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

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.

Figure 1

SNP discovery experiment. We sampled 3 domestic chickens at 1/4 coverage each and compared the resultant sequence to the 6.6x draft genome of Red Jungle Fowl (RJF). Chicken photographs shown here are provided by Bill Payne (RJF), Paul Hocking (broiler), Leif Andersson (layer), and Ning Yang (Silkie).

Figure 2

SNP and indel rates versus chromosome number. We excluded all sequences with “random” chromosome positions. Because of the assembly problems on W, it is not shown. The rates are computed as an average of all 3 domestic lines.

Figure 3

Detailed haplotype patterns in 3 regions, each covered by 2 overlapping BACs from the second layer line (L2). The primary SNP data are labeled B (broiler), L1 (layer), and S (Silkie). All comparisons are to RJF, and we show only those sites where a SNP is identified in at least one of the 4 lines. Hence, the horizontal scale is linear in the number of SNP sites, but non-linear for size. BLUE colors indicate where a particular line agrees with RJF, while RED colors indicate where it does not. Overlapping BACs on GGA1 and GGA7, but not GGA14, are clearly from different haplotypes.

Figure 4

Multi-species alignments for ornithine transcarbamylase (OTC), indicating non-synonymous substitutions relative to human protein. SIFT intolerant position is indicated by site number and bold-faced lettering. WT=wild type. MUT=mutant.