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Review of the initial validation and characterization of a 3K chicken SNP array

Published online by Cambridge University Press:  13 June 2008

W.M. MUIR ,
G.K. WONG ,
Y. ZHANG ,
J. WANG ,
M.A.M. GROENEN ,
R.P.M.A. CROOIJMANS ,
H.-J. MEGENS ,
H.M. ZHANG ,
J.C. MCKAY  and
S. MCLEOD
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W.M. MUIR
Affiliation:
Department of Animal Sciences, Purdue University, West Lafayette, IN 47907, USA
G.K. WONG
Affiliation:
University of Alberta, Department of Biological Sciences and Department of Medicine, Edmonton AB, T6G 2E9 Canada Beijing Institute of Genomics of Chinese Academy of Sciences, Beijing 101300, China
Y. ZHANG
Affiliation:
Beijing Institute of Genomics of Chinese Academy of Sciences, Beijing 101300, China
J. WANG
Affiliation:
Beijing Institute of Genomics of Chinese Academy of Sciences, Beijing 101300, China
M.A.M. GROENEN
Affiliation:
Animal Breeding and Genetics Group, Wageningen University, 6709 PG Wageningen, The Netherlands
R.P.M.A. CROOIJMANS
Affiliation:
Animal Breeding and Genetics Group, Wageningen University, 6709 PG Wageningen, The Netherlands
H.-J. MEGENS
Affiliation:
Animal Breeding and Genetics Group, Wageningen University, 6709 PG Wageningen, The Netherlands
H.M. ZHANG
Affiliation:
USDA-ARS, Avian Disease and Oncology Laboratory, East Lansing, MI 48823, USA
J.C. MCKAY
Affiliation:
Aviagen, Newbridge, Midlothian, EH28 8SZ, Scotland, UK
S. MCLEOD
Affiliation:
Aviagen, Newbridge, Midlothian, EH28 8SZ, Scotland, UK
R. OKIMOTO
Affiliation:
Cobb-Vantress, Inc., Siloam Springs, AR 72761, USA
J.E. FULTON
Affiliation:
Hy-Line International, Dallas Center, IA 50063, USA
P. SETTAR
Affiliation:
Hy-Line International, Dallas Center, IA 50063, USA
N.P. O'SULLIVAN
Affiliation:
Hy-Line International, Dallas Center, IA 50063, USA
A. VEREIJKEN
Affiliation:
Hendrix Genetics, 5831 CK Boxmeer, The Netherlands
A. JUNGERIUS-RATTINK
Affiliation:
Hendrix Genetics, 5831 CK Boxmeer, The Netherlands
G.A.A. ALBERS
Affiliation:
Hendrix Genetics, 5831 CK Boxmeer, The Netherlands
C. TAYLOR LAWLEY
Affiliation:
Illumina, Inc., San Diego, CA 92121, USA
M.E. DELANY
Affiliation:
Department of Animal Science, University of California, Davis, CA 95616, USA
H.H. CHENG*
Affiliation:
USDA-ARS, Avian Disease and Oncology Laboratory, East Lansing, MI 48823, USA
*
Corresponding author: hcheng@msu.edu
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Abstract

In 2004 the chicken genome sequence and more than 2.8 million single nucleotide polymorphisms (SNPs) were reported. This information greatly enhanced the ability of poultry scientists to understand chicken biology, especially with respect to identification of quantitative trait loci (QTL) and genes that control simple and complex traits. To validate and address the quality of the reported SNPs, assays for 3072 SNPS were developed and used to genotype 2576 DNAs isolated from commercial and experimental birds. Over 90% of the SNPs were valid based on the criterion used for segregating, and over 88% had a minor allele frequency of 2% or greater. As the East Lansing (EL) and Wageningen University (WAU) reference panels were genotyped, 1933 SNPs were added to the chicken genetic map, which was used in the second chicken genome sequence assembly. It was also discovered that linkage disequilibrium varied considerably between commercial layers and broilers; with the latter having haplotype blocks averaging 10 to 50 kb in size. Finally, it was estimated that commercial lines have lost 70% or more of their genetic diversity, with the majority of allele loss attributable to the limited number of chicken breeds used.

Keywords

SNPsgeneticsbiodiversitymap
Type
Review Article
Information
World's Poultry Science Journal , Volume 64 , Issue 2 , June 2008 , pp. 219 - 226
Copyright
Copyright © USDA-ARS, USA

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References

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