基于选择信号分析揭示猪终端父本群体间性状趋同的关键基因

doi:10.16431/j.cnki.1671-7236.2022.08.014

摘要/Abstract

摘要： 【目的】试验旨在揭示终端父本皮特兰猪与杜洛克猪在人工选择作用下重要经济性状呈现出表型趋同的基因组变化特征。【方法】利用376头皮特兰猪、451头杜洛克猪品系Ⅰ、841头杜洛克猪品系Ⅱ和497头杜洛克猪品系Ⅲ群体的50K SNP芯片数据,以100 kb窗口、50 kb步长计算综合单倍型评分(iHS)和等位基因频率差(△AF),分别取前5%作为猪群体内、群体间的基因组选择信号候选区域;利用bedtools分别对iHS、△AF按照左右200 kb进行合并,每2个群体间合并后的iHS、△AF统计量的重叠区域定义为性状趋同区域,并挖掘该区域与猪重要经济性状相关的平行选择信号。【结果】iHS结果显示,在皮特兰猪和杜洛克猪4个群体内共检测到5 112个选择信号候选区域,总长约487.51 Mb。基于△AF方法,于皮特兰猪和杜洛克猪每2个群体间共检测到9 579个选择信号显著区域,总长约913.50 Mb。基于合并后的iHS和△AF,共检测到52个性状趋同区域,总长约4.67 Mb,注释到88个与猪的繁殖、胴体和肉质等性状相关的平行选择候选基因。【结论】皮特兰猪和杜洛克猪群体间存在性状趋同的基因组选择区域有52个,平行选择信号主要涉及猪的繁殖、胴体及肉质等重要经济性状,这与瘦肉型猪种相同的育种方向相关,这些关键基因的发现可为后续商业猪品种遗传改良提供参考。

关键词: 皮特兰猪; 杜洛克猪; 遗传改良; 性状趋同; 选择信号; 基因组

Abstract: 【Objective】 This study was aimed to reveal the genomic patterns of the phenotypic convergence of important economic traits in terminal sire Pietrain and Duroc pigs under artificial selection.【Method】 Based on the 50K SNP chips data of 376 Pietrain pigs,451 Duroc pigs line Ⅰ,841 Duroc pigs line Ⅱ and 497 Duroc pigs line Ⅲ,the integrated haplotype score (iHS) and allele frequency difference (△AF) were calculated in 100 kb windows with a step size of 50 kb,and the top 5% statistics of each method were taken as the putative selection signatures of ingroup and intergroup,respectively.The close selection signatures within the distance of 200 kb were merged by bedtools.The overlapping putative selection regions of iHS and △AF statistics between every two populations were defined as the genomic regions associated with trait convergence,and the parallel selection signatures related to important economic traits of pigs were explored based on these putative regions.【Result】 The results showed that 5 112 selection signatures with a total length of 487.51 Mb and 9 579 selection signatures with a total length of 913.50 Mb were detected by iHS and △AF,respectively.After merging the close region,a total of 52 parallel selection regions with the length of approximately 4.67 Mb were found,88 candidate genes were annotated to be related to the traits such as reproduction,carcass and meat quality.【Conclusion】 A total of 52 genomic selection regions might be associated with trait convergence between Pietrain and Duroc pigs,the parallel selection signatures were mainly involved in economically important traits such as reproduction,carcass and meat quality,which was related to the similar breeding direction of lean pigs,and the identification of these key genes could provide a reference for the genetic improvement of subsequent commercial pig breeds.

Key words: Pietrain pigs; Duroc pigs; genetic improvement; trait convergence; selection signature; genome

中图分类号:

S813.3

李望娇, 彭夏, 宋徽, 董文君, 李新云, 赵书红, 马云龙. 基于选择信号分析揭示猪终端父本群体间性状趋同的关键基因[J]. 中国畜牧兽医, 2022, 49(8): 2982-2991.

LI Wangjiao, PENG Xia, SONG Hui, DONG Wenjun, LI Xinyun, ZHAO Shuhong, MA Yunlong. Selection Signature Analysis Reveals the Key Genes Associated with the Convergence Traits Among Porcine Terminal Sire Populations[J]. China Animal Husbandry and Veterinary Medicine, 2022, 49(8): 2982-2991.

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