I would like to congratulate our third and final winner of the 2017-18 Abstract Competition, Suxu Tan, a current PhD Student at Auburn University. Our first and second place winners, Michael Iacocca and Nicole Weaver, performed their research using VarSeq. Suxu, however, used SVS to conduct the research in his paper ‘GWAS analysis of QTL for resistance against Edwardsiella ictaluri in F2 interspecific hybrid catfish’.
Suxu will be sharing his research with the community via webcast on March 14th, 12:00 EST. If you’re interested in joining us for this event, you can register here.
Suxu’s Abstract:
Infectious diseases pose significant threats to the catfish industry. Enteric septicemia of catfish (ESC) caused by Edwardsiella ictaluri is the most devastating disease for catfish aquaculture, causing huge economic losses annually. Channel catfish and blue catfish exhibit great contrast in resistance against ESC, with blue catfish being highly resistant. As such, the interspecific hybrid backcross progenies provide an ideal system for the analysis of resistance QTL. In this study, we conducted GWAS analysis to locate genomic regions associated with ESC resistance by selectively genotyping F2 backcross families with the catfish 690K SNP arrays. Two genomic regions on linkage group (LG) 1 and LG23 were determined to be associated with ESC resistance as revealed by EMMAX in SVS and QFAM in PLINK. A number of genes within QTL have known functions in immunity, making them potential candidates as disease resistance genes. For instance, seven genes on LG1 (nck1, agtr1, trpc1, abi1, apbb1ip, actr3b, and vav3) and three genes on LG23 (mrc1l, prkcq, and gata3) were involved in immune-related functions. These genes mainly function in signaling pathways of phagocytosis and T-cell activation, suggesting their roles in disease resistance. This study demonstrated the power of GWAS analysis for the identification of QTL in the hybrid system. We previously reported one QTL in LG1 using fourth generation of backcross families, which was validated here in the F2 backcross families, suggesting that this QTL is operating in various populations of a broad genetic background, making it useful for application in marker-assisted selection.