A Genome-wide Association Study for Low-oxygen Tolerance in Catfish using the 250K SNP Array

Low-oxygen tolerance is a major performance trait for aquaculture because hypoxia can cause major mortalities. In addition, use of aerators increases production costs. Catfish, a dominant aquaculture species in the US, is highly tolerant to low oxygen, but enormous losses are still caused by exposures to hypoxia each year. Therefore, improving low-oxygen tolerance through genetics is of great interest to the catfish industry. To identify loci associated with hypoxia tolerance, in this work we conducted a genome-wide association study (GWAS) using the catfish 250K SNP array with 376 channel catfish from six different strains, including Marion Random, Marion Select, Thompson, Kansas Random, Kmix (Kansas × Kansas Select), and 103KS (NWAC 103 × Kansas Select). A genomic region on linkage group 6 was found to be significantly associated with low-oxygen tolerance. In addition, six additional suggestively associated QTL regions were identified on linkage group 4, linkage group 5, linkage group 10 and linkage group 12, respectively. The low-oxygen tolerance associated SNPs and candidate genes discovered in this study provided new insights into selection strategies for improving catfish brood stocks in aquaculture. Furthermore, some of these candidate genes are involved in MAPK, PI3K/AKT and mTOR signaling pathways, which are essential to hypoxia-mediated apoptosis, cell proliferation and tumor angiogenesis in cancer tissues, suggesting evolutionary conservation of functions of these genes across a broad range of species.