Genomic dissection of high-temperature resistance in hybrid oysters (Crassostrea gigas ♀ × C. angulata ♂) using SNP- and InDel-GWAS based on whole-genome resequencing

Global warming has significantly impacted the aquaculture industry, creating an urgent need for genetic analysis of traits related to heat tolerance. Oysters are economically vital shellfish, but high summer temperatures cause severe mortality, challenging global aquaculture. Understanding the genetic basis of high-temperature tolerance in oysters and advancing genetic improvement strategies are crucial for rapidly developing heat-tolerant strains. The hybrid lines (GA) between the Pacific oysters (Crassostrea gigas) ♀ and the Fujian oysters (Crassostrea angulata) ♂, as well as the self-cross progeny of these hybrids, have exhibited significant heat tolerance and notable phenotypic variation, making them excellent materials for genetic analysis. In this study, GA oysters that had undergone high-temperature selection for four generations were used as samples and subjected to heat stress experiments at their semi-lethal temperature (LT₅₀, 42 °C). Genotyping through whole-genome resequencing identified 9,692,180 single nucleotide polymorphisms (SNPs) and 3,883,291 insertions/deletions (InDels). Genome-wide association studies (GWAS) revealed 17 SNPs and 14 InDels significantly associated with high-temperature resistance, identifying 25 candidate genes through gene annotation. Gene Ontology (GO) enrichment analysis indicated that the candidate genes are associated with key biological processes such as phosphorylation, centrosome, kinase activity, and molecular adaptor activity. The focused 12 candidate genes were validated by RT-PCR in the sensitive and tolerant groups, identifying four essential regulatory genes (TIMP3, THH, SLC38A11, TRIM2) associated with protein synthesis, degradation, cell stability and other physiological processes related to heat tolerance in oysters. These findings provide valuable insights for marker-assisted selection (MAS) and genomic selection (GS) breeding of heat-tolerant oysters.