Unveiling genetic basis and candidate genes for low-temperature tolerance in golden pompano (Trachinotus ovatus)

Low-temperature stress is one of the major challenges affecting global aquaculture production. Golden pompano ( Trachinotus ovatus ) is a commercially important marine species widely cultured in tropical and subtropical regions. However, the genetic basis of low-temperature tolerance in this species remains unexplored. Here, we conducted a genome-wide association study (GWAS) to identify key genes associated with low-temperature tolerance traits in golden pompano. A total of one significant SNP ( P < 2.38 × 10 −8 ) and 31 suggestive SNPs ( P < 1.0 × 10 −5 ) were detected, and the most significant SNP was located in Chr20. A 10-kb window analysis around these SNPs identified 28 protein-coding genes, most of which were related to low-temperature response. Among them, the most significant SNP was exactly located within the gpr64 gene, encoding an adhesion G protein-coupled receptor. Genotype analysis revealed that gpr64 was significantly associated with low-temperature tolerance. In addition, linkage disequilibrium (LD) block analysis and gene expression profiling under low-temperature stress identified cacna2d3 (Calcium Voltage-Gated Channel Auxiliary Subunit Alpha2delta 3) and rbms3 (RNA Binding Motif Single Stranded Interacting Protein 3) as additional candidate genes. A natural allelic variation ( P < 1.0 × 10 −5 ) in the promoter region of rbms3 was found within a CTCF (CCCTC-binding factor) binding sites. Dual-luciferase assay further showed that this allelic variation caused CTCF-dependent differences in rbms3 promoter activity. Collectively, our findings contribute to the understanding of the genetic mechanism underlying low-temperature tolerance in golden pompano and provide a valuable genetic resource for selective breeding of low-temperature tolerant strains.