Zhong Ziqi, Wang Feng, Xie Xinfeng, Wang Ziyi, Pan Deyou, Wang Zhen, 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.
J Therm Biol. 2025 Aug;132:104264. doi: 10.1016/j.jtherbio.2025.104264. Epub 2025 Sep 4.
In light of the challenges posed by global climate change, the environmental adaptability of organisms is becoming increasingly important. The Wuzhishan (WZS) pig, tolerant to high heat and humidity, is an ideal model for genomic study. By characterizing its genome and assessing its genetic diversity and runs of homozygosity (ROH), we can gain insights into its current conservation status and genomic architecture. To this end, we analyzed whole-genome resequencing data from WZS pigs, identifying a comprehensive set of genetic variations: 12,844,858 single nucleotide polymorphisms (SNPs), 4,723,303 insertions and deletions (InDels), 39,311 copy number variations (CNVs), and 70,392 structural variations (SVs). ROH analysis revealed mostly short segments, indicating limited recent admixture and relatively low inbreeding, reflecting high genetic diversity. Linkage disequilibrium decay and effective population size analyses supported these findings, consistent with previous studies. Population genetic analyses of pig populations from Asia, Europe, and the Americas were conducted using SNPs, InDels, and SVs. The results obtained from different variant types were largely concordant, suggesting that the constructed genomic variation database is robust. Notably, the WZS pig displayed relatively unique genetic characteristics compared to other breeds. By intersecting the top 5 % of genes under selection signatures, we identified key pathways and candidate genes associated with important traits in WZS pigs, including reproduction (ABCC9, APC2, CABS1, CSNK1G1), immunity (ARPIN, CMAS, ITPR1, SLC25A13), meat quality (GANC, OBSCN, SLC5A4), environmental adaptability (MAGI1, PHF3), and heat tolerance (GABPB1, LRRC25). Further integrative analyses based on transcriptomic, single-cell transcriptomic, and epigenomic data were conducted to explore the regulatory mechanisms of key genes such as LRRC25 and ITPR1. We identified relevant expression quantitative trait loci (eQTLs), associated tissues, and distal regulatory elements that potentially influence gene expression. These findings suggest that epigenetic modifications may contribute to the enhanced heat tolerance and immune function observed in WZS pigs. In conclusion, WZS pigs represent a valuable genetic resource. Further research on this breed will deepen our understanding of mechanisms underlying environmental adaptability, and provide important insights into evolutionary biology and breeding strategies for improved resilience in livestock.
鉴于全球气候变化带来的挑战，生物的环境适应性变得越来越重要。五指山（WZS）猪耐高温高湿，是基因组研究的理想模型。通过对其基因组进行表征并评估其遗传多样性和纯合子连续片段（ROH），我们可以深入了解其当前的保护状况和基因组结构。为此，我们分析了五指山猪的全基因组重测序数据，鉴定出了一组全面的遗传变异：12,844,858个单核苷酸多态性（SNP）、4,723,303个插入缺失（InDel）、39,311个拷贝数变异（CNV）和70,392个结构变异（SV）。ROH分析显示大多为短片段，表明近期的混杂有限且近亲繁殖程度相对较低，反映出高遗传多样性。连锁不平衡衰减和有效种群大小分析支持了这些发现，与先前的研究一致。利用SNP、InDel和SV对来自亚洲、欧洲和美洲的猪种群进行了群体遗传学分析。从不同变异类型获得的结果在很大程度上是一致的，表明构建的基因组变异数据库是可靠的。值得注意的是，与其他品种相比，五指山猪表现出相对独特 的遗传特征。通过对选择信号下排名前5%的基因进行交叉分析，我们鉴定出了与五指山猪重要性状相关的关键途径和候选基因，包括繁殖（ABCC9、APC2、CABS1、CSNK1G1）、免疫（ARPIN、CMAS、ITPR1、SLC25A13）、肉质（GANC、OBSCN、SLC5A4）、环境适应性（MAGI1、PHF3）和耐热性（GABPB1、LRRC25）。基于转录组学、单细胞转录组学和表观基因组学数据进行了进一步的整合分析，以探索LRRC25和ITPR1等关键基因的调控机制。我们鉴定出了可能影响基因表达的相关表达数量性状位点（eQTL）、相关组织和远端调控元件。这些发现表明表观遗传修饰可能有助于五指山猪耐热性和免疫功能的增强。总之，五指山猪是一种宝贵的遗传资源。对该品种的进一步研究将加深我们对环境适应性潜在机制的理解，并为进化生物学和提高家畜恢复力的育种策略提供重要见解。
