Association analysis of intraspecific ESC resistance QTL and identification of landscape of promoters in catfish on the genome-wide level

Abstract

Catfish is the most important aquaculture species, accounting for over 50% of aquaculture production in the US. However, disease problems threaten the survival of the catfish industry. Bacterial diseases are a major issue for the catfish industry, with enteric septicemia of catfish (ESC) being the most severe, causing enormous economic losses every year. ESC is caused by the bacterial pathogen Edwardsiella ictaluri, which is a rod-shape and gram-negative bacterium. Genetic architecture and detailed molecular mechanism of ESC disease resistance in catfish can be studied by genome-wide association study (GWAS), which detected the genomic markers significantly associated with the phenotypic variation and then, identified the associated genomic regions (QTL) and potentially influenced genes. Two related, but separate studies of catfish genome analysis have been conducted in this dissertation. In the first study, GWAS was conducted to detect the quantitative trait loci (QTL) associated with ESC resistance in channel catfish. Three significant QTL, two of them located on LG1 and one on LG26, and three suggestive QTL located on LG1, LG3, and LG21, respectively, were identified. This study validated one QTL previously identified using interspecific hybrid backcross progenies and identified additional QTL among channel catfish families. There were only a few major QTL for ESC disease resistance, potentially, making marker-assisted selection an effective approach for genetic improvement of ESC resistance in channel catfish. In the second study, applicability of ChIP-Seq technology in catfish have been confirmed. Genome-wide tri-methylated histone H3 lysine 4 (H3K4me3) profiles were generated using ChIP-Seq technology and the landscape of catfish promoter sequences determined. A total of 14,464 active promoters and 14,346 genes regulated by these promoters were identified. The catfish promoters were characteristic of low GC-content and specific structure of TATA-boxes. A total of 331 and 363 protein-coding genes were regulated by tissue-specific promoters in liver and intestine, respectively. This analysis laid a solid foundation for further analysis of histone modification epigenetic regulators in catfish, and their involvement in regulation of phenotypes such as growth, stress tolerance, and disease resistance in the future.