Hainan Institute, Zhejiang University, Yongyou Industry Park, Yazhou Bay Sci-Tech City, Sanya 572000, China; Key Laboratory of Livestock and Poultry Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, College of Animal Science, Zhejiang University, 866# Yuhangtang Road, Hangzhou, East 310058, China; Hainan Yazhou Bay Seed Lab, Yongyou Industrial Park, Yazhou Bay Sci-Tech City, Sanya 572025, China.
Key Laboratory of Livestock and Poultry Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, College of Animal Science, Zhejiang University, 866# Yuhangtang Road, Hangzhou, East 310058, China.
Animal. 2024 Aug;18(8):101236. doi: 10.1016/j.animal.2024.101236. Epub 2024 Jul 2.
Tunchang pigs, mainly distributed throughout Hainan Province of China, are well-known for their superior meat quality, crude feed tolerance, and adaptability to high temperatures and humidity. Runs of homozygosity (ROH) can provide valuable information about the inbreeding coefficient in individuals and selection signals that may reveal candidate genes associated with key functional traits. Runs of heterozygosity (ROHet) are commonly associated with balance selection, which can help us understand the adaptive evolutionary history of domestic animals. In this study, we investigated ROHs and ROHets in 88 Tunchang pigs. We also compared the estimates of inbreeding coefficients in individuals calculated based on four methods. In summary, we detected a total of 16 ROH islands in our study, and 100 genes were found within ROH regions. These genes were correlated with economically important traits such as reproduction (e.g., SERPIND1, HIRA), meat quality (e.g., PI4KA, TBX1), immunity (e.g., ESS2, RANBP1), adaption to heat stress (TXNRD2 and DGCR8), and crude food tolerance (TRPM6). Moreover, we discovered 18 ROHet islands harbouring genes associated with reproduction (e.g., ARHGEF12, BMPR2), immune system (e.g., BRD4, DNMT3B). These findings may help us design effective breeding and conservation strategies for this unique breed.
屯昌猪主要分布在中国海南省，以其卓越的肉质、对粗饲料的耐受性以及对高温高湿环境的适应性而闻名。纯合度 runs of homozygosity (ROH) 可以提供个体近交系数的有价值信息和可能揭示与关键功能性状相关候选基因的选择信号。杂合度 runs of heterozygosity (ROHet) 通常与平衡选择有关，可以帮助我们了解家畜的适应性进化历史。在本研究中，我们研究了 88 头屯昌猪的 ROH 和 ROHet。我们还比较了基于四种方法计算的个体近交系数估计值。总之，我们在研究中总共检测到 16 个 ROH 岛，其中有 100 个基因位于 ROH 区域内。这些基因与经济上重要的性状有关，如繁殖（例如 SERPIND1、HIRA）、肉质（例如 PI4KA、TBX1）、免疫（例如 ESS2、RANBP1）、对热应激的适应（TXNRD2 和 DGCR8）和粗饲料耐受性（TRPM6）。此外，我们发现了 18 个含有与繁殖（例如 ARHGEF12、BMPR2）、免疫系统（例如 BRD4、DNMT3B）相关基因的 ROHet 岛。这些发现可能有助于我们为这一独特品种设计有效的繁殖和保护策略。
