Reproductive Genomics in Domestic Animals E-Book

• Herausgeber: John Wiley & Sons
• Kategorie: Wissenschaft und neue Technologien
• Sprache: Englisch

Seitenzahl: 1027

Veröffentlichungsjahr: 2011

Beschreibung

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.

Leseprobe

Contents

Contributors

Preface

Part I Quantitative Genomics of Reproduction

1 Reproductive Genomics: Genome, Transcriptome, and Proteome Resources

1.1 Introduction

1.2 Discovery of underlying genetic influences

1.3 Characterization of gene expression

1.4 Resources for protein analysis

1.5 Future research directions References

2 Quantitative Genomics of Female Reproduction

2.1 Introduction

2.2 Female reproductive phenotypes

2.3 Genetic markers and genotyping methods

2.4 Association of phenotypes with genotypes

2.5 Some illustrative examples of reproductive QTL

2.6 Future research directions References

3 Quantitative Genomics of Male Reproduction

3.1 Introduction

3.2 Male reproduction phenotypes

3.3 Genetics, genomics, and quantitative trait loci (QTL)

3.4 QTL identified for male reproduction traits

3.5 Future research directions References

4 Genetics and Genomics of Reproductive Disorders

4.1 Introduction

4.2 Reproductive disorders associated with the ovary

4.3 Reproductive disorders associated with the vagina and uterus

4.4 Reproductive disorders associated with pregnancy and placenta

4.5 Reproductive disorders associated with male reproductive organs

4.6 Reproductive disorders associated with embryos and fetuses

4.7 Future research directions References

5 Genomics of Reproductive Diseases in Cattle and Swine

5.1 Introduction

5.2 Bovine paratuberculosis

5.3 BRD

5.4 Brucellosis in cattle

5.5 Leptospirosis in swine

5.6 Aujeszky’s disease (pseudorabies)

5.7 PRRS

5.8 Future research directions References

6 Comparative Genomics of the Y Chromosome and Male Fertility

6.1 Introduction

6.2 Characteristics of the mammalian Y chromosome

6.3 Sequence and gene content of the Y chromosome

6.4 Function of Y chromosome genes in spermatogenesis and male fertility

6.5 Polymorphisms of the Y chromosome and male fertility

6.6 Future research directions References

7 Mitochondriomics of Reproduction and Fertility

7.1 Introduction

7.2 Cytoplasm mitochondrial genomes in fertility and reproduction

7.3 Nuclear mitochondrial genomes in fertility and reproduction

7.4 Future research directions References

Part II Physiological Genomics of Reproduction

8 Functional Genomics Studies of Ovarian Function in Livestock: Physiological Insight Gained and Perspective for the Future

