永登七山羊全基因组选择信号检测分析

doi:10.11843/j.issn.0366-6964.2023.11.014

Abstract

Abstract: The aim of this study was to detect genomic selection signals in the Yongdeng Qishan sheep population and to mine valuable germplasm trait genes. A total of 40 individuals from 4 sheep populations (Yongdeng Qishan sheep, Minxian black fur sheep, Lanzhou fat-tailed sheep, Tan sheep) were used as study subjects to detect genome-wide single nucleotide polymorphism sites (SNPs) using specific-locus amplified fragment sequencing (SLAF-seq). Based on SNPs data, elgensoft software was used for principal component analysis (PCA), gene flow events were analyzed by Treemix software. Selective sweep analysis was performed using population genetic differentiation index (Fst) and nucleotide diversity ratio (π ratio) and the intersection of top 5% Fst and π ratio was taken to identify selected genomic regions. The GO and KEGG enrichment analysis of candidate genes was performed. A total of 1 658 596 population SNPs were obtained; Principal component analysis (PCA) found that Yongdeng Qishan sheep were able to independently group, gene flow showed that there was weak gene exchange between Yongdeng Qishan sheep and Lanzhou fat-tailed sheep. Yongdeng Qishan sheep were used as the experimental group, and Minxian black fur sheep, Lanzhou fat-tailed sheep and Tan sheep were used as the reference group for selection sweep analysis. The 424, 294 and 301 candidate genes were detected in the selected regions of the 3 comparison groups; GO and KEGG analyses showed that the candidate genes were significantly enriched in 65, 79 and 41 GO terms and 15, 22 and 10 KEGG pathways, respectively (P＜0.05). In addition, SNP datas from 3 populations of Minxian black fur sheep, Lanzhou fat-tailed sheep and Tan sheep were combined into one dataset for comparison with Yongdeng Qishan sheep and 466 candidate genes were significantly enriched to 124 GO terms and 7 KEGG pathways (P＜0.05).Functional genes BMP2, GRM1, and ALDH1A1 related to important economic traits were screened from Yongdeng Qishan sheep. The research shows that the selection signal detection in the whole genome of Yongdeng Qishan sheep can identify candidate genes related to growth and development and fat tail evolution, providing reference for molecular genetic marker mining of Yongdeng Qishan sheep.

Key words: Yongdeng Qishan sheep, specific-locus amplified fragment sequencing, gene flow, selective sweep analysis, functional enrichment

CLC Number:

S826.2

LI Dengpan, MA Keyan, HAN Jintao, BAI Yaqin, LI Taotao, MA Youji. Detection and Analysis of Whole Genome Selection Signal of Yongdeng Qishan Sheep[J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(11): 4577-4588.

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Detection and Analysis of Whole Genome Selection Signal of Yongdeng Qishan Sheep

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