Liu Yuqiang, Xu Lingyang, Yang Liu, Zhao Guoyao, Li Junya, Liu Dewu, Li Yaokun
College of Animal Science, South China Agricultural University, Guangzhou, China.
Innovation Team of Cattle Genetic Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China.
Front Genet. 2020 Dec 18;11:533052. doi: 10.3389/fgene.2020.533052. eCollection 2020.
Chinese local cattle with a high level of genetic diversity mainly originate from two subspecies; the cattle in northern China are primarily , and the cattle in southern China are primarily . Cattle from southern China are characterized by a specific phenotype and adapted to the local environment. This study explored the genetic diversity, degree of admixture, and selection signature in eight local cattle breeds in southern China. The lowest level of heterozygosity was found in Hainan and Nandan cattle from Hainan and Guangxi province, respectively, whereas the highest level of heterozygosity was detected in Zhaotong cattle from Yunnan province. A neighbor-joining phylogenetic tree analysis clearly separated Lufeng cattle from other breeds, whereas Leiqiong and Hainan cattle have some crossover. Based on linkage disequilibrium-filtered single nucleotide polymorphisms (SNPs), the admixture analysis revealed two clusters corresponding to the taurine and indicine cattle lineages, and the local cattle breeds from southern China showed a certain degree of admixture. When = 4 and 9, we found a slight separation among Leiqiong, Lufeng, and Hainan cattle. Meanwhile, we performed a selection signature analysis in Hainan, Leiqiong, and Lufeng cattle distributed in the extreme south of China, using the integrated haplotype score (iHS), Rsb statistic, and BayeScan software. Using the iHS approach, we identified 251, 270, and 256 candidate regions in Lufeng, Leiqiong, and Hainan cattle, respectively. Moreover, we identified 184, 174, and 146 candidate regions in pairwise comparisons of Leiqiong vs. Lufeng, Leiqiong vs. Hainan, and Hainan vs. Lufeng cattle using the Rsb approach. In addition, we identified 76 loci with a total of 48 genes under selection, based on the F approach. Several candidate genes under selection were found to be related to meat quality, immunity, and adaptation to the local environment in southern China. Our results provide significant information about the genetic differences among the cattle breeds from southern China and the possible cause of difference in breed-specific characteristics. Selection signature analysis identified a few candidate SNPs and genes related to certain important traits of these cattle. In general, our results provide valuable insights into the genetic basis of specific traits under selection in certain local cattle breeds.
具有高度遗传多样性的中国本土牛主要起源于两个亚种；中国北方的牛主要是……，而中国南方的牛主要是……。中国南方的牛具有特定的表型特征并适应当地环境。本研究探讨了中国南方八个本地牛品种的遗传多样性、混杂程度和选择印记。分别在来自海南和广西的海南牛和南丹牛中发现了最低水平的杂合度，而在来自云南省的昭通牛中检测到了最高水平的杂合度。邻接法系统发育树分析清楚地将禄丰牛与其他品种区分开来，而雷琼牛和海南牛有一些交叉。基于连锁不平衡过滤的单核苷酸多态性（SNP），混杂分析揭示了对应于普通牛和瘤牛谱系的两个聚类，并且中国南方的本地牛品种表现出一定程度的混杂。当K = 4和9时，我们发现雷琼牛、禄丰牛和海南牛之间有轻微的分离。同时，我们使用综合单倍型评分（iHS）、Rsb统计量和BayeScan软件，对分布在中国最南部的海南牛、雷琼牛和禄丰牛进行了选择印记分析。使用iHS方法，我们分别在禄丰牛、雷琼牛和海南牛中鉴定出251、270和256个候选区域。此外，使用Rsb方法，我们在雷琼牛与禄丰牛、雷琼牛与海南牛以及海南牛与禄丰牛的成对比较中分别鉴定出184、174和146个候选区域。另外，基于F方法，我们鉴定出76个位点，共有48个基因受到选择。发现一些受到选择的候选基因与肉质、免疫力以及对中国南方当地环境的适应性有关。我们的结果提供了关于中国南方牛品种之间遗传差异以及品种特异性特征差异可能原因的重要信息。选择印记分析鉴定出了一些与这些牛某些重要性状相关的候选SNP和基因。总体而言，我们的结果为某些本地牛品种中受到选择的特定性状的遗传基础提供了有价值的见解。