8.1 Introduction

8.2 Transcriptomics of ovarian tissues: EST sequencing

8.3 Transcriptomics of ovarian tissues: Microarray studies

8.4 Proteomics of ovarian tissues

8.5 Future research directions References

9 Physiological Genomics of Preimplantation Embryo Development in Production Animals

9.1 Introduction

9.2 Preimplantation developmental stages and transcriptomics

9.3 Preimplantation developmental systems and transcriptomics

9.4 Future research directions References

10 Physiological Genomics of Conceptus–Endometrial Interactions Mediating Corpus Luteum Rescue

10.1 Introduction

10.2 Physiological genomics of luteal regression

10.3 Physiological genomics of blocking luteal regression

10.4 Future research directions References

11 Physiological Genomics of Placental Growth and Development

11.1 Introduction

11.2 Placental development: Basics

11.3 Placental hormones and peptides

11.4 Transcriptomics of placental development

11.5 Future research directions References

12 Cellular, Molecular, and Genomic Mechanisms Regulating Testis Function in Livestock

12.1 Introduction

12.2 Spermatogenesis

12.3 Transcriptomics of testis in bulls

12.4 Reproductive genomics in boars

12.5 Future research directions References

Part III Genomics and Reproductive Biotechnology

13 The Epigenome and Its Relevance to Somatic Cell Nuclear Transfer and Nuclear Reprogramming

13.1 Introduction

13.2 The epigenome

13.3 Epigenetic reprogramming

13.4 Genomic imprinting

13.5 SCNT and epigenetic abnormalities

13.6 Future research directions References

14 Biotechnology and Fertility Regulation

14.1 Introduction

14.2 Basic aspects in vaccine development

14.3 Specific aspects in vaccine development

14.4 Sperm antigens

14.5 Zona pellucida antigens

14.6 LHRH antigens

14.7 Future research directions References

15 Proteomics of Male Seminal Plasma

15.1 Introduction

15.2 Proteins of seminal plasma

15.3 Function of seminal plasma proteins

15.4 In vitro effects of seminal plasma proteins

15.5 Properties of major proteins of seminal plasma of domestic animals

15.6 Future research directions References

16 Evolutionary Genomics of Sex Determination in Domestic Animals

16.1 Introduction

16.2 State of knowledge of sex differentiation

16.3 Sex differentiation in domestic mammals

16.4 Sex determination in nonmammal domestic species

16.5 Future research directions References

17 Toxicogenomics of Reproductive Endocrine Disruption

17.1 Introduction

17.2 Reproductive endocrine disruption

17.3 Reproductive endocrine disruptors

17.4 Toxicogenomics

17.5 Future research directions References

18 Nutrigenomics for Improved Reproduction

18.1 Introduction

18.2 Nutritional physiology of reproduction: A brief view

18.3 Mechanistic connections between nutrient flux and reproductive processes

18.4 History of integration of physiological state, nutrient flux, and reproduction

18.5 Nutritional physiology of pregnancy and lactation

18.6 Nutrigenetics and nutrigenomics approaches for improved fertility, pregnancy, and lactation

18.7 Future research directions References

Index

Edition first published 2010 © 2010 Blackwell Publishing

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Library of Congress Cataloging-in-Publication Data

Reproductive genomics in domestic animals / editors, Zhihua Jiang, Troy L. Ott.–1st ed.p. cm.Includes bibliographical references and index.ISBN 978-0-8138-1784-2 (hardback: alk. paper) 1. Domestic animals–Genetics.2. Domestic animals–Reproduction. 3. Livestock–Genetics. 4. Livestock–Reproduction.5. Genomics–Research. I. Jiang, Zhihua, 1959– II. Ott, Troy L. SF105.R45 2010 636.08’21–dc22 2009049307

A catalog record for this book is available from the U.S. Library of Congress.

Set in 10 on 13 pt Trump Mediaeval by Toppan Best-set Premedia Limited

Contributors

Steve Bischoff, Department of Molecular Biomedical Sciences and Center of ComparativeMedicine and Translational Research, College of Veterinary Medicine, North Carolina State University, Raleigh, NC 27606

Kyle Caires, Department of Animal Sciences, Center for Reproductive Biology, Washington State University, Pullman, WA

Eduardo Casas, USDA, Agricultural Research Service, U.S. Meat Animal Research Center, Clay Center, NE 68933-0166

Jie Chen, Department of Animal Sciences, Center for Reproductive Biology, Washington State University, Pullman, WA 99164-6351; and College of Animal Sciences and Technology, Nanjing Agricultural University, Nanjing 210095, China

Noelle E. Cockett, Department of Animal, Dairy and Veterinary Sciences, Utah State University, Logan, UT 84322-4900

Valéria Conforti, Cincinnati Zoo & Botanical Garden, 3400 Vine Street, Cincinnati, OH 45220-1399

Corinne Cotinot, CNRS, FRE 2857, F-78350, Jouy-en-Josas, France

Lennart Dencker, Department of Pharmaceutical Sciences at Biomedical Centre, P.O. Box 594, Uppsala University, SE-756 45 Uppsala, Sweden

Peter Dovc, Department of Animal Science, University of Ljubljana, Groblje 3, SI-1230 Domzale, Slovenia

J. Joe Ford, USDA, Agricultural Research Service, U.S. Meat Animal Research Center, Clay Center, NE 68933-166

Zhihua Jiang, Department of Animal Sciences, Center for Reproductive Biology, Washington State University, Pullman, WA 99164-6351

Jiri Jonak, Laboratory of Diagnostic for Reproductive Medicine, Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Videnska 1083, 14220 Prague 4, Czech Republic

Vera Jonakova, Laboratory of Diagnostics for Reproductive Medicine, Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Videnska 1083, 14220 Prague 4, Czech Republic

