基于全基因组重测序的海南黄牛群体遗传多样性分析及热适应相关候选基因筛选  

Genetic diversity of Hainan cattle population based on whole genome resequencing and screening of candidate genes related to heat adaptation

作　　者：吴慧 李世元 蒋俊明 王欢 吴官胜 李连彬 陈巧玲 杜丽 王凤阳 陈思 WU Hui;LI Shi-yuan;JIANG Jun-ming;WANG Huan;WU Guan-sheng;LI Lian-bin;CHEN Qiao-ling;DU Li;WANG Feng-yang;CHEN Si(School of Tropical Agriculture and Forestry,Hainan University/Key Laboratory of Tropical Animal Reproduction&Breeding and Epidemic Disease Research of Hainan,Haikou,Hainan 570228,China)

机构地区：[1]海南大学热带农林学院/海南省热带动物繁育与疫病研究重点实验室,海南海口570228

出　　处：《南方农业学报》2024年第12期3707-3717,共11页Journal of Southern Agriculture

基　　金：中央引导地方科技发展专项(ZY2022HN09);海南省院士创新平台科研专项(2020)。

摘　　要：【目的】基于全基因组重测序分析海南黄牛群体遗传多样性并筛选热适应相关候选基因,为我国地方家牛种质资源的保护与开发利用提供理论参考。【方法】使用FASTP v0.20.0对海南黄牛、蒙古牛和藏牛的全基因组数据进行质量控制和过滤,BWA进行序列比对,GATK v3.5-0-g36282e4进行变异检测,ANNOVAR Documentation构建注释所需的数据库。基于常染色体SNP位点信息,利用MEGA X构建系统发育进化树,通过EIGENSOFT v7.2.1进行主成分分析(PCA)并进行均匀流形近似和投影(UMAP)聚类,使用Structure v2.3.4进行群体结构分析并通过计算核苷酸多样性及连锁不平衡衰减来探究群体遗传多样性。通过PopGenome对全基因组进行扫描,使用核苷酸多样性比值(θπ)和核苷酸多样性及群体间遗传分化系数(FST)筛选海南黄牛基因组中受正向选择的候选区域,并将注释到的基因通过DAVID进行GO功能注释和KEGG信号通路富集分析,挑选与热适应相关的基因,并预测其编码蛋白的结构和理化性质。【结果】经质控后共检测出20075403个高质量常染色体SNP位点。海南黄牛、蒙古牛和藏牛群体不存在血统混杂现象。相较于蒙古牛和藏牛,海南黄牛连锁不平衡衰减速度更快,核苷酸多样性更高,受人工选择强度较低且具有较高的群体遗传多样性。以蒙古牛和藏牛为参考群体,在海南黄牛中共筛选出144个受正向选择的基因。在海南黄牛群体中存在磷酸肌醇3激酶调节亚基5(PIK3R5)基因的错义突变(AC_000176.1:28979868,c.987C>A,p.331D>Y),该突变能引起PIK3R5基因mRNA二级结构和PIK3R5蛋白二级结构的改变。【结论】海南黄牛较高的遗传多样性和较低的人工选择强度表明其在热带环境中保留了丰富的遗传变异。海南黄牛PIK3R5基因存在错义突变,可能通过调控PI3K/Akt/mTOR信号通路影响热应激响应和代谢调节,从而增强其热适应能力。【Objective】The genetic diversity of Hainan cattle population was analyzed based on whole genome resequencing and candidate genes related to heat adaptation were screened to provide theoretical reference for the protection,development and utilization of local domestic cattle germplasm resources in China.【Method】FASTP v0.20.0 was used to perform quality control and filtering on the whole genome data of Hainan cattle,Mongolian cattle and Tibetan cattle,BWA was used for sequence alignment,GATK v3.5-0-g36282e4 was used for variation detection,and ANNOVAR Documentation was used to build the database required for annotation.Based on the autosomal SNP loci information,the phylogenetic tree was constructed using the method of MEGA X,and principal component analysis(PCA),uniform manifold approximation and projection(UMAP)clustering were performed using EIGENSOFT v7.2.1.Structure v2.3.4 was used for population structure analysis and population genetic diversity was studied by calculating nucleotide diversity and linkage disequilibrium decay.The whole genome was scanned using PopGenome,and the nucleotide diversity ratio(θπ)and nucleotide diversity and genetic differentiation coefficient(FST)methods were used to screen candidate regions under positive selection in the Hainan cattle genome.The annotated genes were annotated with GO functional annotation and KEGG signal pathway enrichment analysis using DAVID,and genes related to heat adaptation were selected,and the structures and physicochemical properties of their encoded proteins were analyzed.【Result】A total of 20075403 highquality autosomal SNP loci were detected after quality control.There was no pedigree admixture in the Hainan cattle,Mongolian cattle and Tibetan cattle populations.Compared with Mongolian cattle and Tibetan cattle,Hainan cattle had a faster decay rate of linkage disequilibrium(LD),higher nucleotide diversity,lower artificial selection intensity and higher population genetic diversity.Using Mongolian cattle and Tibetan cattle as reference p

关 键 词：海南黄牛 全基因组重测序 热适应 PIK3R5基因 遗传多样性 

分 类 号：S823.81[农业科学—畜牧学]