Detection of genomic signatures for pig hairlessness using high-density SNP data

Abstract

Hair provides thermal regulation for mammals and protects the skin from wounds, bites and ultraviolet (UV) radiation, and is important in adaptation to volatile environments. Pigs in nature are divided into hairy and hairless, which provide a good model for deciphering the molecular mechanisms of hairlessness. We conducted a genomic scan for genetically differentiated regions between hairy and hairless pigs using 60K SNP data, with the aim to better understand the genetic basis for the hairless phenotype in pigs. A total of 38405 SNPs in 498 animals from 36 diverse breeds were used to detect genomic signatures for pig hairlessness by estimating between-population (F ST ) values. Seven diversifying signatures between Yucatan hairless pig and hairy pigs were identified on pig chromosomes (SSC) 1, 3, 7, 8, 10, 11 and 16, and the biological functions of two notable genes, RGS17 and RB1, were revealed. When Mexican hairless pigs were contrasted with hairypigs, strong signatures were detected on SSC1 and SSC10, which harbor two functionally plausible genes, REV3L and BAMBI. KEGG pathway analysis showed a subset of overrepresented genes involved in the T cell receptor signaling pathway, MAPK signaling pathway and the tight junction pathways. All of these pathways may be important in local adaptability of hairless pigs. The potential mechanisms underlying the hairless phenotype in pigs are reported for the first time. RB1 and BAMBI are interesting candidate genes for the hairless phenotype in Yucatan hairless and Mexico hairless pigs, respectively. RGS17, REV3L, ICOS and RASGRP1 as well as other genes involved in the MAPK and T cell receptor signaling pathways may be important in environmental adaption by improved tolerance to UV damage in hairless pigs. These findings improve our understanding of the genetic basis for inherited hairlessness in pigs.

Genetic Diversity of Indigenous Pigs from South China Area Revealed by SNP Array

“…The formula for F ST was:FST=MSP−MSGMSP+(nC−1)MSG where MSP and MSG denote the observed mean square errors for loci between and within populations, respectively, and nC is the average sample size across samples that also incorporates and corrects for the variance in sample size over the population. More details are shown in Su et al [27]. The top 1% of SNPs were defined as significant [28].…”

Genetic relationships of the Yucatan black hairless pig with Iberian breeds using single nucleotide polymorfisms

“…Lemus-Flores et al (2020), on the other hand, report the EHF, DST, PDE8A, FOXA1, and VCL genes in YBHP compared to the Duroc breed. Su et al (2014) note that RB1 and BAMBI genes are associated with the lack of hair in USYU and Mexico hairless pigs. Jiang et al (2019) report the MAP2 (HR) and FOXI3 genes as candidate markers, considering that hair follicle morphogenesis occurs at an early stage of embryo development, like in humans and mice.…”

Three-Dimensional Organization of Chicken Genome Provides Insights into Genetic Adaptation to Extreme Environments

“…Those genes were found to cluster in two primary categories including biological process and molecular function ( Figure 4 A). The pathway enrichment analysis within the 5% genomic regions revealed that these genes were forcefully in connection with extreme environment adaptation-related pathways, including tight junction [ 27 , 28 ], notch signaling [ 29 , 30 , 31 ], vascular smooth muscle contraction [ 32 ], and RIG-I-like receptor signaling [ 33 , 34 ] ( Figure 4 B and Table 1 ). Within the consistent A/B compartment-switching regions, a series of genes related to cell proliferation and differentiation were identified in the tight junction, notch signaling, and RIG-I-like receptor signaling pathways.…”