Integrating genome-wide association studies and population genomics analysis reveals the genetic architecture of growth and backfat traits in pigs

Abstract

Growth and fat deposition are complex traits, which can affect economical income in the pig industry. Due to the intensive artificial selection, a significant genetic improvement has been observed for growth and fat deposition in pigs. Here, we first investigated genomic-wide association studies (GWAS) and population genomics (e.g., selection signature) to explore the genetic basis of such complex traits in two Large White pig lines (n = 3,727) with the GeneSeek GGP Porcine HD array (n = 50,915 SNPs). Ten genetic variants were identified to be associated with growth and fatness traits in two Large White pig lines from different genetic backgrounds by performing both within-population GWAS and cross-population GWAS analyses. These ten significant loci represented eight candidate genes, i.e., NRG4, BATF3, IRS2, ANO1, ANO9, RNF152, KCNQ5, and EYA2. One of them, ANO1 gene was simultaneously identified for both two lines in BF100 trait. Compared to single-population GWAS, cross-population GWAS was less effective for identifying SNPs with population-specific effect, but more powerful for detecting SNPs with population-shared effects. We further detected genomic regions specifically selected in each of two populations, but did not observe a significant enrichment for the heritability of growth and backfat traits in such regions. In summary, the candidate genes will provide an insight into the understanding of the genetic architecture of growth-related traits and backfat thickness, and may have a potential use in the genomic breeding programs in pigs.

Large scale sequence-based screen for recessive variants allows for identification and monitoring of rare deleterious variants in pigs

“…Additionally, this study reports the KIAA1549 gene, which we also observed in the QTL on chromosome 18 affecting backfat thickness. Another recent study has associated the ANO9 gene (chromosome 2) with increased backfat thickness [ 34 ]. We identified an additive missense SNP in this gene associated with very high backfat thickness, however we consider IGF2 and INS to be more likely candidate genes to cause this effect.…”

Association analysis between Acetyl-Coenzyme A Acyltransferase-1 gene polymorphism and growth traits in Xiangsu pigs

“…Growth traits such as living backfat thickness (LBT), body length (BL), body height (BH), chest circumference (CC), chest depth (CD), and rump circumference (RC) are directly related to the economic efficiency of pigs ( Liu et al, 2021 ; Zhang et al, 2021 ).Growth traits are quantitative traits that are regulated by a few major genes and a large number of minor genes ( Boyle et al, 2017 ). With the rapid development of molecular breeding and sequencing technologies, many genes that regulate pig growth traits have been identified and confirmed ( Shi et al, 2022 ).…”