A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms

Abstract

Summary We describe a genetic variation map for the chicken genome containing 2.8 million single nucleotide polymorphisms (SNPs), based on a comparison of the sequences of 3 domestic chickens (broiler, layer, Silkie) to their wild ancestor Red Jungle Fowl (RJF). Subsequent experiments indicate that at least 90% are true SNPs, and at least 70% are common SNPs that segregate in many domestic breeds. Mean nucleotide diversity is about 5 SNP/kb for almost every possible comparison between RJF and domestic lines, between two different domestic lines, and within domestic lines - contrary to the idea that domestic animals are highly inbred relative to their wild ancestors. In fact, most of the SNPs originated prior to domestication, and there is little to no evidence of selective sweeps for adaptive alleles on length scales of greater than 100 kb.

Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution

“…An impressive list of chicken quantitative trait loci has already been identified 152 , many with combined agricultural and medical relevance. The chicken genome sequence promotes both the development of more refined polymorphic maps (see the accompanying paper 153 ) and the framework for discovering the functional polymorphisms underlying interesting quantitative traits, thus fully exploiting the genetic potential of the chicken.…”

Deciphering the genetic basis of animal domestication

“…There is also evidence from a number of individual genes that nucleotide variation is relatively high in domesticated pigs [77], where sustained gene flow with their wild boar relatives (see §3b) appears to play an important role [78]. Despite the extensive bottleneck and associated loss of alleles that accompanied the commercialization of broiler and layer lines [72], domestic chickens have extensive sequence diversity [79], again presumably owing to a very large ancestral population which had even greater levels of diversity (as also seen in present-day red junglefowl [80]). These high levels of genetic diversity contribute to the continuing ability of breeders to select for production traits.…”

Avian genomics: fledging into the wild!

“…Such genome-wide marker sets can be extensive in model species such as the chicken (Groenen et al 2000;Wong et al 2004). In non-model species, it has usually not been possible to conduct studies in which microsatellite markers were used in sufficiently high densities across chromosomes as to refer to them as genomic studies.…”