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

Abstract

With the development of high-throughput genotyping techniques, selection signatures in the genome of domestic pigs have been extensively interrogated in the last decade. The Duroc, a major commercial pig breed famous for its fast growth rate and high lean ratio, has not been extensively studied focusing on footprints of intensively artificial selection in their genomes by a lot of re-sequencing data. The goal of this study was to investigate genomic regions under artificial selection and their contribution to the unique phenotypic traits of the Duroc using whole-genome resequencing data from 97 pigs. Three complementary methods (di, CLR, and iHH12) were implemented for selection signature detection. In Total, 464 significant candidate regions were identified, which covered 46.4 Mb of the pig genome. Within the identified regions, 709 genes were annotated, including 600 candidate protein-coding genes (486 functionally annotated genes) and 109 lncRNA genes. Genes undergoing selective pressure were significantly enriched in the insulin resistance signaling pathway, which may partly explain the difference between the Duroc and other breeds in terms of growth rate. The selection signatures identified in the Duroc population demonstrated positive pressures on a set of important genes with potential functions that are involved in many biological processes. The results provide new insights into the genetic mechanisms of fast growth rate and high lean mass, and further facilitate follow-up studies on functional genes that contribute to the Duroc's excellent phenotypic traits.

Runs of Homozygosity Uncover Potential Functional-Altering Mutation Associated With Body Weight and Length in Two Duroc Pig Lines

“…HOMER1 ( 67 ) and AKIRIN1 ( 68 ) are related to muscle development. Some candidate genes have been reported in previous selective sweep studies, such as HOMER1 ( 23 , 24 ) and ARSB ( 25 ). These promising genes associated with economic traits may contribute to the genetic breeding process of pigs.…”

“…From the perspective of selection, intense selection reduced the diversity of haplotype, and different selective sweeps contributed to the formation of germplasm characteristics in Duroc pigs (19). For example, numerous studies (20)(21)(22)(23)(24)(25)(26)(27) have used the methods of selection signatures to reveal a lot of candidate genes related to growth, immunity, meat, and carcass quality traits of Duroc pigs. Currently, the ROH pattern has been used to detect genetic diversity and genomic regions putatively under strong selection in Duroc pigs.…”

Lipidomic and Transcriptomic Analysis of the Longissimus Muscle of Luchuan and Duroc Pigs

“…Duroc is one of the main commercial pig breeds, famous for its fast growth rate and high lean meat rate ( 5 ). However, its intramuscular fat (IMF) content is low which may influence the meat quality.…”

Genome-wide analysis of genetic diversity and artificial selection in Large White pigs in Russia

“…The mechanisms underlying phenotypic differentiation induced by pig breeding have been investigated using genome-wide genotype data or high throughput sequencing (Groenen et al, 2012;Yang et al, 2014;Diao et al, 2018;Gurgul et al, 2018;Xu et al, 2020b;Xu et al, 2020a;Bovo et al, 2020). Genomic loci associated with growth traits, reproductive traits, coat color, ear shape, and other phenotypes are now known, as well as the genes that influence these traits (Wilkinson et al, 2013;Zhang et al, 2018;Yu et al, 2020). We compared the Large White pigs of Russian breeding (LW_Old) and modern commercial pigs (LW_New) in this work.…”