Wang Feifan, Zha Zonglin, He Yingzhi, Li Jie, Zhong Ziqi, Xiao Qian, Tan Zhen
School of Animal Science and Technology, Hainan University, Haikou 570228, China.
Animals (Basel). 2023 Jun 1;13(11):1835. doi: 10.3390/ani13111835.
Tunchang pig is one population of Hainan pig in the Hainan Province of China, with the characteristics of delicious meat, strong adaptability, and high resistance to diseases. To explore the genetic diversity and population structure of Tunchang pigs and uncover their germplasm characteristics, 10 unrelated Tunchang pigs were re-sequenced using the Illumina NovaSeq 150 bp paired-end platform with an average depth of 10×. Sequencing data from 36 individuals of 7 other pig breeds (including 4 local Chinese pig breeds (5 Jinhua, 5 Meishan, 5 Rongchang, and 6 Wuzhishan), and 3 commonly used commercial pig breeds (5 Duorc, 5 Landrace, and 5 Large White)) were downloaded from the NCBI public database. After analysis of genetic diversity and population structure, it has been found that compared to commercial pigs, Tunchang pigs have higher genetic diversity and are genetically close to native Chinese breeds. Three methods, F, θπ, and XP-EHH, were used to detect selection signals for three breeds of pigs: Tunchang, Duroc, and Landrace. A total of 2117 significantly selected regions and 201 candidate genes were screened. Gene enrichment analysis showed that candidate genes were mainly associated with good adaptability, disease resistance, and lipid metabolism traits. Finally, further screening was conducted to identify potential candidate genes related to phenotypic traits, including meat quality (, , , , , , , and ), immune regulation (, , , , , , , , and ), growth and development (, , , and ), reproduction ( and ), vision ( and ), energy metabolism (), cell migration (), and olfaction (). In summary, our research results provide a genomic overview of the genetic variation, genetic diversity, and population structure of the Tunchang pig population, which will be valuable for breeding and conservation of Tunchang pigs in the future.
屯昌猪是中国海南省海南猪的一个种群，具有肉质鲜美、适应性强、抗病力高的特点。为了探索屯昌猪的遗传多样性和群体结构，揭示其种质特性，使用Illumina NovaSeq 150 bp双末端平台对10头无亲缘关系的屯昌猪进行重测序，平均深度为10×。从NCBI公共数据库下载了7个其他猪品种的36个个体的测序数据（包括4个中国地方猪品种（5头金华猪、5头梅山猪、5头荣昌猪和6头五指山猪）和3个常用商业猪品种（5头杜洛克猪、5头长白猪和5头大白猪））。在对遗传多样性和群体结构进行分析后，发现与商业猪相比，屯昌猪具有更高的遗传多样性，并且在基因上与中国本土品种接近。使用F、θπ和XP-EHH三种方法检测了屯昌猪、杜洛克猪和长白猪三个猪品种的选择信号。共筛选出2117个显著选择区域和201个候选基因。基因富集分析表明，候选基因主要与良好的适应性、抗病性和脂质代谢性状相关。最后，进行进一步筛选以鉴定与表型性状相关的潜在候选基因，包括肉质（……）、免疫调节（……）、生长发育（……）、繁殖（……）、视觉（……）、能量代谢（……）、细胞迁移（……）和嗅觉（……）。总之，我们的研究结果提供了屯昌猪群体遗传变异、遗传多样性和群体结构的基因组概况，这将对未来屯昌猪的育种和保护具有重要价值。
