Abstract
SummaryThe development of broiler chickens over the last 70 years has been accompanied by large phenotypic changes, so that the resulting genomic signatures of selection should be detectable by current statistical techniques with sufficiently dense genetic markers. Using two approaches, this study analysed high‐density SNP data from a broiler chicken line to detect low‐diversity genomic regions characteristic of past selection. Seven regions with zero diversity were identified across the genome. Most of these were very small and did not contain many genes. In addition, fifteen regions were identified with diversity increasing asymptotically from a low level. These regions were larger and thus generally included more genes. Several candidate genes for broiler traits were found within these ‘regression regions’, including IGF1,GPD2 and MTNR1AI. The results suggest that the identification of zero‐diversity regions is too restrictive for characterizing regions under selection, but that regions showing patterns of diversity along the chromosome that are consistent with selective sweeps contain a number of genes that are functional candidates for involvement in broiler development. Many regions identified in this study overlap or are close to regions identified in layer chicken populations, possibly due to their shared precommercialization history or to shared selection pressures between broilers and layers.
Highlights
In the absence of other factors, positive selection will eventually cause a beneficial allele to become fixed in a population, leading to a reduction in diversity in the population at the selected site
A number of putative selection signatures were identified in a broiler chicken line genotyped with high-density SNPs
Our results suggest that the identification of zero-diversity regions is too restrictive for characterizing regions under selection and that the use of the asymptotic regression method is more promising
Summary
In the absence of other factors, positive selection will eventually cause a beneficial allele to become fixed in a population, leading to a reduction in diversity in the population at the selected site This hitchhiking effect (Maynard Smith & Haigh 1974) causes a statistical association between a selected site and neutral sites linked to it, with a pattern of reduced genetic variation around the selected site. Low-value outliers in the genomic distribution of diversity are considered to be candidates for selected positions. Another class of tests takes advantage of the linkage disequilibrium created by the hitchhiking effect, such as the long-range
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