Linkage disequilibrium and recent selection signatures in commercial broilers
Date
2016
Authors
Journal Title
Journal ISSN
Volume Title
Publisher
University of Delaware
Abstract
Over the past 70 years, modern breeding programs have significantly improved traits of economical importance in commercial broilers. Due to recent strong selection and large reduction in effective population size in the breeding program, linkage disequilibrium (LD) in broiler population has changed over generations. Characterizing LD is of fundamental importance for implementation of both genome-wide association studies and genomic selection as well as identification of recent selection signatures.
Therefore, using a 60K single nucleotide polymorphism (SNP) panel, we firstly estimated LD and haplotype structure in crossbred broiler chickens and their component pure lines and calculated the consistency of LD between these populations. Compared with the pure lines, the crossbred populations consistently showed a lower level of LD, smaller haploblock sizes and lower haplotype homozygosity on autosomes. Furthermore, correlations of LD between markers at short distances were high between crossbred and pure lines (0.83 to 0.94). Our results suggest that using crossbred populations instead of pure lines can be advantageous for high-resolution quantitative trait loci mapping and good persistence of accuracy of genomic breeding values over generations in genomic selection.
Secondly, with better understanding of the extent of LD in commercial broiler populations, we applied two statistical methods to detect signatures of positive selection in five elite lines of commercial broiler chickens, including three broiler sire (male) lines and two broiler dam (female) lines. A total of 321 candidate selection regions were detected by both methods, 42 of which were shared by 2 or more purebred lines. Our results provide a genome-wide scan of recent selection signatures in the five purebred lines. We found several candidate genes for recent selection in multiple lines, such as SOX6 (Sex Determining Region Y-Box 6) and cTR (Thyroid hormone receptor beta), which may have been under selection due to their essential roles in growth, development and reproduction in chickens. Most of the candidate genes in selection regions are novel, and as such they should be of great interest for future research into the genetic architecture of traits relevant to modern broiler breeding.