Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, 243122, India.
Division of Pharmacology & Toxicology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, 243122, India.
Mamm Genome. 2023 Dec;34(4):615-631. doi: 10.1007/s00335-023-10021-4. Epub 2023 Oct 16.
The main objective of the current research was to locate, annotate, and highlight specific areas of the bovine genome that are undergoing intense positive selection. Here, we are analyzing selection signatures in crossbred (Bos taurus X Bos indicus), taurine (Bos taurus), and indicine (Bos indicus) cattle breeds. Indicine cattle breeds found throughout India are known for their higher heat tolerance and disease resilience. More breeds and more methods can provide a better understanding of the selection signature. So, we have worked on nine distinct cattle breeds utilizing seven different summary statistics, which is a fairly extensive approach. In this study, we carried out a thorough genome-wide investigation of selection signatures using bovine 50K SNP data. We have included the genotyped data of two taurine, two crossbreds, and five indicine cattle breeds, for a total of 320 animals. During the 1950s, these indicine (cebuine) cattle breeds were exported with the aim of enhancing the resilience of taurine breeds in Western countries. For this study, we employed seven summary statistics, including intra-population, i.e., Tajima's D, CLR, iHS, and ROH and inter-population statistics, i.e., F, XP-EHH, and Rsb. The NCBI database, PANTHER 17.0, and CattleQTL database were used for annotation after finding the important areas under selection. Some genes, including EPHA6, CTNNA2, NPFFR2, HS6ST3, NPR3, KCNIP4, LIPK, SDCBP, CYP7A1, NSMAF, UBXN2B, UGDH, UBE2K, and DAB1, were shown to be shared by three or more different approaches. Therefore, it gives evidence of the most intense selection in these areas. These genes are mostly linked to milk production and adaptability traits. This study also reveals selection regions that contain genes which are crucial to numerous biological functions, including those associated with milk production, coat color, glucose metabolism, oxidative stress response, immunity and circadian rhythms.
本研究的主要目的是定位、注释和突出牛基因组中正在经历强烈正选择的特定区域。在这里，我们分析了杂交（Bos taurus X Bos indicus）、瘤牛（Bos taurus）和印度野牛（Bos indicus）牛品种的选择特征。在印度发现的印度野牛品种以其更高的耐热性和疾病抵抗力而闻名。更多的品种和更多的方法可以更好地理解选择特征。因此，我们使用了 7 种不同的汇总统计数据，对 9 个不同的牛品种进行了研究，这是一种相当广泛的方法。在这项研究中，我们利用牛 50K SNP 数据对选择特征进行了全面的全基因组研究。我们包括了两种瘤牛、两种杂交品种和五种印度野牛品种的基因型数据，共 320 头动物。在 20 世纪 50 年代，这些印度野牛品种被出口，旨在提高西方国家瘤牛品种的抗逆性。在这项研究中，我们使用了七种汇总统计数据，包括群体内，即 Tajima 的 D、CLR、iHS 和 ROH 以及群体间统计数据，即 F、XP-EHH 和 Rsb。在发现选择下的重要区域后，使用 NCBI 数据库、PANTHER 17.0 和 CattleQTL 数据库进行注释。一些基因，包括 EPHA6、CTNNA2、NPFFR2、HS6ST3、NPR3、KCNIP4、LIPK、SDCBP、CYP7A1、NSMAF、UBXN2B、UGDH、UBE2K 和 DAB1，被证明是三种或更多不同方法共有的。因此，这为这些区域的最强选择提供了证据。这些基因主要与产奶量和适应性性状有关。这项研究还揭示了包含对许多生物功能至关重要的基因的选择区域，包括与产奶量、毛色、葡萄糖代谢、氧化应激反应、免疫和昼夜节律有关的基因。
