A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms: International Chicken Polymorphisms Map Consortium

G.K. Wong, B. Liu, J. Wang, R.P.M.A. Crooijmans, J.J. van der Poel, H. Bovenhuis, M.A.M. Groenen

Research output: Contribution to journalArticleAcademicpeer-review

324 Citations (Scopus)

Abstract

We describe a genetic variation map for the chicken genome containing 2.8 million single-nucleotide polymorphisms ( SNPs). This map is based on a comparison of the sequences of three domestic chicken breeds ( a broiler, a layer and a Chinese silkie) with that of their wild ancestor, red jungle fowl. Subsequent experiments indicate that at least 90% of the variant sites are true SNPs, and at least 70% are common SNPs that segregate in many domestic breeds. Mean nucleotide diversity is about five SNPs per kilobase for almost every possible comparison between red jungle fowl and domestic lines, between two different domestic lines, and within domestic lines - in contrast to the notion that domestic animals are highly inbred relative to their wild ancestors. In fact, most of the SNPs originated before domestication, and there is little evidence of selective sweeps for adaptive alleles on length scales greater than 100 kilobases.
Original languageEnglish
Pages (from-to)717-722
JournalNature
Volume432
Issue number7018
DOIs
Publication statusPublished - 2004

Keywords

  • quantitative trait loci
  • broiler layer cross
  • genome
  • diversity
  • sequence
  • mutation
  • markers
  • growth
  • snp

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