Detection of Selection Signatures in Chinese Landrace and Yorkshire Pigs Based on Genotyping-by-Sequencing Data

Abstract

The domestic pigs have been undergone intense selection pressures for these development of interested traits following domestication and modern breeding. This has altered many traits in most of pig breeds, such as growth rate, body weight, fertility, and immunity. Thus, the objectives of this study were to (1) detect these selection signatures and identify the candidate genes that show evidences of recent artificial selection at the level of whole genome, (2) be beneficial to understand the relationship between genomic structure and phenotypic diversity, and (3) highlight the key roles of these candidate genes in growth and development in the two breeds. The data consisted of total raw number of 345570 single nucleotide polymorphisms (SNPs) in 1200 individuals from the Chinese Landrace pigs (L, n = 600) and Yorkshire pigs (Y, n = 600). Based on these SNPs data, two complementary methods, population differentiation (Fst) and composite likelihood ratio test (CLR), were carried out to detect the selection signatures in this study. A total of 540 potential selection regions (50 kb) which contained 111 candidate genes were detected for Landrace-Yorkshire pair (L-Y) by Fst. In addition, 73 and 125 candidate genes were found for Landrace pigs and Yorkshire pigs by CLR test based on 321 and 628 potential selection regions, respectively. Some candidate genes are associated with important traits and signaling pathways including the ACACA, MECR, COL11A1, GHR, IGF1R, IGF2R, IFNG, and MTOR gene. The ACACA and MECR gene are related to fatty acid biosynthesis. The COL11A1 gene is essential for the development of the normal differentiation. The GHR, IGF1R, and IGF2R gene are significant candidate genes which play major roles in the growth and development in animals. The IFNG gene is associated with some aspects of immune response. The MTOR gene regulates many signaling pathways and signaling transduction pathway.

Genome-Wide Scan Identifies Selection Signatures in Chinese Wagyu Cattle Using a High-Density SNP Array

“…The phenotypic variations among the population are caused by both natural selection and artificial selection in farm animals [34]. Identifying positive selection signatures can provide valuable information about the influence of selection pressures for economically important traits.…”

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].…”

Genome Diversity and Signatures of Selection for Production and Performance Traits in Dromedary Camels

“…GBS has been widely used in plant breeding for genome-wide association analysis, genomic diversity studies, and genomic selection (reviewed in He et al (2014)). In addition, Wang et al (2018) employed GBS to analyze the genomes of Chinese Landrace and Yorkshire pigs, identifying candidate signatures of selection in genes related to fatty acid biosynthesis, animal growth and development, and immune responses.…”