Effects of the Temperature–Humidity Index on Milk Production Traits and Gene–Environment Interactions in Chinese Holstein Cows

Heat stress limits dairy production. The temperature-humidity index (THI), combining temperature and relative humidity, is widely used to assess heat stress. However, in Chinese Holstein cattle, the phenotypic responses of milk traits and genotype-environment interaction mechanisms under different THI conditions are understudied. Based on 63,334 records from 7240 cows (milk yield, fat percentage, protein percentage), matched with meteorological data and 113,297 SNPs, we employed a random-effects GWAS to examine SNP effects across a continuous THI gradient, comparing results with conventional, temperature-, and humidity-interaction GWAS. As THI increased, all traits declined with distinct patterns. Random regression GWAS identified 149 significant SNP × THI interactions (5 for MY, 86 for FP, 58 for PP), distributed across BTA5, BTA6, BTA14, and BTA20. Candidate gene annotation identified 52 candidate genes near significant SNPs, of which 50 core candidate genes were supported in both temperature and humidity GWAS. The most robustly supported core candidate genes include DGAT1, CPSF1, ABCG2, MGST1, VPS28, PPP1R16A, ZNF250, GRID2, KCNC2, and LOC787350—of which DGAT1, ABCG2, and MGST1 have been functionally validated in milk production traits, whereas others represent novel candidates requiring further investigation. Temperature and THI-GWAS showed high consistency, while humidity-GWAS detected both overlapping and specific signals. Incorporating THI as a continuous environmental gradient identifies environment-dependent regulatory signals not captured by conventional GWAS, providing candidate genes that may contribute to future breeding strategies after further validation.