Poultry genetics, breeding, and biotechnology

706 Pages·2003·5.572 MB·English

by  W M Muir, S E Aggrey

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Poultry Genetics, Breeding and Biotechnology
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Poultry Genetics, Breeding and
Biotechnology
Edited by
W.M. Muir
Department of Animal Sciences
Purdue University
West Lafayette, Indiana
USA
and
S.E. Aggrey
Department of Poultry Science
University of Georgia
Athens, Georgia
USA
CABIPublishing
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CABIPublishing is a division of CAB International
CABIPublishing CABIPublishing
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©CAB International 2003. All rights reserved. No part of this publication may
be reproduced in any form or by any means, electronically, mechanically, by
photocopying, recording or otherwise, without the prior permission of the
copyright owners.
A catalogue record for this book is available from the British Library, London,
UK.
Library of Congress Cataloging-in-Publication Data
Poultry genetics, breeding and biotechnology/edited by W.M. Muir and
S.E. Aggrey.
p. cm.
Includes bibliographical references and index.
ISBN 0-85199-660-4 (alk. paper)
1. Poultry--Breeding. 2. Poultry--Genetics. 3. Poultry--Genetic
engineering. I. Muir, W. M. (William M.) II. Aggrey, S. E. (Samuel E.)
III. Title.
SF487.P85 2003
636.5′082--dc21 2002013733
ISBN 0 85199 660 4
Typeset by AMADataSet, UK
Printed and bound in the UK byCromwell Press, Trowbridge
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Contents
Contributors ix
Preface xiii
Part I. Problems and Issues Associated with Poultry Breeding
1. Industrial Perspective on Problems and Issues Associated with Poultry
Breeding 1
James A. Arthur and Gerard A.A. Albers
2. Growth and Reproduction Problems Associated with Selection for Increased
Broiler Meat Production 13
E.Decuypere,V.Bruggeman, G.F. Barbato and J. Buyse
3. Skeletal Problems Associated with Selection for Increased Production 29
Colin C. Whitehead,Robert H. Fleming, Richard J. Julian and Poul Sørensen
4. Meat Quality Problems Associated with Selection for Increased Production 53
HervéRémignonand Elisabeth LeBihan-Duval
5. BehaviourProblems Associated with Selection for Increased Production 67
J.B. Kjaerand J.A. Mench
6. Genotype–Environment Interactions: Problems Associated with Selection
for Increased Production 83
P.K.Mathur
Part II. Breeding Strategies and Objectives
7. Breeding Objectives and Selection Strategies for Layer Production 101
A.F.Groen
8. Breeding Objectives and Selection Strategies for Broiler Production 113
DerekEmmerson
v
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vi Contents
9. Use of Mixed Model Methodology in Breeding Strategies for Layers 127
B. Besbesand V. Ducrocq
10. Application of Mixed Model Methodology in Breeding Strategies for Meat-type
Birds 147
StanislawWfxyk and Jan Jankowski
11. Use of Mixed Model Methodology in Poultry Breeding: Estimation of Genetic
Parameters 165
Tomasz Szwaczkowski
12. Use of Mixed Model Methodology in Poultry Breeding: Assumptions,
Limitations and Concerns of BLUP-based Selection Programmes 203
Margaret Quinton
13. Direct Selection for Improvement of Animal Well-being 221
J.M. Faure,W. Bessei and R.B. Jones
14. Indirect Selection for Improvement of Animal Well-being 247
W.M. Muir
15. Genetic Diversity and Conservation of Poultry 257
Mary E. Delany
Part III. Disease Resistance and Transmission
16. Progress and Prospects in Resistance to Disease 283
U. Kuhnlein,S.E. Aggrey and D. Zadworny
17. Genetics of the Immune System 293
J. Plachy,P. Kaiser and K. Hála
18. Genetic Resistance and Transmission of Avian Bacteria and Viruses 311
N. Bumstead
19. Genetic Resistance and Transmission of Avian Parasites 329
Marie-Helene Pinard-van der Laan,Hyun S. Lillehoj and James J. Zhu
20. Selection for Disease Resistance: Conventional Breeding for Resistance to
Bacteria and Viruses 357
