Genomic Analysis To Identify Signatures of Artificial Selection and Loci Associated with Important Economic Traits in Duroc Pigs

Abstract

Identifying genetic basis of domestication and improvement in livestock contributes to our understanding of the role of artificial selection in shaping the genome. Here we used whole-genome sequencing and the genotyping by sequencing approach to detect artificial selection signatures and identify the associated SNPs of two economic traits in Duroc pigs. A total of 38 candidate selection regions were detected by combining the fixation index and the Composite Likelihood Ratio methods. Further genome-wide association study revealed seven associated SNPs that were related with intramuscular fat content and feed conversion ratio traits, respectively. Enrichment analysis suggested that the artificial selection regions harbored genes, such as MSTN, SOD2, MC5R and CD83, which are responsible for economic traits including lean muscle mass, fertility and immunization. Overall, this study found a series of candidate genes putatively associated with the breeding improvement of Duroc pigs and the polygenic basis of adaptive evolution, which can provide important references and fundamental information for future breeding programs.

Genome-wide analysis of expression QTL (eQTL) and allele-specific expression (ASE) in pig muscle identifies candidate genes for meat quality traits

“…In a previous study, we confirmed that the splicing mutation g.8283C > A is the causative mutation for the eQTL signal and that pigs that carry the mutant allele have a high risk of pale, soft, and exudative meat [30]. Other identified candidate genes that are of interest include NUDT7, which was assigned to a QTL for meat color [47][48][49], and FADS2 and DGAT2, which are involved in the regulation of lipid metabolism and fat deposition [50][51][52]. The discovery of cis-eQTL that regulate the expression of these genes further confirms that these candidate genes affect economic traits in the pig and enhance possibilities to identify the causative mutations for each gene in future studies.…”

Genome-Wide Detection of Selection Signatures in Duroc Revealed Candidate Genes Relating to Growth and Meat Quality

“…Previous study also suggested that combining different selection signature statistics can reduce those selective sweeps merely derived from independent domestication processes ( Ma et al 2015a ). Compared with previous genome-wide scans for selection signatures in Duroc pigs ( Edea et al 2017 ; Diao et al 2018 ; Ma et al 2018 ), a number of overlapping signatures were found with previous studies, such as 7.3–7.4 Mb on SSC1, and 88.1–88.4 Mb on SSC2. These regions contain some important genes, such as IGF2R , HOMER1 and CMYA5 , which are associated with muscle development, carcass traits and meat quality ( Hao et al 2017 ; Xu et al 2011 ).…”

Whole-genome sequencing of European autochthonous and commercial pig breeds allows the detection of signatures of selection for adaptation of genetic resources to different breeding and production systems

“…Other studies that involved a few Asian and European pig breeds investigated signatures of selection in the porcine genome using SNP chip or partial/reduced or wholegenome re-sequencing datasets and highlighted loci of economic importance [7,[31][32][33][34][35][36][37][38][39][40][41][42].…”