The yak is a species of livestock which is crucial for local communities of the Qinghai-Tibet Plateau and adjacent regions and naturally owns one more thoracic vertebra than cattle. Recently, a sub-population of yak termed as the Jinchuan yak has been identified with over half its members own a thoracolumbar vertebral formula of T15L5 instead of the natural T14L5 arrangement. The novel T15L5 positioning is a preferred genetic trait leading to enhanced meat and milk production. Selective breeding of this trait would have great agricultural value and exploration of the molecular mechanisms underlying this trait would both accelerate this process and provide us insight into the development and regulation of somitogenesis. Here we investigated the genetic background of the Jinchuan yak through resequencing fifteen individuals, comprising five T15L5 individuals and ten T14L5 individuals with an average sequencing depth of > 10X, whose thoracolumbar vertebral formulae were confirmed by anatomical observation. Principal component analysis, linkage disequilibrium analysis, phylogenetic analysis, and selective sweep analysis were carried out to explore Jinchuan yak’s genetic background. Three hundred and thirty candidate markers were identified as associated with the additional thoracic vertebrae and target sequencing was used to validate seven carefully selected markers in an additional 51 Jinchuan yaks. The accuracies of predicting 15 thoracic vertebrae and 20 thoracolumbar vertebrae with these 7 markers were 100.00 and 33.33% despite they both could only represent 20% of all possible genetic diversity. Two genes, PPP2R2B and TBLR1, were found to harbour the most candidate markers associated with the trait and likely contribute to the unique somitic number and identity according to their reported roles in the mechanism of somitogenesis. Our findings provide a clear depiction of the Jinchuan yak’s genetic background and a solid foundation for marker-assistant selection. Further exploitation of this unique population and trait could be promoted with the aid of our genomic resource.

中文翻译：

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洞悉unique牛（Bos grunniens）与另外一个胸椎的独特的体发生

牛是一种牲畜，对青藏高原和邻近地区的当地社区至关重要，自然拥有比牛多的一个胸椎。最近，已经确定了一种称为金川牛的​​sub牛亚群，其一半以上的成员拥有T15L5的胸腰椎脊椎公式，而不是自然的T14L5排列。新的T15L5定位是导致肉和奶产量提高的优选遗传特征。该性状的选择性育种将具有巨大的农业价值，对该性状潜在的分子机制的探索将加速这一过程，并为我们提供对体发生的发展和调控的见识。在这里，我们通过对15个人进行重新测序，调查了金川牛的遗传背景，包括5个T15L5个体和10个T14L5个体，平均测序深度> 10X，其胸腰椎脊椎公式已通过解剖学观察得到证实。进行了主成分分析，连锁不平衡分析，系统发育分析和选择性扫描分析，以探索金川牛的遗传背景。确定了330个候选标记与其他胸椎相关，并通过靶标测序验证了另外51头金川牛中七个精心选择的标记。用这7个标记预测15个胸椎和20个胸腰椎椎骨的准确性分别为100.00和33.33％，尽管它们都只能代表所有可能的遗传多样性的20％。PPP2R2B和TBLR1这两个基因，被发现具有与该性状相关的最候选标记，并根据其在体发生机理中的作用报道，可能有助于独特的体细胞数和特性。我们的发现为金川牛的​​遗传背景提供了清晰的描述，并为标记辅助选择提供了坚实的基础。借助我们的基因组资源，可以促进对这一独特种群和性状的进一步开发。