C. Beaumont,G. Dambrine, A.M. Chaussé and D. Flock
21. Selection for Disease Resistance: Molecular Genetic Techniques 385
Hans H. Cheng
22. Selection for Disease Resistance: Direct Selection on the Immune Response 399
Susan J. Lamont,Marie-Helene Pinard-van der Laan, Avigdor Cahaner,
Jan J. van der Poel and Henk K. Parmentier
Part IV. The Use of Genomics and Bioinformatics in Poultry
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Contents vii
23. Genetic Markers: Prospects and Applications in Genetic Analysis 419
Samuel E. Aggreyand Ronald Okimoto
24. Designs and Methods to Detect QTL for Production Traits Based on Mapped
Genetic Markers 439
Johan A.M. van Arendonk and Henk Bovenhuis
25. Designs and Methods to Detect QTL for Production Traits Based on Random
Genetic Models 465
Nengjun Yi and Shizhong Xu
26. Structural Genomics: Integrating Linkage, Physical and Sequence Maps 497
Martien A.M. Groenen and Richard P.M.A. Crooijmans
27. Incorporating Molecular Information in Breeding Programmes: Methodology 537
Rohan L. Fernando and Liviu R. Totir
28. Incorporating Molecular Information in Breeding Programmes: Applications
and Limitations 549
W.M. Muir
29. Comparative Genomics 563
David W. Burt
30. Functional Genomics: Development and Gene Regulation 607
John Killefer and Hakan Kocamis
31. Expressed Sequence Tags, DNA Chip Technology and Gene Expression
Profiling 629
Larry A. Cogburn,Robin Morgan and Joan Burnside
32. DNA Polymorphisms in Functional Genes 647
U. Kuhnlein, S.E. Aggrey, N. Kansaku and D. Zadworny
33. Strategies for the Production of Transgenic Chickens 665
James N. Petitte
34. The Future of Molecular Genetics in Poultry Breeding 685
Jerry B. Dodgson
Index 697
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Contributors
G.A.A. Albers, Nutreco Agriculture Research and Development, Veerstraat 38, PO Box
220, 5830 AE Boxmeer, The Netherlands.
S.E.Aggrey,DepartmentofPoultryScience,TheUniversityofGeorgia,Athens,GA30602,
USA.
J.A.M. van Arendonk, Animal Breeding and Genetics Group, Department of Animal
Sciences, Wageningen University, Marijkeweg 40, 6709 PG Wageningen, The
Netherlands.
J.A. Arthur,Hy-Line International, PO Box 310, Dallas Center, IA 50063, USA.
G.F.Barbato,DepartmentofPoultryScience,201WmL.HenningBuilding,Pennsylvania
State University, University Park, PA 16808, USA.
C. Beaumont, Station de Recherches Avicoles, INRA Centre de Tours, 37380 Nouzilly,
France.
B. Besbes,Hubbard-ISA (Layer Division), BP 27, 35220 Chateaubourg, France.
W.Bessei,UniversitätHohenheim,NutztierethologieundKleintierzucht,70593Stuttgart,
Germany.
H. Bovenhuis, Animal Breeding and Genetics Group, Department of Animal Sciences,
Wageningen University, Marijkeweg 40, 6709 PG Wageningen, The Netherlands.
V.Bruggeman,DepartmentofAnimalSciences,CatholicUniversityofLeuven,Laboratory
for Physiology and Immunology of Domestic Animals, Kasteelpark Arenberg 20,
B-3001 Leuven, Belgium.
N. Bumstead, Institute of Animal Health, Compton Laboratory, Compton, Newbury,
Berkshire RG20 7NN, UK.
J. Burnside, Department of Animal and Food Sciences, University of Delaware, Newark,
DE 19716, USA.
D.W. Burt, Department of Genomics and Bioinformatics, Roslin Institute, Roslin,
Midlothian EH25 9PS, UK.
D.J.Buyse,DepartmentofAnimalSciences,CatholicUniversityofLeuven,Laboratoryfor
Physiology and Immunology of Domestic Animals, Kasteelpark Arenberg 20, B-3001
Leuven, Belgium.
A. Cahaner, Faculty of Agriculture, Hebrew University of Jerusalem, POB 12, Rehovot,
Israel.
A.M. Chaussé, INRA, Station de Pathologie Aviarire et Parasitologie, 37380 Nouzilly,
France.
H.H.Cheng,USDA-ARS,AvianDiseaseandOncologyLab,3606E.MountHopeRoad,East
Lansing, MI 48823, USA.
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x Contributors
L.A.Cogburn,DepartmentofAnimalandFoodSciences,UniversityofDelaware,Newark,
DE 19716, USA.
R.P.M.A. Crooijmans, Animal Breeding and Genetics Group, Department of Animal
Sciences, Wageningen University, Marijkeweg 40, 6709 PG Wageningen, The
Netherlands.
