【作者】 胡昀雅；

【导师】 陈善元；

【作者基本信息】 云南大学 ， 动物学， 2021， 硕士

【摘要】 为了摸清云南家牛地方品种遗传背景和加强其保护,本研究通过长纯合片段(Runs of homozygosity,ROH)分析和拷贝数变异(copy number variation,CNV)分析对六个云南家牛地方品种的遗传多样性进行了研究。通过生物信息学方法对各云南家牛地方品种的遗传信息进行分析可以帮助我们挖掘埋藏在已知遗传数据中的相关表型、种群信息,丰富其基础遗传资源的研究。在本研究中,我们采用Illumina公司的770K高密度牛SNP芯片进行基因分型,获得云南六个地方品种家牛:邓川牛、迪庆牛、云南高峰牛、文山牛、昭通牛以及滇中牛的SNP分型数据,据此进行了ROH分析和CNV分析。最后对分析结果进行了GO-KEGG富集分析并寻找候选基因。ROH检测结果可以计算近交系数、推测群体历史、寻找候选基因。而CNV作为一种重要的遗传变异,可对多种复杂性状及疾病产生影响。本研究旨在通过ROH分析对各家牛地方品种群体进行近交程度分析和推测各品种家牛群体的近交历史;通过CNV分析探究各家牛品种的基因组结构变异及其与疾病等性状的关联。得到的结果如下:1.在本研究中一共在六个地方家牛品种中检测到了3357个ROH片段,并根据计算的近交系数与ROH数据结合分析,发现滇中牛是这六个品种中最近世代中近交强度最大的品种,而文山牛与云南高峰牛在最近世代中的近交强度则相对最小。2.对ROH片段相关基因进行GO-KEGG通路富集,得到一系列与代谢、免疫与疾病相关的通路,并通过筛选出富集到多个重复的GO功能与KEGG通路的基因来查找相应的候选基因。在生物合成抗生素、B细胞受体信号通路、癌症相关通路、EB病毒感染、细胞外基质受体互相作用、补体和凝血级联、阿米巴虫病、慢性粒细胞白血病、美洲锥虫病等与关键经济性状相关的通路中筛选得到了PIK3CD、TLR4、IL10、NFKB1、TP53、RAC2、PLCG1、CDK2、TCF7、LEF1、STAT3等基因。3.本研究还对这六个云南家牛品种进行了CNV的预测。在六个品种中共预测出了7469个CNVs。对与这些CNVs片段重叠的相关基因进行GO-KEGG通路富集分析并对富集在多个通路及功能的基因进行筛选,在抗原加工提呈、金黄色葡萄球菌感染、单疱疹病毒感染、炎症性肠病、弓形虫病、利什曼原虫病、甲型流感、结核病、单疱疹感染、病毒性心肌炎、破骨细胞分化等与关键经济性状相关的通路中筛选得到了JSP.1、BOLA-DQA2、BLA-DQB、IFNAH、CIITA和OAS1X等基因。本研究揭示了六种云南家牛地方品种群体的近交历史,推测了六个家牛品种的全基因组内的拷贝数变异。通过评估各群体的遗传多样性,探究影响关键表型性状的遗传分子信息。可以为后续的云南家牛品种遗传资源的保护工作如育种和保种工作提供一定的科学依据。更多还原

【Abstract】 To understand the genetic background of Yunnan native cattle breeds and strengthen their protection,in this study,genetic diversity of six Yunnan native cattle breeds was studied through Runs of Homozygosity(ROH)analysis and Copy Number Variation(CNV)analysis.Bioinformatics analysis of the genetic information of Yunnan native cattle breeds can help us dig out the relevant phenotypes and population information buried in the known genetic data and enrich the research on their basic genetic resources.In this study,we used Illumina Bovine 770 k high-density SNP genotyping chip,for six Yunnan native cattle breeds which are Dengchuan cattle,Diqing cattle,Wenshan cattle,Zhaotong cattle,Dianzhong cattle and Yunnan Humped cattle,to get the SNP classification data,and on the basis of that analyse the ROH and the CNV of those Yunnan native cattles.Finally,the results were enriched by GO-KEGG analysis and candidate genes were found.The results of ROH analyse can be used to calculate inbreeding number,predict population history and search for candidate genes.As an important genetic variation,CNV can affect a variety of complex traits and diseases.The purpose of this study was to analyze the inbreeding degree of native cattle breeds and to predict the inbreeding history of native cattle breeds by ROH analysis.CNV analysis was used to explore the genomic structural variation of the six native cattle breeds and its association with diseases and other traits.The obtained results are as follows:1.In this study,with in a total of six cattle breeds,we have detected 3357 ROH,and according to the calculation of inbreeding coefficient and ROH data analysis,found that Dianzhong cattle has the largest intensity of inbreeding in recent generation of all six varieties,Wenshan cattle and Yunnan Humped cattle in the latest generation of inbreeding strength is relatively minimal.2.GO-KEGG pathway enrichment was performed on ROH related genes to obtain a series of pathways related to metabolism,immunity and disease,and multiple genes enriched into GO function and KEGG pathway were choose to find the corresponding candidate genes.PIK3 CD,TLR4,IL10,NFKB1,TP53,RAC2,PLCG1,CDK2,TCF7,LEF1,STAT3 genes were found in biosynthesis of antibiotics pathway,B cell receptor signaling pathway,cancer related pathways,Epstein-Barr virus infection pathway,extracellular matrix receptor interactions pathway,ECM-receptor interaction pathway,salmonella infection pathway,amoebiasis pathway,chronic myeloid leukemia pathway,et al.3.CNV was also predicted for Yunnan Humped cattle and Dengchuan cattle.A total of 2006 CNVs were predicted in the two cultivars,and 964 CNVRs were found by merging and overlapping CNVs.The relevant genes overlapping with these CNVs were enriched by GO-KEGG pathway enrichment analysis,and the genes enriched in multiple pathways and functions were chosen and relevant literature was consulted to find a series of candidate genes.Such as JSP.1,Bo LA-DQA2,BLA-DQB,IFNAH,CIITA and OAS1 X genes were found in biosynthesis of antibiotics pathway,staphylococcus aureus infection pathway,toxoplasmosis pathway,et al.This study revealed the inbreeding history of six Yunnan native cattle breeds,and speculated the CNV variation in the whole genome of those cattle.The genetic diversity of each population was evaluated to explore the genetic molecular information influencing key phenotypic traits.It can provide a scientific basis for the protection of Yunnan domestic cattle genetic resources.更多还原