Genome-wide association and transcriptome analysis provide the SNPs and molecular insights into the hypoxia tolerance in large yellow croaker (Larimichthys crocea)

The large yellow croaker (Larimichthys crocea) is a commercially important marine fish indigenous to the southeastern coast of China. Cultured L. crocea is frequently subjected to hypoxia which causes huge economic losses to the aquaculture industry. Therefore, it is crucial to elucidate the molecular mechanisms of hypoxia tolerance in L. crocea. Here, we combined a genome-wide association study (GWAS) and transcriptome analysis to reveal single-nucleotide polymorphisms (SNPs) and the mechanisms by which they regulate hypoxia tolerance in L. crocea. We used liquid chips to genotype 400 L. crocea individuals, obtained 120,815 high-quality SNPs, identified seven SNPs with significant suggestive association levels, and found a significant peak on chromosome 1. We then combined the potential candidate genes obtained from GWAS with the differentially expressed genes (DEGs) obtained by transcriptome sequencing. We found that the genes and processes related to glucose transport and metabolism, erythropoiesis, ion regulation, DNA replication and repair, and cell cycle were critical to hypoxia adaptation in L. crocea. We also identified the gene lias that might regulate hypoxia-inducible factor (HIF)-1α. The results of the present study provided insight into the molecular mechanisms of hypoxia tolerance in fish and may facilitate the genetic selection and breeding of hypoxia tolerance in L. crocea. •We identified candidate genes by GWAS and DEGs by transcriptome analyses.•Seven SNPs with significant suggestive association levels were identified.•Molecular mechanisms regulating hypoxia tolerance of L. crocea were elucidated.