World's Poultry Science Journal

Review Article

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

W.M. MUIRa1, G.K. WONGa2a3, Y. ZHANGa3, J. WANGa3, M.A.M. GROENENa4, R.P.M.A. CROOIJMANSa4, H.-J. MEGENSa4, H.M. ZHANGa5, J.C. MCKAYa6, S. MCLEODa6, R. OKIMOTOa7, J.E. FULTONa8, P. SETTARa8, N.P. O'SULLIVANa8, A. VEREIJKENa9, A. JUNGERIUS-RATTINKa9, G.A.A. ALBERSa9, C. TAYLOR LAWLEYa10, M.E. DELANYa11 and H.H. CHENGa5 c1

a1 Department of Animal Sciences, Purdue University, West Lafayette, IN 47907, USA

a2 University of Alberta, Department of Biological Sciences and Department of Medicine, Edmonton AB, T6G 2E9 Canada

a3 Beijing Institute of Genomics of Chinese Academy of Sciences, Beijing 101300, China

a4 Animal Breeding and Genetics Group, Wageningen University, 6709 PG Wageningen, The Netherlands

a5 USDA-ARS, Avian Disease and Oncology Laboratory, East Lansing, MI 48823, USA

a6 Aviagen, Newbridge, Midlothian, EH28 8SZ, Scotland, UK

a7 Cobb-Vantress, Inc., Siloam Springs, AR 72761, USA

a8 Hy-Line International, Dallas Center, IA 50063, USA

a9 Hendrix Genetics, 5831 CK Boxmeer, The Netherlands

a10 Illumina, Inc., San Diego, CA 92121, USA

a11 Department of Animal Science, University of California, Davis, CA 95616, USA

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.

(Received October 14 2007)

(Accepted December 12 2007)

Correspondence:

c1 Corresponding author: hcheng@msu.edu