Wang Ziyi, Pan Deyou, Xie Xinfeng, Zhong Ziqi, Wang Feng, Xiao Qian
Hainan Key Laboratory of Tropical Animal Reproduction & Breeding and Epidemic Disease Research, School of Tropical Agriculture and Forestry, Hainan University, Haikou, 570228, China.
Institute of Animal Science and Veterinary Medicine, Hainan Academy of Agricultural Sciences, Haikou, 571100, China.
BMC Genomics. 2025 Mar 31;26(1):316. doi: 10.1186/s12864-025-11501-4.
Ding'an (DA) pig, a native Chinese breed, is renowned for its excellent meat quality, disease resistance, high reproductive performance, and adaptability. Its meat quality traits hold significant economic value. However, its conservation population has been declining due to the impact of commercialized breeds and African swine fever, which is not conducive to its development and utilization.
This study utilized whole-genome resequencing data from 15 DA pigs to reveal their genetic characteristics and current resource status. We analyzed the length, number, and distribution patterns of Runs of Homozygosity (ROH) in DA pigs, as well as high-frequency ROH regions. The results identified 23,208,098 single nucleotide polymorphisms (SNPs), 4,497,242 insertion and deletion (InDels), 13,622 copy number variation (CNVs), and 399,934 structure variation (SVs). Further analysis revealed relatively high genetic diversity and low inbreeding levels in DA pigs. Through functional gene enrichment analysis of high-frequency ROH regions, we identified multiple candidate genes associated with specific traits in DA pigs, including meat quality (ANKRD1, CPNE5, MYOM1), fat deposition (OBSCN, MAPK4, PNPLA1, PACSIN1, GRM4), and skeletal muscle development (LRPPRC, WNT9A).
This study conducted whole-genome sequencing and ROH analysis on DA pigs, revealing high genetic diversity and low inbreeding levels within the population. Through functional gene enrichment analysis of high-frequency ROH regions, we identified multiple candidate genes associated with meat quality, fat deposition, and skeletal muscle development. These findings not only enhance our understanding of the genetic mechanisms underlying the unique traits of DA pigs but also provide valuable insights for practical applications. Specifically, the identified candidate genes and genomic regions can guide conservation efforts to maintain genetic diversity and mitigate inbreeding risks. Meanwhile, these genetic insights can be integrated into breeding programs to improve meat quality and other economically important traits, thereby supporting the sustainable development and utilization of DA pigs.
定安猪是中国本土猪种，以其优良的肉质、抗病性、高繁殖性能和适应性而闻名。其肉质性状具有重要的经济价值。然而，由于商业化品种和非洲猪瘟的影响，其保种群数量一直在下降，这不利于其开发利用。
本研究利用15头定安猪的全基因组重测序数据，揭示了它们的遗传特征和当前资源状况。我们分析了定安猪纯合子连续片段（ROH）的长度、数量和分布模式，以及高频ROH区域。结果鉴定出23,208,098个单核苷酸多态性（SNP）、4,497,242个插入缺失（InDel）、13,622个拷贝数变异（CNV）和399,934个结构变异（SV）。进一步分析表明，定安猪具有较高的遗传多样性和较低的近交水平。通过对高频ROH区域进行功能基因富集分析，我们鉴定出多个与定安猪特定性状相关的候选基因，包括肉质（ANKRD1、CPNE5、MYOM1）、脂肪沉积（OBSCN、MAPK4、PNPLA1、PACSIN1、GRM4）和骨骼肌发育（LRPPRC、WNT9A）。
本研究对定安猪进行了全基因组测序和ROH分析，揭示了群体内较高的遗传多样性和较低的近交水平。通过对高频ROH区域进行功能基因富集分析，我们鉴定出多个与肉质、脂肪沉积和骨骼肌发育相关的候选基因。这些发现不仅增进了我们对定安猪独特性状遗传机制的理解，也为实际应用提供了有价值的见解。具体而言，鉴定出的候选基因和基因组区域可指导保护工作，以维持遗传多样性并降低近交风险。同时，这些遗传见解可纳入育种计划，以改善肉质和其他重要经济性状，从而支持定安猪的可持续开发利用。
