State Key Laboratory of Animal Biotech Breeding, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
National Animal Breeding and Genetics Research Centre, Nepal Agricultural Research Council, Lalitpur, Nepal.
BMC Genomics. 2024 Nov 14;25(1):1082. doi: 10.1186/s12864-024-10993-w.
Indigenous buffaloes, as the important livestock species contributing to economy of the country, are the lifeline of livelihood in Nepal. They are distributed across diverse geographical regions of the country and have adapted to various feeding, breeding, and management conditions. The larger group of these native buffalo breeds are present in narrow and stiff hilly terrains. Their dispersal indicates a possible environmental adaptation mechanism, which is crucial for the conservation of these breeds.
We utilized whole-genome sequencing (WGS) to investigate the genetic diversity, population structure, and selection signatures of Nepalese indigenous buffaloes. We compared 66 whole-genome sequences with 118 publicly available sequences from six river and five swamp buffalo breeds. Genomic diversity parameters indicated genetic variability level in the Nepalese buffaloes comparable to those of Indian breeds, and population genetic structure revealed distinct geography-mediated genetic differentiation among these breeds. We used locus-specific branch length analysis (LSBL) for genome-wide scan, which revealed a list of potentially selected genes in Lime and Parkote breeds that inhabit the hilly region. A gene ontology (GO) analysis discovered that many GO terms were associated with cardiac function regulation. Furthermore, complementary analyses of local selection signatures, tissue expression profiles, and haplotype differences identified candidate genes, including KCNE1, CSF1R, and PDGFRB, related to the regulation of cardiac and pulmonary functions.
This study is a comprehensive WGS-based genetic analysis of the native Nepalese buffalo breeds. Our study suggested that the Nepalese "hilly" buffaloes, especially the Lime and Parkote breeds, have undergone some characteristic genetic changes and evolved increased cardiac and pulmonary function for their adaptation to the steep hilly terrains of the country.
印度野牛作为对国家经济有重要贡献的畜种，是尼泊尔生计的生命线。它们分布在该国的不同地理区域，适应各种饲养、繁殖和管理条件。这些本地水牛品种的较大群体存在于狭窄而坚硬的丘陵地形中。它们的扩散表明存在一种可能的环境适应机制，这对于保护这些品种至关重要。
我们利用全基因组测序（WGS）来研究尼泊尔本地水牛的遗传多样性、群体结构和选择特征。我们将 66 个全基因组序列与来自六个河流和五个沼泽水牛品种的 118 个公开序列进行了比较。基因组多样性参数表明，尼泊尔水牛的遗传变异性水平可与印度品种相媲美，种群遗传结构揭示了这些品种之间存在明显的地理介导遗传分化。我们使用特定基因座分支长度分析（LSBL）进行全基因组扫描，发现栖息在丘陵地区的 Lime 和 Parkote 品种中存在一些潜在的选择基因。GO 分析发现，许多 GO 术语与心脏功能调节有关。此外，对局部选择特征、组织表达谱和单倍型差异的补充分析确定了候选基因，包括与心脏和肺功能调节有关的 KCNE1、CSF1R 和 PDGFRB 基因。
本研究是对尼泊尔本地水牛品种进行的综合 WGS 遗传分析。我们的研究表明，尼泊尔“丘陵”水牛，特别是 Lime 和 Parkote 品种，经历了一些特征性的遗传变化，为适应该国陡峭的丘陵地形，进化出了增强的心脏和肺部功能。
