Transcriptome and Expression Profiling of Response to Acute Hypoxia in the Gill of Adult Catfish

Low oxygen levels (hypoxia) in water can adversely affect the performance and survival of aquaculture fish species. Such negative impacts include reduced metabolic rate, suppressed growth and also increased susceptibility to diseases. In the US, catfish is the major aquaculture species. In the catfish industry, channel catfish, blue catfish, and the channel catfish × blue catfish interspecific hybrid are all utilized, but channel catfish and the interspecific hybrid are the major genotypes. In spite of the very strong low oxygen tolerance of channel catfish, high mortalities can still happen due to hypoxia. In addition, use of aerators significantly increase the energy cost for production. Therefore, selection for low oxygen tolerance is one of the breeding objectives. Here we report the identification and characterization of hypoxia-related genes in catfish by analysis of RNA-Seq datasets. Genome expression profiles in the gill were determined between tolerant and susceptible fish with and without low oxygen challenges. A total of 376 million reads were obtained and assembled into contigs. The transcriptome assembly allowed identification of hypoxia-induced genes, and novel genes associated with low oxygen challenge. RNA-Seq data are being validated by quantitative real-time PCR. Gene set enrichment analysis and gene pathway analysis are being conducted to identify the related genes enriched in response to hypoxia. Because the backcross of F₁ hybrid fish was used, the RNA-Seq data also allowed us to determine the expressed SNP allele distributions. Apparently, strong differences existed between the tolerant fish and intolerant fish in their allele usages, indicating candidate genes important for low oxygen tolerance.