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 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.