Animal Husbandry Institute of Guangxi Zhuang Autonomous Region, Guangxi Key Laboratory of Livestock Genetic Improvement, Nanning, 530001, China.
College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China.
BMC Genomics. 2020 Sep 29;21(1):674. doi: 10.1186/s12864-020-07095-8.
Fuzhong buffalo, a native breed of Guangxi Zhuang Autonomous Region, is traditionally used as a draft animal to provide farm power in the rice cultivation. In addition, the Fuzhong buffalo also prepared for the bullfighting festival organized by the locals. The detection of the selective signatures in its genome can help in elucidating the selection mechanisms in its stamina and muscle development of a draft animal.
In this study, we analyzed 27 whole genomes of buffalo (including 15 Fuzhong buffalo genomes and 12 published buffalo genomes from Upper Yangtze region). The ZHp, ZFst, π-Ratio, and XP-EHH statistics were used to identify the candidate signatures of positive selection in Fuzhong buffalo. Our results detected a set of candidate genes involving in the pathways and GO terms associated with the response to exercise (e.g., ALDOA, STAT3, AKT2, EIF4E2, CACNA2D2, TCF4, CDH2), immunity (e.g., PTPN22, NKX2-3, PIK3R1, ITK, TMEM173), nervous system (e.g., PTPN21, ROBO1, HOMER1, MAGI2, SLC1A3, NRG3, SNAP47, CTNNA2, ADGRL3). In addition, we also identified several genes related to production and growth traits (e.g., PHLPP1, PRKN, MACF1, UCN3, RALGAPA1, PHKB, PKD1L). Our results depicted several pathways, GO terms, and candidate genes to be associated with response to exercise, immunity, nervous system, and growth traits.
The selective sweep analysis of the Fuzhong buffalo demonstrated positive selection pressure on potential target genes involved in behavior, immunity, and growth traits, etc. Our findings provided a valuable resource for future research on buffalo breeding and an insight into the mechanisms of artificial selection.
富钟水牛是广西壮族自治区的本地品种，传统上被用作水稻种植的役用动物提供农场动力。此外，富钟水牛也为当地人组织的斗牛节做准备。检测其基因组中的选择性特征有助于阐明其耐力和肌肉发育作为役用动物的选择机制。
在这项研究中，我们分析了 27 头水牛的全基因组（包括 15 头富钟水牛基因组和 12 头来自长江上游地区的已发表水牛基因组）。使用 ZHp、ZFst、π-Ratio 和 XP-EHH 统计数据来识别富钟水牛中阳性选择的候选特征。我们的结果检测到一组候选基因，涉及与运动反应相关的途径和 GO 术语（例如，ALDOA、STAT3、AKT2、EIF4E2、CACNA2D2、TCF4、CDH2）、免疫（例如，PTPN22、NKX2-3、PIK3R1、ITK、TMEM173）、神经系统（例如，PTPN21、ROBO1、HOMER1、MAGI2、SLC1A3、NRG3、SNAP47、CTNNA2、ADGRL3）。此外，我们还鉴定了几个与生产和生长性状相关的基因（例如，PHLPP1、PRKN、MACF1、UCN3、RALGAPA1、PHKB、PKD1L）。我们的结果描绘了几个与运动反应、免疫、神经系统和生长性状相关的途径、GO 术语和候选基因。
富钟水牛的选择性扫描分析表明，潜在的目标基因受到行为、免疫和生长性状等方面的正选择压力。我们的研究结果为未来的水牛养殖研究提供了有价值的资源，并深入了解了人工选择的机制。