G. Dambrine,INRA, BioAgresseurs, Santé et Environnement, 37380 Nouzilly, France.
E.Decuypere,DepartmentofAnimalSciences,CatholicUniversityofLeuven,Laboratory
forPhysiologyandImmunogyofDomesticAnimals,KasteelparkArenberg30,B-3001
Leuven, Belgium.
M.E.Delany,DepartmentofAnimalScience,2131DMeyerHall,UniversityofCalifornia,
One Shields Avenue, Davis, CA 95616, USA.
J.B.Dodgson,DepartmentofMicrobiologyandMolecularGenetics,GiltnerHall,Michigan
State University, East Lansing, MI 48824, USA.
V. Ducrocq, Station de Génétique Quantitative et Appliquée, INRA, 78352 Jouy-en-Josas,
Cedex, France.
D. Emmerson, Aviagen North America, Cumming Research Park, 5015 Bradford Avenue,
Huntsville, AL 35805, USA.
J.M. Faure, Station de Recherches Avicoles, INRA Centre de Tours, 37380 Nouzilly,
France.
R.L. Fernando, Department of Animal Science, 255 Kildee Hall, Iowa State University,
Ames, IA 50011-3150, USA.
R.H. Fleming,Bone Biology Group, Roslin Institute, Roslin, Midlothian EH25 9PS, UK.
D. Flock,Akazienweg 5, 27478 Cuxahaven, Germany.
A.F. Groen, Animal Breeding and Genetics Group, Department of Animal Sciences,
Wageningen University, Marijkeweg 40, 6709 PG Wageningen, The Netherlands.
M.A.M. Groenen, Animal Breeding and Genetics Group, Wageningen University,
Marijekweg 40, 6709 PG Wageningen, The Netherlands.
K. Hála, Institute of Pathophysiology, University of Innsbruck Medical School,
Friz-Pregl-Strasse 3, A-6020 Innsbruck, Austria.
J. Jankowski,University of Warmia and Mazury, Olsztyn, Poland.
R.B. Jones,Roslin Institute (Edinburgh), Roslin, Midlothian EH25 9PS, UK.
R.J.Julian,DepartmentofPathobiology,OntarioVeterinaryCollege,UniversityofGuelph,
Guelph, Ontario N1G 2W1, Canada.
P.Kaiser,InstituteofAnimalHealth,ComptonLaboratory,Compton,Newbury,Berkshire
RG20 7NN, UK.
N.Kansaku,LaboratoryofAnimalGeneticsandBreeding,AzabuUniversity,Sagamihara,
Japan.
J. Killefer, College of Agriculture, Division of Animal and Veterinary Sciences,
1022 Agricultural Sciences Building, West Virginia University, Morgantown, WV
26506-6108, USA.
J.B. Kjaer, Department of Animal Health and Welfare, Danish Institute of Agricultural
Sciences, Research Centre Foulum, PO Box 50, DK-8830, Tjele, Denmark.
H. Kocamis, College of Agriculture, Division of Animal and Veterinary Sciences,
1022 Agricultural Sciences Building, West Virginia University, Morgantown, WV
26506-6108, USA.
U. Kuhnlein, Department of Animal Science, McGill University, 21111 Lakeshore Road,
Ste Anne de Bellevue, Quebec H9X 3V9, Canada.
S.J. Lamont, Department of Animal Science, 2255 Kildee Hall, Iowa State University,
Ames, IA 50011-3150, USA.
E.LeBihan-Duval,StationdeRecherchesAvicoles,INRACentredeTours,37380Nouzilly,
France.
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Contributors xi
H.S. Lillehoj, USDA, Agricultural Research Service, Parasite Biology, Epidemiology and
Systematics Laboratory, Beltsville, MD 20705, USA.
P.K. Mathur, Canadian Centre for Swine Improvement, Central Experimental Farm,
54 Maple Drive, Ottawa, Ontario K1A 0C6, Canada.
J.A.Mench,DepartmentofAnimalScience,UniversityofCalifornia,OneShieldsAvenue,
Davis, CA 95616, USA.
R.Morgan,DelawareBiotechnologyInstitute,UniversityofDelaware,Newark,DE19717,
USA.
W.M. Muir, Department of Animal Sciences, 1151 Lilly Hall, Purdue University,
West Lafayette, IN 47907, USA.
R. Okimoto, Department of Poultry Science, University of Arkansas, Fayetteville,
AR 72701, USA.
H.K. Parmentier, Animal Health and Reproduction Group, Wageningen University,
Marijkeweg 40, 6709 PG Wageningen, The Netherlands.
J.N. Petitte, Department of Poultry Science, North Carolina State University, Box 7608,
Raleigh, NC 27695, USA.
