Tyagi Shiv K, Mehrotra Arnav, Singh Akansha, Kumar Amit, Dutt Triveni, Mishra Bishnu P, Pandey Ashwni K
Animal Genetics Division, ICAR-Indian Veterinary Research Institute, Izatnangar, Bareilly, India.
Livestock Production and Management, Indian Council of Agricultural Research (ICAR)-Indian Veterinary Research Institute, Bareilly, India.
Front Genet. 2021 Oct 19;12:673697. doi: 10.3389/fgene.2021.673697. eCollection 2021.
India is home to a large and diverse buffalo population. The Murrah breed of North India is known for its milk production, and it has been used in breeding programs in several countries. Selection signature analysis yield valuable information about how the natural and artificial selective pressures have shaped the genomic landscape of modern-day livestock species. Genotype information was generated on six buffalo breeds of India, namely, Murrah, Bhadawari, Mehsana, Pandharpuri, Surti, and Toda using ddRAD sequencing protocol. Initially, the genotypes were used to carry out population diversity and structure analysis among the six breeds, followed by pair-wise comparisons of Murrah with the other five breeds through XP-EHH and methodologies to identify regions under selection in Murrah. Admixture results showed significant levels of Murrah inheritance in all the breeds except Pandharpuri. The selection signature analysis revealed six regions in Murrah, which were identified in more than one pair-wise comparison through both XP-EHH and analyses. The significant regions overlapped with QTLs for milk production, immunity, and body development traits. Genes present in these regions included , , , , , , , , , , , , and . These genes emerged as candidates for future polymorphism studies of adaptability and performance traits in buffaloes. The results also suggested ddRAD sequencing as a useful cost-effective alternative for whole-genome sequencing to carry out diversity analysis and discover selection signatures in Indian buffalo breeds.
印度拥有庞大且多样的水牛种群。印度北部的摩拉水牛品种以其产奶量而闻名，并且已在多个国家的育种计划中得到应用。选择特征分析能够提供有关自然和人工选择压力如何塑造现代家畜物种基因组格局的宝贵信息。使用ddRAD测序方案，对印度的六个水牛品种，即摩拉水牛、巴达瓦里水牛、梅赫萨纳水牛、潘德哈普里水牛、苏尔蒂水牛和托达水牛进行了基因型信息测定。最初，这些基因型用于六个品种之间的群体多样性和结构分析，随后通过XP-EHH和其他方法对摩拉水牛与其他五个品种进行成对比较，以确定摩拉水牛中受选择的区域。混合分析结果显示，除潘德哈普里水牛外，所有品种中都有显著水平的摩拉水牛遗传成分。选择特征分析在摩拉水牛中发现了六个区域，通过XP-EHH和其他分析在不止一对比较中都识别出了这些区域。这些显著区域与产奶量、免疫力和身体发育性状的数量性状基因座重叠。这些区域中存在的基因包括……（此处原文未完整列出基因名称）。这些基因成为未来水牛适应性和生产性能性状多态性研究的候选基因。结果还表明，ddRAD测序是全基因组测序的一种有用且具有成本效益的替代方法，可用于进行印度水牛品种的多样性分析和发现选择特征。
