A genome-wide association study of resistance to Pseudomonas plecoglossicida infection in the large yellow croaker (Larimichthys crocea)
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Cultured large yellow croaker (Larimichthys crocea) is frequently infected by bacteria, thus developing small white granulomas in the spleen and kidneys with high mortality in a few days. We performed a genome-wide association study (GWAS) on the trait of resistance to Pseudomonas plecoglossicida infection in a large yellow croaker population in 222 extreme-phenotype samplings using the whole-genome resequencing technology. With the 254,110 detected SNPs for the trait, three candidate regions associated with disease resistance were found on chromosomes 3, 5 and 20. By combing our GWAS results with the biological functional analysis of immunity genes, we found that IL10, THBS1, IGSF21, IGR and IGH as well as IRF8, TRAIL, CC, TNF and LINGO1 are candidate genes of the disease resistance trait in the large yellow croaker. Moreover, after comparison with transcriptome sequencing data, we found that the candidate genes from GWAS were actually up-regulated or down-regulated. This is the first time that a GWAS combined with a transcriptome-wide study was performed on disease resistance to detect candidate loci and find potential functionally relevant genes in the large yellow croaker.
KeywordsGWAS Pseudomonas plecoglossicida Large yellow croaker Disease resistance
Thanks a lot for two reviewers’ thorough guidance and careful help. We thank Kun Ye, Shuangbin Xu and other colleagues in the laboratory that participated in fish sampling and measuring of the trait.
ZW conceived the research and revised the manuscript. LW drafted the manuscript and conducted the experiments. WW performed the SNP calling. LG performed the transcriptome analysis. LD conducted the GWAS. WL performed the data analysis. ZH extracted DNA. KY reared the fish. Two reviewers revised our manuscript and gave very valuable advice. All the authors read and approved the final manuscript.
Thanks for this work was supported by the Key Projects of the Xiamen Southern Ocean Research Centre (14GZY70NF34), China Agriculture Research System (CARS-47-G04), and South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences (FREU2016-05).
Compliance with ethical standards
The authors declare that they have no competing interests.
The sample collection and experiments in the study were approved by the Animal Care and Use Committee of Fisheries College of Jimei University (Animal Ethics approval no. 1067).
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