M.-H. Pinard-van der Laan, UMR Génétique et diversité Animales, INRA, 78352
Jouy-en-Josas, Cedex, France.
J. Plachy, Institute of Molecular Genetics, Academy of Sciences of the Czech Republic,
Prague, Czech Republic.
J.J. van der Poel, Animal Breeding and Genetics Group, Wageningen University,
Marijkeweg 40, 6709 PG Wageningen, The Netherlands.
M. Quinton, Department of Animal and Poultry Science, University of Guelph, Guelph,
Ontario N1G 2W1, Canada.
H. Rémignon, INPT-ENSAT, Avenue de l’Agrobiopole, BP 107, 31326 Castanet-Tolosan
Cedex, France.
P.Sørensen,DepartmentofAnimalBreedingandGenetics,DanishInstituteofAgricultural
Sciences, Foulum, DK-8830 Tjele, Denmark.
T. Szwaczkowski, Department of Genetics and Animal Breeding, August Cieszkowski
Agricultural University of Poznan, Wolynska 33, PL 60-637 Poznan, Poland.
L.R.Totir,Department ofAnimalScience,255KildeeHall,IowaStateUniversity,Ames,
IA 50011-3150, USA.
S. Wfxyk, National Research Institute of Animal Production, Krowoderskich Zuchow
20/15, PL 31-272 Krakow, Poland.
C.C. Whitehead,Bone Biology Group, Roslin Institute, Roslin, Midlothian EH25 9PS, UK.
S. Xu, Department of Botany and Plant Science, University of California, Riverside,
CA 92521-0124, USA.
N. Yi, Department of Botany and Plant Sciences, University of California, Riverside,
CA 92521-0124, USA.
D. Zadworny, Department of Animal Science, McGill University, 21111 Lakeshore Road,
Ste Anne de Bellevue, Quebec H9X 3V9, Canada.
J.J. Zhu, USDA, Agricultural Research Service, Parasite Biology, Epidemiology and
Systematics Laboratory, Beltsville, MD 20705, USA.
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Preface
Thewheelontheaxisofsciencerotateseverycoupleofyearswithnewinnovativebasic
ideasthatrevolutionizetraditionalthinkinganddirectscientiststoareasunimaginableto
theminthepast.Improvementsinpoultryandotherlivestockspecieshavebeenpursued
through empirical statistical approaches with underlying genetic principles. Since the
publicationofPoultryBreedingandGenetics(1990),newideashaveemergedinmolecular
genetics, computation strategies and bioinformatics with concurrent breeding-related
problems in poultry. It was the combination of the rotating axis of science coupled with
emerging new problems in poultry breeding that led to the birth of this book.
Thisbookrepresentsthefirstcompleteintegrationofthestateoftheartinquantitative
and molecular genetics as applied to poultry breeding. Our approach is first to define
problemsencounteredinpoultrybreedingin‘ProblemsandIssuesAssociatedwithPoultry
Breeding’.Thenmethodstoaddresstheseissuesareexamined,includingbothquantitative
and molecular genetics, which are simply different tools to address these problems with
differing strengths and weakness. Quantitative approaches are examined in ‘Breeding
Strategies and Objectives’ while molecular approaches and integration with quantitative
ones are examined in‘Use of Genomics and Bioinformatics in Poultry’.
Coverage of genomics includes structural, comparative and functional. Use of trans-
genictechnologyinpoultryisalsoexamined.Transgenictechnologiesofferthepromiseof
beingabletoaddressissuesbycreatingnewgeneticvariability,ratherthanbeingrestricted
to existing variation as with quantitative and genomics methods. In addition, transgenic
technology can develop new uses for egg products, particularly as a bioreactor for other
applications.Oneofthegreatestissuesinthepoultryindustryisthatofdiseaseresistance
and transmission. A special section is devoted to the genetics of disease resistance.
Wefeelthatwehaveachievedourgoalofproducinganoutstandingbook,withthetop
scientistsintheirfieldaddressingeachsubtopic.Althoughthefieldofmoleculargeneticsis
progressingrapidly,wefeeltheissuesandmethodsoutlinedinthisbookwillbewithusfora
longtime.Wethankalltheauthorsfortheiroutstandingcontributionstowhatwillsurelybe
a standard of excellence against which all future books will be measured.
WealsowishtothankTimHardwick(CABIPublishing)forgivingustheopportunity
toputthisbooktogether,andMarianKaiserforherkindassistanceandtechnicalskillsin
editing the final drafts.
William M. Muir, PhD
Samuel E. Aggrey, PhD
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