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

  • W.M. MUIR (a1), G.K. WONG (a2) (a3), Y. ZHANG (a3), J. WANG (a3), M.A.M. GROENEN (a4), R.P.M.A. CROOIJMANS (a4), H.-J. MEGENS (a4), H.M. ZHANG (a5), J.C. MCKAY (a6), S. MCLEOD (a6), R. OKIMOTO (a7), J.E. FULTON (a8), P. SETTAR (a8), N.P. O'SULLIVAN (a8), A. VEREIJKEN (a9), A. JUNGERIUS-RATTINK (a9), G.A.A. ALBERS (a9), C. TAYLOR LAWLEY (a10), M.E. DELANY (a11) and H.H. CHENG (a5)...

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.

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Corresponding author

Corresponding author: hcheng@msu.edu

References

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AERTS, J., MEGENS, H.J., VEENENDAAL, T., OVCHARENKO, I., CROOIJMANS, R., GORDON, L., STUBBS, L. and GROENEN, M. (2007) Extent of linkage disequilibrium in chicken. Cytogenetics and Genome Research 117: 338-345.
INTERNATIONAL CHICKEN GENOME SEQUENCING CONSORTIUM, (2004) Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature 432: 695-716.
INTERNATIONAL CHICKEN POLYMORPHISM MAP CONSORTIUM, (2004) A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms. Nature 432: 717-722.
MUIR, W. and CHENG, H. (2007) A world wide and genome wide assessment of biodiversity in commercial poultry populations. Proceedings of the National Breeders Roundtable. In press.
NG, P.C. and HENIKOFF, S. (2001) Predicting deleterious amino acid substitutions. Genome Research 11: 863-874.

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