德南牛全基因组变异解析和功能基因挖掘

[目的]研究德南牛的群体遗传结构和解析影响其重要性状的关键基因。[方法]通过主成分分析、群体进化树分析、群体遗传结构分析等方法,研究德南牛的遗传结构和与其他品种的亲缘关系；同时,利用全基因组SNP数据,计算德南牛与德国黄牛、南阳牛群体固定指数(Fst)和核苷酸多样性比值(π ratio)、复合似然比(CLR)、XP-EHH等多种选择信号指标,以筛选出德南牛基因组上受到选择的信号,鉴定出重要的候选基因。[结果] 德南牛具有欧洲普通牛(0.789)、东亚牛(0.176)、中国瘤牛(0.035)的混合血统。在θπ和CLR方法中鉴定出93个共有基因,使用FST和XP-EHH方法鉴定出17个共有基因。进行富集以及基因功能注释后,发现这些基因可能与生殖性能(TUBB3、NSD2、GRM1、ERBB4)、生长性状(RFX3、FGFR3、GABRB1、PDE4D)、环境适应性(PGR、GRIA4)和免疫系统反应(P2RY12、P2RY13、GPR87、P2RY14、GPR171)有关。[结论]本项研究发现德南牛血统受德国黄牛影响较多,且挖掘了德南牛基因组内可能具有经济意义的性状相关的选择特征,为德南牛种群的选育提高提供理论支撑。

Whole-genome variation analysis and functional gene mining of Denan cattle

[Purpose] In order to study the progress of genetic breeding of German cattle to improve Nanyang cattle, and to explore the population genetic structure of Denan cattle. [Method] Through principal component analysis, population evolutionary tree analysis, population genetic structure analysis and other methods, the genetic structure of Denan cattle and its genetic relationship with other breeds were studied. At the same time, whole-genome SNP data is used to calculate Denan cattle, German cattle, Nanyang cattle population fixation index (Fst) and nucleotide diversity ratio (π ratio), composite likelihood ratio (CLR), XP-EHH and other options. Signal indicators were used to screen out the selected signals on the Denan cattle genome and identify important candidate genes. [Results] Denan cattle have a mixed ancestry of European common cattle (0.789), East Asian cattle (0.176), and Chinese Zebu (0.035). 93 consensus genes were identified in the θπ and CLR methods, and 17 consensus genes were identified using the FST and XP-EHH methods. After enrichment and gene functional annotation, it was found that these genes may be related to reproductive performance (TUBB3, NSD2, GRM1, ERBB4), growth traits (RFX3, FGFR3, GABRB1, PDE4D), environmental adaptability (PGR, GRIA4) and immune system response (P2RY12, P2RY13, GPR87, P2RY14, GPR171) related.