Molecular and Quantitative Animal Genetics

331 Pages·2015·18.11 MB·English

by  Hasan Khatib

Molecular and
Quantitative Animal
Genetics

Molecular and
Quantitative Animal
Genetics
edited by
Hasan Khatib
University of Wisconsin-Madison
Madison, WI, USA
Copyright © 2015 by John Wiley & Sons, Inc. All rights reserved
Published by John Wiley & Sons, Inc., Hoboken, New Jersey
Published simultaneously in Canada
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Library of Congress Cataloging-in-Publication Data
Molecular and quantitative animal genetics / edited by Hasan Khatib.
p. ; cm.
Includes bibliographical references and index.
ISBN 978-1-118-67740-7 (paperback)
1. Animal genetics. 2. Intellectual property. I. Khatib, Hasan, editor.
[DNLM: 1. Animals. 2. Genetics. 3. Molecular Biology. QH 432]
QH432.M65 2015
591.3'5–dc23
2014036482
10 9 8 7 6 5 4 3 2 1
Contents
Contributors, ix  4 Basic Genetic Model for Quantitative Traits, 33
Guilherme J. M. Rosa
Manuscript reviewers, xi
Introduction, 33
Preface, xiii
Quantitative traits, 33
Expected value and variance: the normal distribution, 33
 1 Decoding and Encoding the “DNA” of Teaching 
Basic genetic model for quantitative traits, 35
and Learning in College Classrooms, 1
Heritability and selection, 35
Michel A. Wattiaux
Predicting rate of genetic change from selection, 36
Introduction, 1 Further reading, 37
Teaching and learning: definitions, 1 References, 37
Understanding learning, 2
Understanding teaching, 5
 5 Heritability and Repeatability, 39
Implications for classroom design in the twenty-first
Guilherme J. M. Rosa
century, 6
Final thoughts, 9 Introduction, 39
References, 10 Heritability, 39
Review questions, 11 Estimation of heritability and variance components, 40
Prediction of breeding values and of response to selection, 41
Section 1: Quantitative and Population Genetics, 13 Repeatability, 41
References, 42
 2 Mating Systems: Inbreeding and  
Inbreeding Depression, 15  6 Applications of Statistics in Quantitative  
David L. Thomas Traits, 43
Hayrettin Okut
Introduction, 15
Inbreeding, 15 Population and sample, 43
Cause of inbreeding depression, 18 Descriptive statistics, 43
Quantifying inbreeding, 20 Graphically examining the distribution of the data, 47
Genomics and inbreeding, 23 Normal distribution, 49
Summary, 23 Exploring relationships between variables, 53
Further reading, 24 Summary, 59
References, 24 Appendix 6.1, 62
Review questions, 24 Further reading, 62
References, 62
 3 Genomic Selection, Inbreeding, and  Review questions, 63
Crossbreeding in Dairy Cattle, 25
Kent Weigel
Section 2: Applications of Genetics and Genomics to 
Introduction, 25
Livestock and Companion Animal Species, 65
Genomic selection, 25
Crossbreeding, 28
 7 Genetic Improvement of Beef Cattle, 67
Inbreeding and genetic defects, 29
Michael D. MacNeil
Summary, 30
References, 30 Introduction, 67
Review questions, 31 Single trait selection, 67
v
Contents
National cattle evaluation, 69 11 Equine Genetics, 107
Multiple trait selection, 71 Jennifer Minick Bormann
Summary, 71
Color, 107
Further reading, 71
Genetic defects, 110
References, 72
Inbreeding and relationship, 113
Selection and improvement, 114
 8 Genetic Improvement in  
New technologies, 116
Sheep through Selection, 73
Further reading, 117
David L. Thomas
References, 119
Products from sheep, 73 Review questions, 119
Selection among breeds, 73
Selection within a breed or population and the Key
12 Genetics and Genomics of the Domestic Dog, 121
Equation, 73
Leigh Anne Clark and Alison Starr-Moss
Adjustment for environmental effects, 73
Phenotypic selection, 75 Introduction to canine research, 121
Estimated breeding values (EBV), 75 The dog genome, 122
Using multiple sources of information, 76 Uncovering the genetic basis of phenotypes, 125
Genetic correlations, 76 Future challenges, 127
Selection intensity, 78 Summary, 128
Generation interval (L), 79 Further reading, 129
Predicting progress from selection, 79 References, 130
National genetic improvement programs, 80 Review questions, 130
