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Front. Genet. | doi: 10.3389/fgene.2019.01167

Genome-wide association mapping and gene expression analyses reveal genetic mechanisms of disease resistance variations in Cynoglossus semilaevis

 QIAN ZHOU1,  Zhencheng Su2,  Yangzhen Li1, Yang Liu1, Lei Wang1, Sheng Lu1, Shuangyan Wang1, Tian Gan1, Feng Liu1, Xun Zhou1, Min Wei1,  Guangjian Liu2* and  Songlin Chen1*
  • 1Yellow Sea Fisheries Research Institute (CAFS), China
  • 2Novogene Bioinformatics Technology Co., Ltd, China

The sustainable development of aquaculture has been impeded by infectious diseases worldwide. However, the genomic architecture and the genetic basis underlying the disease resistance remain poorly understood, which severely hampers both the understanding of the evolution of fish disease resistance traits and the prevention of these diseases in the aquaculture community. Cynoglossus semilaevis is a representative and commercially-important flatfish species. Here we combined GWAS and Fst and nucleotide diversity filtration to identify loci important for the disease resistance. Based on 1,076,778 SNPs identified from 650 Gb genome re-sequencing data of 505 individuals, we detected 33 SNPs significantly associated with disease resistance and 79 candidate regions after filtration steps. Both the allele frequencies and genotype frequencies of the associated loci were significantly different between the resistant and susceptible fish, suggesting a role in the genetic basis of disease resistance. The SNP with strongest association with disease resistance was located in Chr 17, at 145 bp upstream of fblx19 gene, and overlapped with the major QTL previously identified. Several genes, such as plekha7, nucb2 and fgfr2, were also identified to potentially play roles in the disease resistance. Furthermore, the expression of some associating genes were likely under epigenetic regulations between the bacterial resistant and susceptible families. These results provide insights into the mechanism that enable variation of disease resistance to bacterial pathogen infection. The identified polymorphisms and genes are valuable targets and molecular resources for disease resistance and other traits, and for advanced breeding practice for superior germplasm in fish aquaculture.

Keywords: genome re-sequencing, GWAS, Disease Resistance, Cynoglossus semilaevis, Gene Expression, Fst and nucleotide diversity filtration

Received: 19 Mar 2019; Accepted: 23 Oct 2019.

Copyright: © 2019 ZHOU, Su, Li, Liu, Wang, Lu, Wang, Gan, Liu, Zhou, Wei, Liu and Chen. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

* Correspondence:
Dr. Guangjian Liu, Novogene Bioinformatics Technology Co., Ltd, Beijing, Beijing Municipality, China,
Prof. Songlin Chen, Yellow Sea Fisheries Research Institute (CAFS), Qingdao, Shandong Province, China,