Genome-wide detection of runs of homozygosity in Ding'an pigs revealed candidate genes relating to meat quality traits
文献类型： 外文期刊
作者： Wang, Ziyi 1 ; Pan, Deyou 1 ; Xie, Xinfeng 1 ; Zhong, Ziqi 1 ; Wang, Feng 2 ; Xiao, Qian 1 ;
作者机构： 1.Hainan Univ, Sch Trop Agr & Forestry, Hainan Key Lab Trop Anim Reprod & Breeding & Epide, Haikou 570228, Peoples R China
2.Hainan Acad Agr Sci, Inst Anim Sci & Vet Med, Haikou 571100, Peoples R China
关键词： Ding'an pigs; Runs of homozygosity; Selection signature; Meat quality traits; Inbreeding coefficients
期刊名称：BMC GENOMICS （ 影响因子：3.7； 五年影响因子：4.2 ）
ISSN： 1471-2164
年卷期： 2025 年 26 卷 1 期
页码：
收录情况： SCI
摘要： Background 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. Results 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). Conclusions 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.
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