 Quantitative Genomics of Female Reproduction 23Jeffrey L. Vallet, Dan J. Nonneman, and Larry A. Kuehn2.1 Introduction 232.2 Female reproductive phenotypes 232.3 Genetic markers and genotyping methods 262.4 Association of phenotypes with genotypes 282.5 Some illustrative examples of reproductive QTL 372.6 Future research directions 41References 433 Quantitative Genomics of Male Reproduction 53Eduardo Casas, J. Joe Ford, and Gary A. Rohrer3.1 Introduction 533.2 Male reproduction phenotypes 533.3 Genetics, genomics, and quantitative trait loci (QTL) 553.4 QTL identified for male reproduction traits 563.5 Future research directions 60References 614 Genetics and Genomics of Reproductive Disorders 67Peter Dovc, Tanja Kunej, and Galen A. Williams4.1 Introduction 674.2 Reproductive disorders associated with the ovary 684.3 Reproductive disorders associated with the vagina and uterus 734.4 Reproductive disorders associated with pregnancy and placenta 764.5 Reproductive disorders associated with male reproductive organs 784.6 Reproductive disorders associated with embryos and fetuses 854.7 Future research directions 89References 905 Genomics of Reproductive Diseases in Cattle and Swine 99Holly Neibergs and Ricardo Zanella5.1 Introduction 995.2 Bovine paratuberculosis 1005.3 BRD 1025.4 Brucellosis in cattle 1065.5 Leptospirosis in swine 1085.6 Aujeszky’s disease (pseudorabies) 1105.7 PRRS 1115.8 Future research directions 113References 1136 Comparative Genomics of the Y Chromosome and Male Fertility 129Wansheng Liu6.1 Introduction 1296.2 Characteristics of the mammalian Y chromosome 1296.3 Sequence and gene content of the Y chromosome 1316.4 Function of Y chromosome genes in spermatogenesis and male fertility 1366.5 Polymorphisms of the Y chromosome and male fertility 1426.6 Future research directions 145References 1467 Mitochondriomics of Reproduction and Fertility 157Zhihua Jiang, Galen A. Williams, Jie Chen, and Jennifer J. Michal7.1 Introduction 1577.2 Cytoplasm mitochondrial genomes in fertility and reproduction 1587.3 Nuclear mitochondrial genomes in fertility and reproduction 1627.4 Future research directions 174References 174Part II Physiological Genomics of Reproduction 1818 Functional Genomics Studies of Ovarian Function in Livestock: Physiological Insight Gained and Perspective for the Future 183Beau Schilling and George W. Smith8.1 Introduction 1838.2 Transcriptomics of ovarian tissues: EST sequencing 1848.3 Transcriptomics of ovarian tissues: Microarray studies 1898.4 Proteomics of ovarian tissues 1968.5 Future research directions 197References 1999 Physiological Genomics of Preimplantation Embryo Development in Production Animals 205Luc J. Peelman9.1 Introduction 2059.2 Preimplantation developmental stages and transcriptomics 2069.3 Preimplantation developmental systems and transcriptomics 2149.4 Future research directions 219References 22010 Physiological Genomics of Conceptus–Endometrial Interactions Mediating Corpus Luteum Rescue 231Troy L. Ott and Thomas E. Spencer10.1 Introduction 23110.2 Physiological genomics of luteal regression 23210.3 Physiological genomics of blocking luteal regression 23510.4 Future research directions 242References 24311 Physiological Genomics of Placental Growth and Development 251Sukanta Mondal11.1 Introduction 25111.2 Placental development: Basics 25211.3 Placental hormones and peptides 25311.4 Transcriptomics of placental development 26111.5 Future research directions 263References 26312 Cellular, Molecular, and Genomic Mechanisms Regulating Testis Function in Livestock 269Kyle Caires, Jon Oatley, and Derek McLean12.1 Introduction 26912.2 Spermatogenesis 27012.3 Transcriptomics of testis in bulls 27212.4 Reproductive genomics in boars 27912.5 Future research directions 283References 284Part III Genomics and Reproductive Biotechnology 29113 The Epigenome and Its Relevance to Somatic Cell Nuclear Transfer and Nuclear Reprogramming 293Jorge A. Piedrahita, Steve Bischoff, and Shengdar Tsai13.1 Introduction 29313.2 The epigenome 29313.3 Epigenetic reprogramming 29713.4 Genomic imprinting 30113.5 SCNT and epigenetic abnormalities 30713.6 Future research directions 310References 31014 Biotechnology and Fertility Regulation 317Valéria Conforti14.1 Introduction 31714.2 Basic aspects in vaccine development 31814.3 Specific aspects in vaccine development 32014.4 Sperm antigens 32314.5 Zona pellucida antigens 32614.6 LHRH antigens 32814.7 Future research directions 332References 33315 Proteomics of Male Seminal Plasma 339Vera Jonakova, Jiri Jonak, and Marie Ticha15.1 Introduction 33915.2 Proteins of seminal plasma 34015.3 Function of seminal plasma proteins 34315.4 In vitro effects of seminal plasma proteins 34715.5 Properties of major proteins of seminal plasma of domestic animals 34815.6 Future research directions 352References 35216 Evolutionary Genomics of Sex Determination in Domestic Animals 367Eric Pailhoux and Corinne Cotinot16.1 Introduction 36716.2 State of knowledge of sex differentiation 36916.3 Sex differentiation in domestic mammals 37416.4 Sex determination in nonmammal domestic species 38016.5 Future research directions 382References 38317 Toxicogenomics of Reproductive Endocrine Disruption 397Ulf Magnusson and Lennart Dencker17.1 Introduction 39717.2 Reproductive endocrine disruption 39817.3 Reproductive endocrine disruptors 40117.4 Toxicogenomics 40417.5 Future research directions 408References 40818 Nutrigenomics for Improved Reproduction 413John P. McNamara18.1 Introduction 41318.2 Nutritional physiology of reproduction: A brief view 41418.3 Mechanistic connections between nutrient flux and reproductive processes 41718.4 History of integration of physiological state, nutrient flux, and reproduction 42118.5 Nutritional physiology of pregnancy and lactation 42218.6 Nutrigenetics and nutrigenomics approaches for improved fertility, pregnancy, and lactation 42718.7 Future research directions 434References 435Index 439