Using High-Density SNP Array to Reveal Selection Signatures Related to Prolificacy in Chinese and Kazakhstan Sheep Breeds

Abstract

Selection signature provides an efficient tool to explore genes related to traits of interest. In this study, 176 ewes from one Chinese uniparous breed and three Kazakhstan multiparous breeds are genotyped using Affymetrix 600K HD single nucleotide polymorphism (SNP) arrays, F-statistics (Fst), and a Cross Population Extend Haplotype Homozygosity Test (XPEHH). These are conducted to identify genomic regions that might be under selection in three population pairs comprised the one multiparous breed and the uniparous breed. A total of 177 and 3072 common selective signatures were identified by Fst and XPEHH test, respectively. Nearly half of the common signatures detected by Fst were also captured by XPEHH test. In addition, 1337 positive and 1735 common negative signatures were observed by XPEHH in three Kazakhstan multiparous breeds. In total, 242 and 798 genes were identified in selective regions and positive selective regions identified by Fst and XPEHH, respectively. These genes were further clustered in 50 gene ontology (GO) functional terms and 66 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways in enrichment analysis. The GO terms and pathways were relevant with reproductive processes, e.g., oxytocin signaling pathway, thyroid hormone synthesis and GnRH signaling pathway, vascular smooth muscle contraction and lipid metabolism (alpha-Linolenic acid metabolism and Linoleic acid metabolism), etc. Based on the findings, six potential candidate genes ESR1, OXTR, MAPK1, RYR1, PDIA4, and CYP19A1, under positive selection related to characteristics of multiparous sheep breeds were revealed. Our results improve our understanding of the mechanisms of selection that underlies the prolificacy trait in sheep, and provide essential references for future sheep breeding.

Genomic Regions Associated with Wool, Growth and Reproduction Traits in Uruguayan Merino Sheep

“…The gene CDH10 was associated with several reproduction traits in buffaloes [64]. Furthermore, PDIA4 was found to be involved in the litter size in sheep and pigs [65,66]. In our work, LEPR was identified as a candidate gene for the pregnancy rate.…”

Genetic architecture and selection of Anhui autochthonous pig population revealed by whole genome resequencing

“…In a previous study, population high-density SNP array analysis of multiparous and uniparous sheep revealed that MAPK1 is a selected gene among Kazakhstan sheep (Wang et al, 2020), highlighting its role in reproduction. One synonymous SNV was also identified in MAPK1 (Supplementary Table S15; exon1:c.C144T: p.L48L).…”

“…Furthermore, a signal adequate for promoting trophoblast proliferation and invasion can decrease below thresholds if MAPK1 protein expression is insufficient ( Saba et al, 2003 ; Jeong et al, 2013 ). In a previous study, population high-density SNP array analysis of multiparous and uniparous sheep revealed that MAPK1 is a selected gene among Kazakhstan sheep ( Wang et al, 2020 ), highlighting its role in reproduction. One synonymous SNV was also identified in MAPK1 ( Supplementary Table S15 ; exon1:c.C144T: p.L48L).…”

Identification of Signatures of Selection for Litter Size and Pubertal Initiation in Two Sheep Populations

“…Wei et al [ 13 ] used Fst and XP-EHH methods on 122 Chinese native sheep and found that EPASI genes play an important role in hypoxia adaptation. By selective signature analysis between polytocous and monotocous sheep populations, Wang et al identified six genes (ESR1, OXTR, MAPK1, RYR1, PDIA4, and CYP19A1) associated with polytocous traits in sheep [ 14 ]. Yao et al used selective signature analysis between high and low fertility populations in Bamei mutton sheep and found that JUN, ITPR3, PLCB2, HERC5 and KDM4B genes might be associated with polytocous traits [ 15 ].…”