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GWAS analysis of QTL for enteric septicemia of catfish and their involved genes suggest evolutionary conservation of a molecular mechanism of disease resistance

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Abstract

Disease problems cause major economic losses for the aquaculture industries. In catfish, enteric septicemia of catfish (ESC), caused by the bacterial pathogen Edwardsiella ictaluri, is the leading disease problem, causing tens of millions of dollars of annual economic losses. In this study, we conducted a genome-wide association study to determine quantitative trait loci (QTL) for resistance against ESC using an interspecific hybrid system. Five hundred fish were used in the analysis and 192 phenotypic extremes were used for genotyping with the catfish 250K SNP arrays. A genomic region on linkage group (LG) 1 was found significantly associated with ESC disease resistance. In addition, two suggestively associated QTL for ESC resistance were identified on LG 12 and LG 16. The nlrc3 duplicates were identified within all the three QTL, suggesting their importance in association with the QTL. Within the significant QTL on LG 1, 16 genes with known functions in immunity were identified. Of particular interest is the nck1 gene nearby the most significantly associated SNP. Nck1 was known to function as an adaptor to facilitating the pathogenesis of enteropathogenic Escherichia coli (EPEC) in humans. E. ictaluri and EPEC pathogens belong to the same bacterial family and share many common characteristics. The fact that nck1 is mapped in the QTL and that it was significantly upregulated in channel catfish intestine after ESC challenge suggested its candidacy of being involved in resistance/susceptibility of ESC.

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Acknowledgements

This project was supported by Agriculture and Food Research Initiative Competitive Grant No. 2015-67015-22975 from the USDA National Institute of Food and Agriculture (NIFA). Tao Zhou is supported by a scholarship from the China Scholarship Council (CSC).

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  1. Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University, 202 Samford Hall, Auburn, AL, 36849-5112, USA

    Tao Zhou, Shikai Liu, Xin Geng, Yulin Jin, Chen Jiang, Lisui Bao, Jun Yao, Yu Zhang, Jiaren Zhang, Luyang Sun, Xiaozhu Wang, Ning Li, Suxu Tan & Zhanjiang Liu

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438_2016_1269_MOESM1_ESM.tif

Fig. S1 Manhattan plot of genome wide association analysis for ESC disease resistance. GWAS was conducted by using family based association test for quantitative trait (QFAM) (TIFF 1761 kb)

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Zhou, T., Liu, S., Geng, X. et al. GWAS analysis of QTL for enteric septicemia of catfish and their involved genes suggest evolutionary conservation of a molecular mechanism of disease resistance. Mol Genet Genomics 292, 231–242 (2017). https://doi.org/10.1007/s00438-016-1269-x

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