Larry A. Kuehn, USDA, Agricultural Research Service, U.S. Meat Animal Research Center, Clay Center, NE 68933

Tanja Kunej, Department of Animal Science, University of Ljubljana, Groblje 3, SI-1230 Domzale, Slovenia

Wansheng Liu, Department of Dairy and Animal Science, Center for Reproductive Biology and Health, The Pennsylvania State University, University Park, PA 16802

Ulf Magnusson, Department of ClinicalSciences and Centre for Reproductive Biology in Uppsala, P.O. Box 7054, Swedish University of Agricultural Sciences, SE-750 07 Uppsala, Sweden

Derek McLean, Department of AnimalSciences, Center for Reproductive Biology, Washington State University, Pullman, WA

John P. McNamara, Department of AnimalSciences, Center for Reproductive Biology,Washington State University, Pullman, WA 99164-6351

Jennifer J. Michal, Department of Animal Sciences, Center for Reproductive Biology,Washington State University, Pullman, WA 99164-6351

Sukanta Mondal, Division of AnimalPhysiology, National Institute of AnimalNutrition and Physiology (Indian Council ofAgricultural Research), Adugodi, Bangalore—560 030, Karnataka, India

Holly Neibergs, Department of AnimalSciences, Center for Reproductive Biology, Washington State University, Pullman, WA99164-6351

Dan J. Nonneman, USDA, AgriculturalResearch Service, U.S. Meat AnimalResearch Center, Clay Center, NE 68933

Jon Oatley, Department of Dairy andAnimal Sciences, Center for ReproductiveBiology and Health, The Pennsylvania StateUniversity, University Park, PA

Troy L. Ott, Department of Dairy andAnimal Sciences, Center for ReproductiveBiology and Health, The Pennsylvania StateUniversity, University Park, PA 16802

Eric Pailhoux, INRA, UMR 1198 Biologie duDéveloppementet Reproduction, F-78350 Jouy-en-Josas, France

Luc J. Peelman, Department of Nutrition, Genetics and Ethology, Faculty of VeterinaryMedicine, Ghent University, 9820Merelbeke, Belgium

Jorge A. Piedrahita, Department of MolecularBiomedical Sciences and Center ofComparative Medicine and TranslationalResearch, College of Veterinary Medicine, North Carolina State University, Raleigh, NC 27606

Gary A. Rohrer, USDA, Agricultural ResearchService, U.S. Meat Animal Research Center, Clay Center, NE 68933-0166

Beau Schilling, Laboratory of MammalianReproductive Biology and Genomics, Departmentof Animal Science, Michigan State University, East Lansing, MI 48824-1225

George W. Smith, Laboratory of MammalianReproductive Biology and Genomics, Department of Physiology, Michigan StateUniversity, East Lansing, MI 48824-1225

Thomas E. Spencer, Department of AnimalScience, Center for Animal Biotechnologyand Genomics, Texas A & M University,College Station, TX 77843-2471

Marie Ticha, Laboratory of Diagnostic forReproductive Medicine, Institute of MolecularGenetics, Academy of Sciences of theCzech Republic, Videnska 1083, 142 20Prague 4, Czech Republic

Shengdar Tsai, Department of MolecularBiomedical Sciences and Center of ComparativeMedicine and Translational Research,College of Veterinary Medicine, NorthCarolina State University, Raleigh,NC 27606

Jeffrey L. Vallet, USDA, AgriculturalResearch Service, U.S. Meat Animal ResearchCenter, Clay Center, NE 68933

Galen A. Williams, Devers Eye Institute,1225 NE 2nd Ave., Portland, OR 97232

Ricardo Zanella, Department of AnimalSciences, Center for Reproductive Biology,Washington State University, Pullman,WA 99164-6351

Preface

Reproductive efficiency has been considered one of the most critical factors affecting the productivity and profitability of the livestock industries. Unfortunately, in spite of a significant improvement in growth, feed efficiency, and carcass and meat quality due to genetic selection and management advances, reproductive efficiency has declined in most livestock species. Due to low heritabilities, and sex-limited complexity, it has been very difficult to improve reproductive traits using traditional selection methods. The rapid development of molecular genetics and genomics in recent years has, however, enabled the identification, characterization, and utilization of genes and pathways that contribute to the genetic complexity of reproduction in domestic animals. This book reviews the current status of reproductive genomics, transcriptomics, and proteomics and highlights the current and potential genomics tools and reagents for improving reproductive efficiency in domestic animals. It is our goal to have in the book a broad coverage on genome sciences and bio-technologies that can help address and understand various aspects of fertility and infertility in domestic animals.

