基于全基因组重测序检测中国地方猪的体型选择信号

doi:10.16431/j.cnki.1671-7236.2024.08.022

摘要/Abstract

摘要： 【目的】利用全基因组选择信号检测方法探索中国地方猪基因组中与体型相关的候选基因,分析中国地方猪在进化和驯化过程中的受选择情况。【方法】基于310头地方猪的全基因组重测序数据,利用跨群体扩展单倍型纯合(cross population extended haplotype homozygosity,XP-EHH)和固定分化指数F_ST统计量(fixation index)两种方法进行全基因组选择信号检测。取两种方法各前0.1%位点的交集作为候选位点,分别向上、下游延伸200 kb作为潜在受选择区域。通过富集分析进一步探索选择信号的生物学功能。【结果】使用XP-EHH和F_ST两种方法共检测到633个潜在受选择位点,获得633个潜在区域,共注释到133个基因。数量性状基因座(quantitative trait locus,QTL)富集分析发现,不同体型中国地方猪之间的选择信号与肉质和胴体性状相关;染色质状态富集结果发现,不同体型中国地方猪群体之间的差异组织为内脏、消化系统和小脑。GO功能和KEGG通路富集分析发现16个基因在6个功能条目(P＜0.05,count＞3)上显著富集,主要集中在生长代谢相关通路,其中ACSM5、ACSM4、FXR1和FOXA2作为候选基因主要富集于脂肪酸合成与代谢、肌肉生长发育等信号通路。【结论】本研究采用两种选择信号检测方法对不同体型的中国地方猪进行了分析,筛选到一系列候选位点和基因,重点挖掘了参与猪生长发育的候选基因,如ACSM5、ACSM4、FXR1和FOXA2。

关键词: 中国地方猪; 选择信号; 全基因组重测序; 跨群体扩展单倍型纯合(XP-EHH); 固定分化指数(F_ST)

Abstract: 【Objective】 The purpose of this study was to investigate candidate genes associated with body size in the genomes of Chinese indigenous pigs using whole-genome selection signal detection methods,and analyze the selection patterns during their evolution and domestication of Chinese indigenous pigs.【Method】 Based on whole-genome resequencing data of 310 indigenous pigs,two methodologies were employed:Cross population extended haplotype homozygosity (XP-EHH) and fixation index statistic (F_ST),a comprehensive genome-wide selection signal scan was conducted.The intersection of the top 0.1% sites identified by both methods was designated as candidate loci,and their upstream and downstream 200 kb regions were designated as potential selection regions.Through enrichment analysis,the biological functions of selected signals were further explored.【Result】 A total of 633 potential selection loci were detected by XP-EHH and F_ST methods,633 potential regions were obtained,and 133 genes were annotated.The quantitative trait locus (QTL) enrichment analysis showed that the selection signals in different body types of Chinese indigenous pigs were related to meat and carcass traits.The results of chromatin state enrichment analysis showed that the tissues with differences in different body types of Chinese indigenous pigs were concentrated in viscera,digestive system and cerebellum.GO function and KEGG pathway enrichment analysis showed that 16 genes were significantly enriched in 6 functional items (P＜0.05,count＞3),mainly concentrated in growth and metabolism-related pathways.Among them,ACSM5,ACSM4,FXR1 and FOXA2 were candidate genes,which were mainly enriched in fatty acid synthesis and metabolism,muscle growth and development and other signaling pathways.【Conclusion】 In this study,two detection methods were used to analyze Chinese indigenous pigs with different body sizes,and a series of genetic differentiation genes were screened.The candidate genes involved in the regulation of growth and development in pigs,such as ACSM5,ACSM4,FXR1 and FOXA2,were excavated.

Key words: Chinese indigenous pigs; selective signals; whole-genome resequencing; XP-EHH; F_ST

中图分类号:

S813.3

马烨, 刘玉强, 吴煜伟, 李广祯, 冯雪燕, 刁淑琪, 高亚辉. 基于全基因组重测序检测中国地方猪的体型选择信号[J]. 中国畜牧兽医, 2024, 51(8): 3438-3446.

MA Ye, LIU Yuqiang, WU Yuwei, LI Guangzhen, FENG Xueyan, DIAO Shuqi, GAO Yahui. Detection of Body Shape Selection Signals in Chinese Indigenous Pigs Based on Whole Genome Resequencing[J]. China Animal Husbandry and Veterinary Medicine, 2024, 51(8): 3438-3446.

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