基于SNP芯片的海南猪全基因组选择信号分析

doi:10.11843/j.issn.0366-6964.2022.02.003

Abstract

Abstract: The purpose of this study was to screen the selection signatures on the whole genome of Hainan pigs, discover the candidate genes of the important economical traits, and analyze the selected process of Hainan pigs in the history of evolution and domestication. Based on the GeneSeek Genomic Profiler (GGP) Procine SNP 80K BeadChip genotypes of 68 Hainan pigs, the integrated haplotype score (iHS) method was carried out to detect the selection signatures for Hainan pigs across the whole genome, and the runs of homozygosity (ROH) analysis was employed. The SNPs with Standard iHS scores > 1.96 (P<0.05) were used as candidate SNPs, and candidate regions detected by iHS were the 200 kb window around the candidate SNPs. In this analysis, the completely overlapping candidate regions detected by both iHS and ROH were defined as potential selected regions. To further explore the biological functions of the selection signatures on Hainan pigs, bioinformatics analysis including gene annotation, quantitative trait locus (QTL) analysis and enrichment analysis were applied. In this study, a total of 44 578 SNPs was remained after quality control. Moreover, 395 candidate selected SNPs were detected by iHS method, 172 ROH segments were detected. And 469 candidate genes were annotated totally in the 136 potential selected regions overlapped. The QTL analysis of the potential selected regions showed that selection signatures of Hainan pigs were associated with meat quality, growth and disease resistance traits. In addition, the QTLs associated with the age of puberty were mostly reported to be overlapped with the potential selected regions on the SSC12 (Sus Scrofa chromosome 12). Moreover, enrichment analysis of gene ontology (GO) and kyoto encyclopedia of genes and genomes (KEGG) pathway of candidate genes showed that 91 candidate genes were significantly enriched in 21 function (P<0.05) terms totally, which were mainly associated with growth and metabolism, immunoresponse and estrogen signaling pathway. This study reveals the possible selection process of Hainan pigs populations in their domestication history. This research suggests that screening the selection signatures on the whole genome of Hainan pigs contributes to a better understanding of the evolution progress and the genetic mechanisms of the important traits, which also provides reference for further analysis about protection and utilization of germplasm resource and related research about southern China pig breeds.

Key words: Hainan pigs, selection signatures, SNP, iHS, ROH

CLC Number:

S828.2

FENG Xueyan, DIAO Shuqi, LIU Yuqiang, XU Zhiting, WEI Chen, YUAN Xiaolong, LI Jiaqi, ZHANG Zhe. Analysis of Selection Signatures for Hainan Pigs across the Whole Genome Based on SNP BeadChips[J]. Acta Veterinaria et Zootechnica Sinica, 2022, 53(2): 349-359.

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Analysis of Selection Signatures for Hainan Pigs across the Whole Genome Based on SNP BeadChips

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