The book consists of three main parts. Part I has seven chapters that focus on genome resources and quantitative genomics of reproduction. Chapter 1 demonstrates genome resources specifically available to livestock species, such as well-characterized genome maps, whole genome and cDNA sequences, expression arrays, and high-density genetic marker chips. Chapter 2 defines the female reproductive phenotypes and updates the genes/quantitative trait loci associated with the traits. Chapter 3 defines the male reproductive phenotypes and updates the genes/quantitative trait loci associated with these traits. Chapters 2 and 3 also include methods and technologies for the development and discovery of genomic markers as well as their genotyping formats. Chapter 4 covers genetic and genomic aspects of reproductive disorders associated with the ovary, vagina, and uterus; pregnancy and placenta; male reproductive organs; and embryos and fetuses. Chapter 5 deals with genetic and genomic aspects of reproductive diseases, such as paratuberculosis, respiratory disease, and brucellosis in cattle, and leptospirosis, Aujeszky’s disease, and porcine reproductive and respiratory syndrome in swine. Chapter 6 focuses on the structure, function, and evolution of the Y chromosome and its effect on male fertility. Chapter 7 describes both mitochondrial genomes in the cytoplasm and nucleus and their involvements in male reproduction, female reproduction, embryo development, and reproductive aging.

Part II of this book possesses five chapters that target transcriptomics and physiological genomics of reproduction, which link genes to physiology and pathways critical for reproductive success. Chapter 8 deals with transcriptomics of ovarian tissues involved in follicular growth and development, luteinization of the dominant follicle, corpus luteum regression, oocyte maturation, and oocyte competence. Chapter 9 focuses on transcriptomics related to different preimplantation development stages and systems. Chapter 10 focuses on the genomics endometrial responses to conceptus signals mediating corpus luteum rescue. Chapter 11 reviews hormones and peptides, and transcriptomics involved in placental development. Chapter 12 targets cellular, molecular, and genomic mechanisms regulating testis function in livestock with emphasis on transcriptomics of the testis in bulls and reproductive genomics in boars.

Part III has six chapters that deal with genomics of reproductive biotechnology and their applications. Chapter 13 discusses the importance of nuclear reprogramming during somatic cell nuclear transfer and its implications for normal fetal and placental development. Chapter 14 describes how to use immunocontraception and immunosterilization as methods of fertility control in animals. Chapter 15 deals with the structure and properties of seminal plasma proteins and their potential roles in fertilization affecting the oviductal reservoir, and as capacitation modulators, gamete interaction enhancers, and enzyme inhibitors. Chapter 16 reports the state of knowledge on sex differentiation in domestic mammals and sex determination in nonmammal domestic species. Chapter 17 addresses the disruption of the reproductive endocrine systems and the mechanisms of action of endocrine disrupting chemicals that exert hormone-like activity in humans and animals. Chapter 18 focuses on the mechanistic connections between nutrient flux and reproductive processes with emphasis on nutritional physiology of pregnancy and lactation and demonstrates how nutrigenetics and nutrigenomics approaches can improve fertility, pregnancy, and lactation.

This book is for researchers, instructors, extension experts, and students in animal, veterinary, and biomedical sciences who are interested in quantitative genomics, physiological genomics, mitochondriomics, pathological genomics, epigenomics, nutrigenomics, evolutionary genomics, and proteomics of reproduction. The 37 contributors to the book are all internationally recognized experts in their field, and they represent 15 different institutions from seven different countries. We thank them for their contributions to this first book on reproductive genomics of domestic animals. Support from both families has been essential for us to finish the book project, and we are grateful for their patience. Thanks also to Justin Jeffryes, Susan Engelken, Shelby Allen, the Wiley-Blackwell publishing team, and the team at Toppan Best-set Premedia for their extra care and patience in publishing the book.

