Genome-wide association analysis of intra-specific QTL associated with the resistance for enteric septicemia of catfish

Huitong Shi, Tao Zhou, Xiaozhu Wang, Yujia Yang, Chenglong Wu, Shikai Liu, Lisui Bao, Ning Li, Zihao Yuan, Yulin Jin, Suxu Tan, Wenwen Wang, Xiaoxiao Zhong, Guyu Qin, Xin Geng, Dongya Gao, Rex Dunham, Zhanjian "John" Liu

Research output: Contribution to journalArticle

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Abstract

Disease resistance is one of the most important traits for aquaculture industry. For catfish industry, enteric septicemia of catfish (ESC), caused by the bacterial pathogen Edwardsiella ictaluri, is the most severe disease, causing enormous economic losses every year. In this study, we used three channel catfish families with 900 individuals (300 fish per family) and the 690K catfish SNP array, and conducted a genome-wide association study to detect the quantitative trait loci (QTL) associated with ESC resistance. Three significant QTL, with two of located on LG1 and one on LG26, and three suggestive QTL located on LG1, LG3, and LG21, respectively, were identified to be associated with ESC resistance. With a well-assembled- and -annotated reference genome sequence, genes around the involved QTL regions were identified. Among these genes, 37 genes had known functions in immunity, which may be involved in ESC resistance. Notably, nlrc3 and nlrp12 identified here were also found in QTL regions of ESC resistance in the channel catfish × blue catfish interspecific hybrid system, suggesting this QTL was operating within both intra-specific channel catfish populations and interspecific hybrid backcross populations. Many of the genes of the Class I MHC pathway, for mediated antigen processing and presentation, were found in the QTL regions. The positional correlation found in this study and the expressional correlation found in previous studies indicated that Class I MHC pathway was significantly associated with ESC resistance. This study validated one QTL previously identified using the second and fourth generation of the interspecific hybrid backcross progenies, and identified five additional QTL among channel catfish families. Taken together, it appears that there are only a few major QTL for ESC disease resistance, making marker-assisted selection an effective approach for genetic improvements of ESC resistance.

Original languageEnglish (US)
Pages (from-to)1-14
Number of pages14
JournalMolecular Genetics and Genomics
DOIs
StateAccepted/In press - Jul 2 2018

Fingerprint

Catfishes
Quantitative Trait Loci
Genome-Wide Association Study
Sepsis
Ictaluridae
Disease Resistance
Antigen Presentation
Edwardsiella ictaluri
Industry
Genes
MHC Class I Genes
Aquaculture
Population
Single Nucleotide Polymorphism
Immunity
Fishes
Economics
Genome

Keywords

  • Channel catfish
  • ESC resistance
  • GWAS
  • Immunity
  • QTL

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics

Cite this

Genome-wide association analysis of intra-specific QTL associated with the resistance for enteric septicemia of catfish. / Shi, Huitong; Zhou, Tao; Wang, Xiaozhu; Yang, Yujia; Wu, Chenglong; Liu, Shikai; Bao, Lisui; Li, Ning; Yuan, Zihao; Jin, Yulin; Tan, Suxu; Wang, Wenwen; Zhong, Xiaoxiao; Qin, Guyu; Geng, Xin; Gao, Dongya; Dunham, Rex; Liu, Zhanjian "John".

In: Molecular Genetics and Genomics, 02.07.2018, p. 1-14.

Research output: Contribution to journalArticle

Shi, H, Zhou, T, Wang, X, Yang, Y, Wu, C, Liu, S, Bao, L, Li, N, Yuan, Z, Jin, Y, Tan, S, Wang, W, Zhong, X, Qin, G, Geng, X, Gao, D, Dunham, R & Liu, ZJ 2018, 'Genome-wide association analysis of intra-specific QTL associated with the resistance for enteric septicemia of catfish', Molecular Genetics and Genomics, pp. 1-14. https://doi.org/10.1007/s00438-018-1463-0
Shi, Huitong ; Zhou, Tao ; Wang, Xiaozhu ; Yang, Yujia ; Wu, Chenglong ; Liu, Shikai ; Bao, Lisui ; Li, Ning ; Yuan, Zihao ; