Yunling cattle, a three-breed cross consisting of 1/2 Brahman cattle, 1/4 Murray Grey cattle and 1/4 Yunnan Yellow cattle, has advantage of rapid growth, good meat quality, enhanced tolerance towards a hot and humid climate, tick resistance and crude feed forbearance. Here, we investigated the genetic diversity, global and local ancestry proportions by sequencing the genomes of 131 Yungling cattle and 31 Brahman cattle (for control). Furthermore, we used 35 published genomes of ancestry breeds (including Angus cattle [ancestry of Murray Grey], Wannan cattle [ancestry of Yunnan Yellow cattle: Wenshan and Dianzhong], Wenshan and Dianzhong cattle) to characterize the formation process of Yunling cattle. The highest nucleotide diversity was found in the Wannan cattle, followed by Wenshan, Dianzhong, Brahman, Yunling and Angus cattle. The results of LD decay in each breed was largely consistent with the results of nucleotide diversity, except for the faster decay in Angus cattle out of a smaller effective population size and a strong bottleneck during the breed formation. The population-structure analysis revealed that the cross-breed Yunling cattle harboured the ancestry with Angus (0.44), Brahman (0.48) and Wannan cattle (0.08). Subsequently, we used RFmix to infer local ancestry in Yunling cattle and then performed chi-squared test to obtain the segments whose proportions of a certain ancestry were excessive compared with the whole-genome level, leading to 391 Angus, 49 Brahman and 2,312 Wannan segments. Gene annotation and KEGG enrichment analysis revealed that the excessive Angus, Brahman and Wannan segments might contribute to the rapid growth, immune resistance and indigenous adaptation, respectively, in Yunling cattle. Our results help understand ancestry components and formation process in Yunling cattle and will provide an opportunity for selective breeding by molecular approaches in future.

中文翻译：

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全基因组重测序揭示云岭牛的多样性、全球和本地血统比例

云岭牛由1/2婆罗门牛、1/4墨累灰牛和1/4云南黄牛组成的三品种杂交，具有生长快、肉质好、对湿热气候耐受性强、蜱抗性和粗饲料耐受性。在这里，我们通过对 131 头云岭牛和 31 头婆罗门牛（对照）的基因组进行测序，研究了遗传多样性、全球和本地血统比例。此外，我们使用35个已发表的祖先品种基因组（包括安格斯牛[墨累灰的祖先]、皖南牛[云南黄牛的祖先：文山和滇中]、文山和滇中牛）来表征云岭牛的形成过程。核苷酸多样性最高的是皖南牛，其次是文山牛、滇中牛、婆罗门牛、云岭牛和安格斯牛。每个品种的LD衰减结果与核苷酸多样性的结果基本一致，除了安格斯牛由于较小的有效种群规模和品种形成过程中的强大瓶颈而衰减更快。种群结构分析表明，杂交云岭牛与安格斯牛（0.44）、婆罗门牛（0.48）和皖南牛（0.08）有血缘关系。随后，我们使用RFmix推断云岭牛的局部血统，然后进行卡方检验，得到与全基因组水平相比某个血统比例过高的片段，导致391个Angus片段、49个Brahman片段和2312个皖南片段. 基因注释和KEGG富集分析表明，过多的安格斯、婆罗门和皖南段可能有助于快速增长，分别是云岭牛的免疫抗性和本土适应。我们的研究结果有助于了解云岭牛的祖先成分和形成过程，并将为未来通过分子方法进行选择性育种提供机会。