Genome-wide mapping of signatures of selection using a high-density array identified candidate genes for growth traits and local adaptation in chickens

Abstract

Background Availability of single nucleotide polymorphism (SNP) genotyping arrays and progress in statistical analyses have allowed the identification of genomic regions and genes under selection in chicken. In this study, SNP data from the 600 K Affymetrix chicken array were used to detect signatures of selection in 23 local Italian chicken populations. The populations were categorized into four groups for comparative analysis based on live weight (heavy vs light) and geographical area (Northern vs Southern Italy). Putative signatures of selection were investigated by combining three extended haplotype homozygosity (EHH) statistical approaches to quantify excess of haplotype homozygosity within (iHS) and between (Rsb and XP-EHH) groups. Presence of runs of homozygosity (ROH) islands was also analysed for each group. Results After editing, 541 animals and 313,508 SNPs were available for statistical analyses. In total, 15 candidate genomic regions that are potentially under selection were detected among the four groups: eight within a group by iHS and seven by combining the results of Rsb and XP-EHH, which revealed divergent selection between the groups. The largest overlap between genomic regions identified to be under selection by the three approaches was on chicken chromosome 8. Twenty-one genomic regions were identified with the ROH approach but none of these overlapped with regions identified with the three EHH-derived statistics. Some of the identified regions under selection contained candidate genes with biological functions related to environmental stress, immune responses, and disease resistance, which indicate local adaptation of these chicken populations. Conclusions Compared to commercial lines, local populations are predominantly reared as backyard chickens, and thus, may have developed stronger resistance to environmental challenges. Our results indicate that selection can play an important role in shaping signatures of selection in local chicken populations and can be a starting point to identify gene mutations that could have a useful role with respect to climate change.

A genome‐wide comparison between selected and unselected Valle del Belice sheep reveals differences in population structure and footprints of recent selection

“…This was performed by comparing the genomes of a group of animals subjected to a directional selection process with an unselected population, using three statistical approaches that have been successfully applied in other studies on various livestock species (e.g. Brito et al, 2017; Mastrangelo et al, 2023; Moscarelli et al, 2021; Nolte et al, 2019). Genome scans comparing breeds under artificial selection with their unselected founder population have been previously applied in cattle (e.g.…”

Ancestral alleles defined for 70 million cattle variants using a population-based likelihood ratio test

“…BovineHD and BovineSNP50). In the absence of a comprehensive list of ancestral alleles, an alternate practice is to use major or common alleles as the ancestral alleles [ 17 – 19 ], but it is known that the major alleles are not always the ancestral ones. For example, up to 19% of the identified ancestral alleles in previous studies were minor alleles [ 10 , 20 ].…”

Genetic characteristics and selection signatures between Southern Chinese local and commercial chickens

“…Therefore, it is crucial to study the population genetic structure, admixture patterns, and selection signals in chickens from southern China with specific environmental characteristics subjected to artificial selection. Currently, numerous studies have analyzed selection signals among different types of chickens such as laying hens versus broilers ( Boschiero et al, 2018 ), fighting hens versus red native chickens ( Guo et al, 2016 ), and commercial chickens versus noncommercial ones ( Elferink et al, 2012 ; Goraga et al, 2012 ; Mekchay et al, 2014 ; Cho et al, 2021 ; Mastrangelo et al, 2023 ). However, most comparisons focus on exotic commercial varieties against local ones within our research scope.…”