Application of genome-wide association studies in channel catfish to identify QTL associated with hypoxia tolerance

Abstract

Catfish is the dominant aquaculture species in the United States. The production of the domestic catfish industry rapidly increased in the last two decades. However, as imported catfish from Southeast Asia have kept increasing, the domestic catfish industry faces a great challenge in these few years. To compete with the imported catfish, the domestic catfish industry need to reduce the production costs and enhance the production efficiency by improving various performance traits. However, little information is known about the genetic architecture controlling economically important traits, which hinders marker-assisted selection. Hypoxia is common in aquaculture conditions because of high stocking densities. Although channel catfish (Ictalurus punctatus) is highly tolerant to low concentration of dissolved oxygen, hypoxia still causes enormous economic losses each year. Understanding how genetic architecture and environmental factors affect the hypoxia tolerance is of great interest to aquaculture. In this project, the aim was to investigate the effects of genetic background and environmental factors on hypoxia tolerance in channel catfish. Firstly, the effects of environmental factors such as gender and body size on hypoxia tolerance were investigated. Secondly, six strains of channel catfish were compared for their tolerance to hypoxic stress, including Marion Random, Marion Select, Thompson, Kansas Random, Kmix (Kansas × Kansas Select), and 103KS (NWAC 103 × Kansas Select). Thirdly, multiple within-strain and across-strain QTL were identified to be associated with the hypoxia tolerance in channel catfish by conducting a genome-wide association study (GWAS). Finally, genes within the associated genomic regions were identified for their potential involvement in responses to hypoxia. Six strains of channel catfish were compared for their hypoxia tolerance under a lethal level of dissolved oxygen (0.1 mg/L) by using survival analysis. 103KS and Marion S strains had significantly higher hypoxia tolerance, while Marion strain had the poorest hypoxia tolerance. In addition, effects of gender and body weight on hypoxia tolerance were also identified in catfish. Body weight was positively correlated with the tolerance to hypoxic stress when catfish were in relatively small size range (within 200 g). No significant difference of hypoxia tolerance was observed between female and male channel catfish. To reveal the genetic architecture of hypoxia tolerance in catfish, a GWA study was conducted to identify QTL for hypoxia tolerance using the catfish 250K SNP array with channel catfish families from six strains. Multiple significant and suggestive QTL were identified both across strains and within strains. One significant QTL and four suggestive QTL were identified across strains. Six significant QTL and many suggestive QTL were identified within strains. There were rare overlaps among the QTL identified within the six strains, suggesting a complex genetic architecture of hypoxia tolerance. Overall, within-strain QTL explained larger proportion of phenotypic variation than across-strain QTL. Many of genes within these identified genomic regions have known functions for regulation of oxygen metabolism and involvement in hypoxia responses. Pathway analysis indicated that most of these genes were involved in MAPK and/or PI3K/AKT/mTOR signaling pathways that were known to be important for hypoxia-mediated angiogenesis, cell proliferation, apoptosis and survival.