Detecting signatures of selection in nine distinct lines of broiler chickens

Abstract

Modern commercial chickens have been bred for one of two specific purposes: meat production (broilers) or egg production (layers). This has led to large phenotypic changes, so that the genomic signatures of selection may be detectable using statistical techniques. Genetic differentiation between nine distinct broiler lines was calculated using Weir and Cockerham's pairwise FST estimator for 11 003 genome-wide markers to identify regions showing evidence of differential selection across lines. Differentiation measures were averaged into overlapping sliding windows for each line, and a permutation approach was used to determine the significance of each window. A total of 51 regions were found to show significant differentiation between the lines. Several lines were consistently found to share significant regions, suggesting that the pattern of line divergence is related to selection for broiler traits. The majority of the 51 regions contain QTL relating to broiler traits, but only five of them were found to be significantly enriched for broiler QTL, including a region on chromosome 27 containing 39 broiler QTL and 114 genes. Additionally, a number of these regions have been identified by other selection mapping studies. This study has identified a large number of potential selection signatures, and further tests with higher-density marker data may narrow these regions down to individual genes.

Genetic diversity and signatures of selection in various goat breeds revealed by genome-wide SNP markers

“…Recent advances in genomic technologies resulting in the availability of the Illumina Goat 50K SNP BeadChip [6] have offered the opportunity to search for genomic regions that may have undergone selection. Such studies in cattle [7–9], sheep [10, 11], chickens [12] and pigs [13, 14] have each identified genes that have undergone positive selection and are likely to contribute directly to phenotypic variation. However, in goats there are only a few studies using the SNP arrays and most of them focused on local breeds (e.g.…”

Use of high‐density SNP data to identify patterns of diversity and signatures of selection in broiler chickens

“… (G) Study of commercial broiler lines (Stainton et al . ). Includes regions showing statistically significant between‐line differentiation (Table ). …”

“…In our previous study of nine broiler chicken lines (including line 3, analysed in the current study) genotyped using a low‐density SNP chip, a number of highly differentiated regions were identified in multiple lines (Stainton et al . ). Eight of the 15 regression regions were located within 1 Mb of the highly differentiated regions (Table ), consistent with the theoretical expectation of negative relationship between diversity and F ST (Charlesworth ; Cruickshank & Hahn ).…”

“…Two of the regression regions directly overlapped the differentiated regions: Reg.6 (chrom 4), which overlapped differentiated regions 24 and 25, and region Reg.9 (chrom 5), which overlapped differentiated region 29 (Table from Stainton et al . ). One of the zero‐diversity regions (ZD.6) was located within 1 Mb of a differentiated region (region 27), but they did not directly overlap.…”

“…This region also overlaps with a highly differentiated region identified in our previous study of nine broiler lines (Stainton et al . ) (see below). Forty genes overlap with this region as well as four broiler QTL related to feed intake, shank length and meat quality.…”