Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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Record number 372465
Title Review of the initial validation and characterization of a chicken 3K SNP array.
Author(s) Muir, W.M.; Wong, G.K.; Zhang, Y.; Wang, J.; Groenen, M.A.M.; Crooijmans, R.P.M.A.; Zhang, H.M.; McKay, J.; McLeod, C.W.; Okimoto, R.
Source Worlds Poultry Science Journal 64 (2008). - ISSN 0043-9339 - p. 219 - 226.
Department(s) Crop and Weed Ecology
Animal Breeding and Genetics
Publication type Refereed Article in a scientific journal
Publication year 2008
Keyword(s) dierveredeling - genetische bronnen van diersoorten - kippen - pluimvee - biodiversiteit - genetica - genetische kartering - dna - dna-sequencing - genotypen - genetische diversiteit - kippenrassen - single nucleotide polymorphism - animal breeding - animal genetic resources - fowls - poultry - biodiversity - genetics - genetic mapping - dna sequencing - genotypes - genetic diversity - fowl breeds
Categories Animal Gene Banks and Genetic Resources / Poultry
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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