Institute of Biotechnology, School of Agriculture, Shiraz University, Iran.
Department of System Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran.
Genome Biol Evol. 2021 Jan 7;13(1). doi: 10.1093/gbe/evaa231.
The application of high-throughput genotyping or sequencing data helps us to understand the genomic response to natural and artificial selection. In this study, we scanned the genomes of five indigenous buffalo populations belong to three recognized breeds, adapted to different geographical and agro-ecological zones in Iran, to unravel the extent of genomic diversity and to localize genomic regions and genes underwent past selection. A total of 46 river buffalo whole genomes, from West and East Azerbaijan, Gilan, Mazandaran, and Khuzestan provinces, were resequenced. Our sequencing data reached to a coverage above 99% of the river buffalo reference genome and an average read depth around 9.2× per sample. We identified 20.55 million SNPs, including 63,097 missense, 707 stop-gain, and 159 stop-loss mutations that might have functional consequences. Genomic diversity analyses showed modest structuring among Iranian buffalo populations following frequent gene flow or admixture in the recent past. Evidence of positive selection was investigated using both differentiation (Fst) and fixation (Pi) metrics. Analysis of fixation revealed three genomic regions in all three breeds with aberrant polymorphism contents on BBU2, 20, and 21. Fixation signal on BBU2 overlapped with the OCA2-HERC2 genes, suggestive of adaptation to UV exposure through pigmentation mechanism. Further validation using resequencing data from other five bovine species as well as the Axiom Buffalo Genotyping Array 90K data of river and swamp buffaloes indicated that these fixation signals persisted across river and swamp buffaloes and extended to taurine cattle, implying an ancient evolutionary event occurred before the speciation of buffalo and taurine cattle. These results contributed to our understanding of major genetic switches that took place during the evolution of modern buffaloes.
高通量基因分型或测序数据的应用有助于我们了解基因组对自然和人工选择的反应。在这项研究中，我们扫描了属于三个公认品种的五个本地水牛群体的基因组，这些品种适应于伊朗不同的地理和农业生态区，以揭示基因组多样性的程度，并定位经历过过去选择的基因组区域和基因。总共对来自东阿塞拜疆省、西阿塞拜疆省、吉兰省、马赞达兰省和胡齐斯坦省的 46 头河流型水牛全基因组进行了重测序。我们的测序数据达到了河流型水牛参考基因组的覆盖率超过 99%，每个样本的平均读取深度约为 9.2×。我们鉴定了 2055 万个 SNP，包括 63097 个错义突变、707 个终止增益和 159 个终止丢失突变，这些突变可能具有功能后果。基因组多样性分析表明，在最近的过去，伊朗水牛群体之间存在适度的结构，存在频繁的基因流动或混合。使用分化（Fst）和固定（Pi）指标调查了正选择的证据。固定分析表明，在所有三个品种中，BBU2、20 和 21 上都存在异常多态性含量的三个基因组区域存在固定信号。BBU2 上的固定信号与 OCA2-HERC2 基因重叠，提示通过色素沉着机制适应紫外线暴露。使用来自其他五个牛种的重测序数据以及河流型和沼泽型水牛的 Axiom Buffalo Genotyping Array 90K 数据进行进一步验证表明，这些固定信号在河流型和沼泽型水牛中持续存在，并扩展到牛科动物，这意味着在水牛和牛科动物的物种分化之前，发生了一个古老的进化事件。这些结果有助于我们理解现代水牛进化过程中发生的主要遗传变化。
