Genome-wide association study identifies candidate genes and SNPs associated with heat tolerance in the Chinese mitten crab (Eriocheir sinensis)

The Chinese mitten crab ( Eriocheir sinensis ) is one of the most economically important aquaculture species in China. However, rising water temperatures associated with global climate change and summer heat waves pose significant threats to crab survival, growth, and productivity. Enhancing heat tolerance through selective breeding has become critical for sustaining this industry. In this study, we measured heat tolerance of crabs under acute high-temperature stress (38 °C) and conducted whole-genome resequencing, generating 401,711 high-quality single-nucleotide polymorphisms (SNPs) after stringent quality control. A genome-wide association study (GWAS) identified 20 SNPs significantly associated with heat tolerance distributed across multiple chromosomes, with 362 candidate genes annotated in genomic regions flanking these loci. KEGG functional enrichment analysis revealed that the pathways were significantly enriched in multiple processes, including beta-alanine metabolism and hormone signaling. Through protein–protein interaction (PPI) analysis, 7 core hub genes were identified, which were involved in diverse functions such as cell cycle progression ( CDK7 ) and mitochondrial function ( MPRL19 ). Quantitative real-time PCR (qRT-PCR) validation revealed that two candidate genes ( GPT and MRPL19 ) exhibited significantly higher expression levels in heat-tolerant individuals compared with heat-sensitive individuals. Functional annotation indicated that these candidate genes participate in biological processes related to heat stress responses. Our findings provide new insights into the genetic architecture underlying heat tolerance in Chinese mitten crab and establish a foundation for marker-assisted selection programs aimed at developing heat-tolerant strains for aquaculture. • The first GWAS was conducted for thermal response in Eriocheir sinensis . • 20 significant SNPs and 362 candidate genes associated with heat tolerance were detected. • GWAS identified candidate genes ( GPT and MRPL19) linked to heat-tolerant. • Heat stress significantly affected amino acid metabolism and mitochondrial function. • Results will contribute to the breeding of heat tolerant E. sinensis based on genomics.