Summary, 81
Further reading, 82
References, 82 13 The Sheep Genome, 131
Review questions, 82 Noelle E. Cockett and Chunhua Wu
Investment in sheep genome research, 131
 9 Genetic Improvement Programs for  
Overview of the sheep genome, 131
Dairy Cattle, 85
Genomic resources in sheep, 131
Kent Weigel
Application of genomic resources, 134
Introduction, 85 Summary, 134
Data collection infrastructure, 85 References, 135
Estimation of breeding values, 87 Review questions, 136
Selection for increased productivity, 89
Selection for functional traits, 91
14 Goat Genetics and Genomic Progress, 137
Sire selection, 94
Mulumebet Worku
Summary, 94
Further reading, 95 Introduction, 137
References, 95 Genetics and goat domestication, 137
Review questions, 96 Taxonomy, 138
Goat chromosome number and structure, 138
10 Genetic and Genomic Improvement of Pigs, 97 Patterns of inheritance, 139
Max F. Rothschild Quantitative trail loci (QTL), 139
Progress in goat genomics, 139
Introduction, 97
Biotechnologies and goat genetics, 140
Domestication of swine and breed development, 97
Summary, 140
Methods of selection and mating systems, 98
Further reading, 140
Traits of economic importance, 99
Review questions, 141
Development of molecular genetic approaches, 100
QTL, candidate genes, and genetic improvement, 100
Section 3: Molecular Genetics of Production and 
Sequencing the pig genome, 101
Economically Important Traits, 143
Genomic selection, 102
Databases, 103
15 Bioinformatics in Animal Genetics, 145
Cloning, transgenics, and breeding pigs as biological
José A. Carrillo and Jiuzhou Song
models, 103
Future applications to genetic improvement, 103 Introduction, 145
Acknowledgments, 104 Bioinformatics and animal genetics, 145
Further reading, 104 The importance of bioinformatics in genomics research, 146
References, 104 Gene expression, 148
Review questions, 105 Gene regulation, 150
vi
Contents
Epigenetics, 151 20 Molecular Genetics-Nutrition Interactions  
Genomic data manipulation, 151 in Ruminant Fatty Acid Metabolism and  
Bioinformatics perspectives in animal genetics, 153 Meat Quality, 197
References, 153 Aduli E.O. Malau-Aduli and Benjamin W.B. Holman
Review questions, 154
Introduction, 197
Genetics-nutrition interactions in ruminants, 197
16 Genome-wide Association Studies in Pedigreed 
Educating Australian undergraduate students in molecular
Populations, 155
genetics-nutrition interactions in ruminants, 198
Dirk-Jan de Koning
Review of fatty acids and their manipulation, metabolism,
Introduction, 155 and effect on quality in ruminants, 200
Methods and tools for GWAS in Concluding remarks, 205
pedigreed populations, 159 Appendix 20.1: Fats and beef quality laboratory practicals,
Things to remember about analysis, 160 206
What did we miss?, 160 Appendix 20.2: Sensory evaluation of meat quality in
Acknowledgments, 162 grain-fed versus grass-fed beef, 206
References, 162 Appendix 20.3: Total lipid extraction from a beef cut for
fatty acid analysis, 206
Appendix 20.4: Molecular genetics laboratory practical, 207
17 Molecular Genetics Techniques and High 
References, 212
Throughput Technologies, 163
Wen Huang
21 Nutritional Epigenomics, 215
Central dogma of molecular biology, 163
Congjun Li
Review of properties of nucleic acids, 163
Purification of nucleic acids from cells, 164 Introduction, 215
Determining the quantity and purity of Epigenomic machinery and gene regulation, 216
nucleic acids, 165 Nutrients and histone modification, 219
Polymerase chain reaction (PCR), 166 Nutrients and epigenetics in bovine cells: one definitive
Determining the identity of DNA, 167 example of the nutrient-epigenetic-phenotype
Concept of parallelization and high relationship, 221
throughput assays, 168 Summary, 224
Next generation sequencing technology, 171 References, 224
Summary, 174 Review questions, 225
Further reading, 174
Review questions, 174
Section 4: Genetics of Embryo Development and 
Fertility, 227
18 Single Genes in Animal Breeding, 177
Brian W. Kirkpatrick
22 Genomics of Sex Determination and  