Zhihua JiangTroy L. Ott

Part I

Quantitative Genomics of Reproduction

1

Reproductive Genomics: Genome, Transcriptome, and Proteome Resources

Noelle E. Cockett

1.1 Introduction

Genomic resources, tools, and technologies that can be applied to studies in livestock species, including investigations related to reproduction, have been under development for the last decade. While many of the genomic approaches were originally developed for use in humans or laboratory model animals, they have been successfully applied to studies in livestock. There are now a myriad of resources specific to livestock species, such as well-characterized genome maps, high-resolution genome, and complementary DNA (cDNA) sequences, expression arrays, and high-density genetic marker chips. In addition, there is an explosion of high-throughput technology that will enhance these investigations, increasing the scope and accuracy of the results beyond anything that was imagined just 5 years ago. These technologies advance studies of single gene expression to full gene networks, from single gene sequences to whole genomes,and from hundreds of genetic markers to tens of thousands markers—all assayable in a few weeks to months as opposed to years.

These resources and technologies can be combined in innovative ways to advance two areas of research on reproductive traits, specifically the identification of genes or genetic regions influencing phenotypes and the characterization of expression of genes that are associated with traits.

1.2 Discovery of underlying genetic influences

The first area of interest for researchers studying reproductive traits is the characterization of genetic variation among animals or populations underlying a phenotypic trait, leading to the identification of the genetic cause of the phenotype. Two general approaches have been successfully used over the last 10–15 years, with a third approach now on the horizon. In the first approach,polymorphisms in a candidate gene likely to be involved in the phenotype are tested for associations with different manifestations or phenotypes of the trait. The candidate genes are selected for analysis based on an understanding of trait physiology and/or because of their involvement in similar traits in other species. In the second approach, genetic markers are analyzed for linkage with the phenotype using pedigrees of animals segregating for the trait and the markers. This analysis identifies genetic regions that contain associated genes. By testing additional markers through the families, the interval is narrowed so candidate genes can be selected. The third approach, referred to as whole genome associations, will soon be possible for livestock species now that the development of high-density single nucleotide polymorphism (SNP) arrays are readily available. However, the application of whole genome associations requires very large numbers of phenotyped animals, which is a limitation for most research projects.

1.2.1 Candidate gene associations

As mentioned, the candidate gene approach uses information of the trait to determine likely candidates for the underlying gene(s). The choice of the gene is strengthened by its involvement in comparable traits in other species or its location in a region previously identified as containing a quantitative trait loci (QTL) with similar attributes.

In the past, polymorphisms in a candidate gene were routinely detected by polymerase chain reaction—restriction fragment length polymorphisms (PCR-RFLP), which involves steps of amplifying the gene, digesting the amplicon with a restriction enzyme, and then using gel electrophoresis to separate the resulting fragments. In the PCR-RFLP technique, gene sequence differences among animals are detected by whether or not a restriction enzyme cuts, resulting in different-sized fragments. The genetic differences are usually due to an SNP within the restriction enzyme recognition site, although there might be genetic differences due to insertions/deletions (in/del) in the gene, which will also result in fragment size differences, although there is no variation in the restriction enzyme recognition site. Animals are expected to have two alleles for every gene except those on the X and Y chromosomes in males, so that the presence of one fragment on the electrophoresis gel would indicate that an animal is homozygous for the PCR-RFLP allele whereas the presence of two different-sized fragments would suggest that an animal is heterozygous. However, an animal might be misclassified as a homozygote if there is a polymorphism in the PCR primer sequence, which prevents that allele from being amplified and therefore, not detected on the electrophoresis gel—referred to as a “null” allele. A null allele will often be detected when misparentages are routinely found for a marker system. An animal might also be misclassified if another, nonallelic form of the gene is amplified with the PCR primers and digestion with the restriction enzyme results in a different-sized fragment. A nonallelic form is revealed by sequencing the fragments contained within the electrophoretic bands, which is a recommended step when establishing any marker system.

However, new technologies have significantly advanced our ability to identify SNPs and then explore multiple candidate genes at one time at a much lower cost/ polymorphism than the PCR-RFLP method. The identification of SNPs within a gene or genetic region is now relatively easy. To do this, the genomic DNA of key animals within a population is sequenced using high throughput automatic sequencing and then compared with other sequences within the population or to sequences in publically available databases. The later approach is referred to as SNP detection. Regardless of the approach, confidence of the SNP is dependent on the quality of the sequence across the multiple sources of data.