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 (d_i, 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.

Keywords: Duroc pig; Selection signatures; Whole-genome sequencing.

Figure 1

Genome-wide distribution of detected SNVs on 19 chromosomes for the Duroc. X-axis represents 18 autosomes and X chromosome. Y-axis represents the number of SNVs.

Figure 2

Genome-wide annotation of genetic variations. X-axis represents the number of genetic variations (log10) within various functional regions. Y-axis represents various functional regions in genes.

Figure 3

Genome-wide distribution of selection signatures detected by d_i on 18 chromosomes. X-axis represents 18 autosomes, and Y-axis represents d_i values for non-overlapping 100 kb windows. Red line displays the threshold level of 5%.

Figure 4

Genome-wide distribution of selection signatures detected by CLR on 18 chromosomes. X-axis represents 18 autosomes, and Y-axis represents CLR values for non-overlapping 100 kb windows. Red line displays the threshold level of 5%.

Figure 5

Genome-wide distribution of selection signatures detected by iHH12 on 18 chromosomes. X-axis represents 18 autosomes, and Y-axis represents iHH12 values for non-overlapping 100 kb windows. Red line displays the threshold level of 5%.

Figure 6

Genomic distribution of selection signatures detected by d_i, CLR and iHH12 on 18 chromosomes. In the figure, “d_i”,” CLR” and “iHH12” represent the regions detected by only one method; “d_i,CLR”, “d_i,iHH12” and “CLR,iHH12” represent the regions detected by two different methods; “d_i,CLR,iHH12” represents the regions detected by all three methods.

Figure 7

Venn diagram for numbers of candidate regions detected by different methods. Blue represents the numbers of candidate regions detected by d_i; green represents the numbers of candidate regions detected by CLR; orchid represents the numbers of candidate regions detected by iHH12.