Introduction, 177 Dosage Compensation, 229
Mapping and identifying single genes, 177 Jenifer Cruickshank and Christopher H. Chandler
What types of DNA sequence alterations create single gene
Genotypic sex determination (GSD), 229
effects?, 180
Environmental sex determination (ESD), 232
Examples of single genes in animal breeding, 181
Dosage compensation in mammals: X chromosome
Summary, 185
inactivation, 232
References, 185
Activity patterns of sex chromosomes during
Review questions, 186
gametogenesis, 233
Escape from X inactivation, 234
19 Molecular Genetics of Coat Color: It is more than 
Abnormalities in chromosomal sex, 235
Just Skin Deep, 187
Sex reversal, 235
Samantha Brooks
Summary, 236
Introduction, 187 Further reading, 236
Pathways of melanocyte migration and differentiation from Review questions, 237
the neural crest, 187
Melanocyte signaling and regulation, 188
23 Functional Genomics of Mammalian Gametes and 
Melanin production and transport, 190
Preimplantation Embryos, 239
Conclusions, 192
Şule Doğan, Aruna Govindaraju, Elizabeth A. Crate,
Summary, 192
and Erdoğan Memili
Key terms, 192
References, 193 Introduction, 239
Review questions, 195 Gamete and embryo development, 239
vii
Contents
Transcriptomics, 242 Further reading, 282
Proteomics, 248 Review questions, 282
Systems biology, 251
Conclusion, 253 27 Animal Genetics and Welfare, 283
Further reading, 253 Amin A. Fadl and Mark E. Cook
References, 253
Introduction, 283
A continued need for genetic improvements and
24 The Genetics of In Vitro Produced Embryos, 257 knowledge, 283
Ashley Driver Welfare, 284
Genetic advancement and animal welfare, 284
In vitro production: from livestock to humans, 257
Genetic selection that adversely affects farmed animal
Unlocking developmentally important genes in the
welfare, 286
pre-implantation embryo, 258
Summary, 287
IVP: potential source of genetic alteration?, 259
References, 287
PGD: genetic screening and human embryos, 259
Review questions, 288
Screening the embryo: to infinity and beyond?, 260
Embryogenetics: what’s next?, 260
Summary, 260
28 Animal Biotechnology: Scientific, Regulatory  
Key terms, 260
and Public Acceptance Issues Associated  
References, 261
with Cloned and Genetically Engineered  
Review questions, 262
Animals, 289
Supplementary videos, 262
Alison L. Van Eenennaam
What is animal biotechnology?, 289
Cloning, 290
Section 5: Genetics of Animal Health  
Genetic engineering, 293
and Biotechnology, 263
Ethical, moral, and animal welfare concerns, 297
Summary, 299
25 Understanding the Major Histocompatibility 
Further reading, 300
Complex and Immunoglobulin Genes, 265
References, 300
Michael G. Gonda
Review questions, 301
Introduction, 265
Overview of the immune system, 265
The major histocompatibility complex loci, 267 29 Intellectual Property Rights and Animal Genetic 
Immunoglobulin loci, 268 Resources, 303
Summary, 272 Jennifer Long and Max F. Rothschild
Key terms, 273
Introduction, 303
Further reading and references, 274
Old M/cDonald’s Farm meets Dolly
Review questions, 274
(and her lawyer), 303
What is intellectual property?, 303
26 Livestock and Companion Animal Genetics: 
Forms of intellectual property, 303
Genetics of Infectious Disease  
Here a patent, there (not) a patent, 304
Susceptibility, 275
Forms of payment or remuneration, 305
Michael G. Gonda
Case studies, 306
Introduction, 275 E-I-E-I-O: The alphabet soup of domestic and international
Why is studying the genetics of disease susceptibility issues, 307
important?, 275 Public sector research and IP – domestic and international,
Present applications of genetic selection tools for predicting 307
disease susceptibility, 276 Access to animal genetic resources, 307
Current research into genetic selection for Summary, 308
livestock health, 279 Further reading, 308
Challenges faced when studying the genetics of disease References, 308
resistance in livestock, 280 Review questions, 309
Should we select for increased disease resistance?, 281
Summary, 281
Key terms, 281 Index, 311
viii