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

Abstract

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

CLC Number:

S813.3

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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Detection of Body Shape Selection Signals in Chinese Indigenous Pigs Based on Whole Genome Resequencing

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