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驯化、自然选择和人工选择都会在基因组上留下选择信号，研究这些选择信号是筛选功能基因的重要策略之一。本研究基于野牦牛(Bos mutus)和天祝白牦牛(Bos grunniens)的重测序数据，利用GATK (genome analysis toolkit)获得SNP (single nucleotide polymorphisms)变异位点，然后利用群体分化指数FST和Tajima’s D法分析两个牦牛群体的选择信号分布情况。选择FST值的top 5%和Tajima’s D值两端前2.5%(top 2.5%和bot 2.5%)作为选择阈值，将阈值以内的位点定义为强选择信号位点。经SnpEff注释后，利用FST选择信号方法筛选得到868个候选基因，GO分析富集到细胞增殖的正向调节、肌动蛋白细胞骨架组织、镁离子结合等肌肉相关条目。KEGG富集到肌肉发育相关通路与低氧适应相关的通路，包括MAPK信号通路、肌动蛋白细胞骨架的调节、PI3K-Akt信号通路、ECM受体相互作用、细胞周期、Rap1信号通路。Tajima’s D法分析结果显示，在天祝白牦牛基因组中筛选出377 214个(Tajima’s D>1.974 72)和539 869个(Tajima’s D<-1.780 03)个位点，分别注释得到38个和22个候选基因。在野牦牛基因组中筛选出413 240个(Tajima’s D>1.854 31)和332 871个(Tajima’s D<-1.512 31)位点，分别注释得到30个和24个候选基因。对两种方法筛选出的强选择信号重叠位点进行注释，分别在野牦牛和天祝白牦牛基因组上中得到90和83个候选基因，从中鉴定出2个驯化相关基因(SCRIB1、SNCA)、1个低氧适应相关基因(THADA)、2个毛色相关基因(MAPK3、NNT)。本研究通过FST和Tajima’s D法筛选到一系列与野牦牛和天祝白牦牛遗传分化和表型差异相关的基因和通路，为进一步研究牦牛基因组与表型之间的关系以及确定控制牦牛重要经济性状的基因提供理论基础。
Abstract：Domestication, natural selection, and artificial selection will leave selection signals on the genome. Studying these selection signals is one of the important strategies for screening functional genes. Based on the resequencing data of Wild yak(Bos mutus) and Tianzhu white yak(Bos grunniens), GATK(genome analysis toolkit) was uesd to obtain SNP(single nucleotide polymorphisms) mutation sites, and then the population differentiation index FST and Tajima's D method were uesd to analyze the selection signal distribution of the two yak populations in the study. The top 5% of the FST value and the top 2.5% at both ends of the Tajima's D value(top 2.5% and bot 2.5%) were selected as the selection threshold, and the sites beyond the threshold were defined as strong selection signal sites. After gene annotation by SnpEff, 868 candidate genes were detected by the FST method. These genes were enriched in some GO items related to muscle, such as positive regulation of cell proliferation, actin cytoskeleton organization, and magnesium ion binding. The analysis of KEGG showed that these genes were involved in muscle development and hypoxia adaptation, including MAPK signaling pathway, actin cytoskeleton regulation, PI3 K-Akt signaling pathway, ECM receptor interaction, cell cycle, and Rap1 signaling pathway. The results of Tajima's D analysis showed that 377 214(Tajima's D>1.974 72) and 539 869(Tajima's D<-1.780 03) loci were detected from the Tianzhu white yak genome, and 38 and 22 candidate genes were annotated, respectively. In the wild yak genome, 413 240(Tajima's D>1.854 31) and 332 871(Tajima's D<-1.512 31) loci were detected, and 30 and 24 candidate genes were annotated, respectively. After annotating the overlap sites of strong selection signals screened by the two methods, 90 and 83 candidate genes were obtained from the genomes of wild yak and Tianzhu white yak, respectively. Two domestication-related genes(SCRIB1, SNCA), one gene related to hypoxia adaptation(THADA), and two genes related to hair color(MAPK3, NNT) were selected from these candicate genes. In this study, a series of genes and pathways related to genetic differentiation and phenotypic differences in wild yak and Tianzhu white yak were screened by FST and Tajima's D method, which provides a theoretical basis for further studying the relationship between the yak genome and phenotype, and determining the genes that control important economic traits of the yak.
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基本信息:
DOI：10.13417/j.gab.041.000731
中图分类号:S823.85
引用信息:
[1]鲍麒,梁春年,郭宪,等.全基因组选择信号解析野牦牛和天祝白牦牛的遗传差异[J].基因组学与应用生物学,2022,41(04):731-741.DOI:10.13417/j.gab.041.000731.
基金信息:
中国农业科学院创新工程项目(CAAS-ASTIP-2014-LIHPS-01); 科技援青合作专项(2020-QY-212); 现代农业(肉牛牦牛)产业技术体系建设专项资金(CARS-37); 甘肃省科技计划项目(20JR5RA580)共同资助
2021-04-12
2021
2021-08-24
2022-06-17
2022
2
2022-05-12
2022-05-12
2022-05-12