GWAS analysis for tolerance to heat stress and milk production, in subtropical Egyptian goats

The conservation of local Egyptian goat genotypes has been a national program since 2009. Our study investigated different subtropical Egyptian goat populations (367 does) from different harsh ecological zones(hot Upper Egypt, Coastal Zone of Western Desert, and Wahati Desert Oasis) to identify genes associated with heat stress. We examined the physiological response of animals that were exposed to simulated summer grazing conditions, and physiological parameters including respiration rate, gas volume, rectal temperature, and skin temperature. Temperature Humidity Index ranged from 98.6 to 109.3, indicating that the animals were under severe heat stress. Results showed significant differences between the populations in their tolerance to heat stress, with Saidi goats being the most adapted to hot-dry conditions. Respiration rate was found to be the most reliable physiological trait for differentiating between animals in their tolerance to heat stress. The GWAS analysis involved 157 genotypes and 54,032 marker-SNPs, revealing 90 SNPs associated with heat stress and 70 SNPs associated with milk production. Chromosome 1 had the highest number of SNPs associated with heat-stress traits, while chromosome 4 exhibited the largest number of significant SNPs associated with milk production. Several genes were associated with heat stress response and tolerance in goats. These genes were categorized into three main groups: heat stress response, stress response, and reproduction, and feed intake. The first group includes USP54, KDM6A, and ETNPPL, which have multiple functions, such as steroid biosynthesis, metabolism, and stress response, and are also involved in key biological processes such as reproduction, immune response, and metabolism. The second group, which is mostly associated with immune response, includes GLTSCR2 and NAALADL2. Finally, a group of genes that may control animal feed intakes, including TRPM3 and ZBTB8A. Additionally, several genes, such as FHIT, GALNT18, RAPGEF5, and RBFOX1, linked to milk production, are known to be linked fertility, and fatty acid composition. These findings provide insights into the potential roles of these genes in heat stress response and tolerance in goats, and the genetic basis for improved milk production and animal welfare and can be used as selection markers in the ongoing breeding programs.自2009年起，埃及本土山羊基因型保护便已成为一项国家级项目。本研究针对来自三大严苛生态区——上埃及炎热区域、西沙漠沿海地带与瓦哈提沙漠绿洲——的367头雌性亚热带埃及山羊群体展开调研，旨在筛选与热应激相关的功能基因。研究团队检测了暴露于模拟夏季放牧环境条件下的山羊生理响应，并测定了多项生理指标，包括呼吸频率、呼吸容积、直肠温度与皮肤温度。受试环境的温湿度指数介于98.6至109.3之间，表明所有受试山羊均处于严重热应激状态。结果显示，不同山羊群体的热应激耐受能力存在显著差异，其中赛义德山羊（Saidi goats）最适应炎热干旱的生存环境。研究证实，呼吸频率是区分山羊热应激耐受能力的最可靠生理性状。本次全基因组关联分析（Genome-Wide Association Study, GWAS）共纳入157份基因型样本与54032个标记单核苷酸多态性（Single Nucleotide Polymorphism, SNPs），最终鉴定出90个与热应激相关的SNPs以及70个与产奶性状相关的SNPs。1号染色体上与热应激性状相关的SNPs数量最多，而4号染色体上与产奶性状相关的显著SNPs数量位居首位。已有多项基因被证实与山羊的热应激响应及耐受能力密切相关，可将其划分为三大功能类群：热应激响应类、应激响应类，以及繁殖与采食量调控类。第一类基因包括USP54、KDM6A与ETNPPL，它们具备类固醇生物合成、物质代谢与应激响应等多重生物学功能，同时也参与繁殖、免疫应答与能量代谢等关键生理过程。第二类基因主要与免疫应答相关，涵盖GLTSCR2与NAALADL2。第三类为调控动物采食量的功能基因，包括TRPM3与ZBTB8A。此外，FHIT、GALNT18、RAPGEF5与RBFOX1等与产奶性状相关的基因，同时也被证实与繁殖性能及脂肪酸组成存在显著关联。本研究结果为解析这些基因在山羊热应激响应与耐受中的潜在作用，以及阐明提升产奶性能与动物福利的遗传基础提供了全新视角，相关成果可作为正在开展的育种项目中的选择标记予以应用。