Genome-wide association analysis reveals SNPs and candidate genes associated with thermal tolerance in the Yesso scallop (Patinopecten yessoensis)

The Yesso scallop ( Patinopecten yessoensis ) is a commercially important aquaculture species in northern China. However, as a cold-water species, it has been severely impacted by the continuous rise in seawater temperatures caused by global warming. Frequent high summer temperatures have recently triggered mass mortality events of the species, resulting in substantial economic losses. To reveal single nucleotide polymorphisms (SNPs) and genes related to thermal tolerance, this study conducted a long-term thermal stress experiment on a Yesso scallop population consisting of 1000 individuals, using a gradual temperature elevation method, and thermal-sensitive and thermal-tolerant groups were distinguished. Subsequently, whole-genome resequencing was performed on 100 individuals from each group. A total of 2543.33 Gb of high-quality sequencing data was obtained, corresponding to an average depth of 11.77 × . A total of 14,769,450 SNPs and 2171,314 Indels were detected in the Yesso scallop genome. Through genome-wide association studies (GWAS), 16 SNPs were identified as being suggestively associated with thermal tolerance trait ( p < 10 −6 ). There were 56 candidate genes linked with these SNPs. Functional enrichment analysis of the candidate genes revealed GO functions and KEGG pathways related to fatty acid synthesis, elongation, and desaturation were significantly enriched. Furthermore, these processes were significantly regulated under thermal stress in the gill transcriptomes of the Yesso scallop, suggesting the potential involvement of fatty acid metabolism in thermal tolerance. Expression patterns of eight candidate genes under thermal stress were further validated by qRT-PCR. The present research offers new perspectives on the molecular mechanisms underlying thermal adaptation in scallops and provides important candidate loci for the molecular breeding of thermal-tolerant Yesso scallops.