阿勒泰白头牛基因组结构变异分析

Identification of Genomic Structure Variation in Altay White-headed Cattle

中文关键词: 阿勒泰白头牛  基因组  结构变异  种质特征

英文关键词: Altay white-headed cattle, Genome, Structure variations, Germplasm characteristics

中文摘要:

      阿勒泰白头牛是新疆阿勒泰地区的乳肉役兼用地方品种，具有白头、抗病力强和性情温顺特点。结构变异（Structure Variations，SVs）是影响牛表型性状的重要遗传变异形式。本研究旨在获得阿勒泰白头牛基因组SVs的特征和种质特征的候选基因。以20头阿勒泰白头牛测序深度为17.32X的基因组序列为基础，通过Delly、Lumpy和Manta三个软件进行SVs的检测，并通过SURVIVOR软件取交集进行整合，总共鉴定到37847个SVs。从类型看，缺失、易位、倒位、复制和插入的比例分别为55.5%、26.7%、8.7%、8.9%和不足0.1%。从长度看，缺失、倒位和复制的分布呈现右偏态。以频率大于0.9为标准，获得636个高频SVs，涉及865个蛋白编码基因。基因注释和富集分析发现，阿勒泰白头牛的高频SVs与免疫抗病和神经功能相关，契合了抗病力强和性情温顺特征，可作为相关特征的候选基因（免疫抗病：BolA-DQB、TNIP3、IL1RAP和IL1R1，神经性情：EPHA6、GRM7和HTR2A）。值得注意的是，我们发现ASIP基因5′非编码区存在一个缺失，该基因可减少真黑素的合成，在哺乳动物毛色调控中起着重要作用。研究的结果可以为阿勒泰白头牛种质特征的遗传机制解析奠定基础，也可以为阿勒泰白头牛的资源利用提供基础资料。

英文摘要:

      Altay white-headed cattle, an indigenous breed for dairy, beef and draft purpose in the Altay region of Xinjiang, China, displays white head, strong disease resistance and gentle temperament. Structural variation (SV) is an important genetic variation that affect phenotypic traits in cattle. This study aims to characterize the SVs in the genome of Altay white cattle and identify candidate genes associated with their phenotypic features. Based on the whole genome sequences of 20 Altay white-headed cattle with a sequencing depth of 17.32X, SVs were detected using three software tools: Delly, Lumpy and Manta. Based on the intersection of two or three strategies, the SVs were further integrated using SURVIVOR software, resulting in a total of 37,847 SVs being identified. In terms of type, the proportions of deletion, translocation, inversion, duplication, and insertion were 55.5%, 26.7%, 8.7%, 8.9% and less than 0.1%, respectively. Regarding the length distribution, deletions, inversions, and duplications showed a right-skewed pattern. Using a frequency threshold of greater than 0.9, we obtained 636 high-frequency SVs, which involved 865 protein-coding genes. Gene annotation and enrichment analysis revealed that the high-frequency SVs in Altay white cattle were associated with immune response, disease resistance and neural functions, aligning with the breed''s characteristics of strong disease resistance and gentle temperament. These genes, such as BolA-DQB, TNIP3, IL1RAP and IL1R1 (immune response), EPHA6, GRM7 and HTR2A (neural temperament), may serve as candidate genes related to these traits. It is worth noting that we identified a deletion in the 5'' non-coding region of the ASIP gene, which plays an important role in regulating melanin synthesis and is involved in mammalian coat color determination. The findings of this study provide insights into the genetic mechanisms underlying the phenotypic traits of Altay white-headed cattle and serve as fundamental information for the utilization and conservation of this breed.