Genetic analysis of loci controlling heat tolerance and ESC disease resistance in catfish

Abstract

Catfish is one of the main aquaculture species in the US. However, the catfish industry is under the threat of various of environmental stresses and diseases, with heat stress and ESC are two major representatives. One promising strategy for reducing the magnitude of the threats is to select and develop catfish lines that are genetically resistant to heat stress and ESC disease. Understanding the fundamental mechanism conferring tolerance to heat stress and ESC disease have been studies for decades, and it is of great essential for genetic enhancement programs. However, it is still far from unrevealing the causal genes and genomics locus responsible for these performance traits. In this dissertation, I aim to characterize genes and genomic loci controlling heat tolerance and ESC disease resistance in catfish using integrated genetic, genomic and transcriptomic analyses. Firstly, a genome-wide association study (GWAS) identified three significant SNP markers conferring response to heat stress at the genome-wide significance level in F2 hybrid catfish. The SNP located on linkage group 14 explained 12.1% of phenotypical variation. The other two SNPs located on linkage group 16 explained 11.3% and 11.5% of phenotypical variation, respectively. A total of 14 genes with heat stress related functions were detected within the significant associated regions, with the centrality of genes involved in protein degradation process through ubiquitination pathway. Secondly, a bulked segregant RNA-Seq (BSR-Seq) analysis was conducted to profile DEGs and map ESC resistant QTLs in channel catfish using both liver and intestine tissues. Transcriptomic profiling analysis revealed divergent cellular responses between liver and intestine after infection, demonstrating they could collaborate closely while keep hemostasis using own specific strategies and potential unique mechanisms after infection. Five significant SNPs with large ED values were identified, with three significant SNPs were from liver and physically linked on LG1, the other two were from intestine and located on LG12 and LG26, respectively. Collectively, these significant SNPs suggest three associated QTLs with ESC resistance, which are successfully verified our previous GWAS studies. Eleven genes were found to be differentially regulated between resistant fish and susceptible fish within the three QTL regions, indicating their important involvements in disease resistance. Of particular interest is the Apo-14 kDa gene displayed both differentially up-regulation and significantly allelic segregation of SNP between resistant fish and susceptible fish, indicating Apo-14 kDa could be a promising candidate gene involved in ESC resistance. Overall, my research identified significantly SNPs, genomic regions and potential candidate genes associated with heat stress and ESC resistance by using GWAS and BSR-Seq, respectively. GWAS and BSR-Seq are approved as two major efficient and powerful approaches to mapping genomic loci responsible for many catfish performance traits. The associated SNPs could be promising candidates for selecting heat-tolerant or ESC resistance catfish lines after validating their effects on larger and various catfish populations. The isolation, functional study and regulation networks of these potential candidate genes will be the focus in future study, which will facilitate the better knowledge of heat stress and ESC resistance in catfish.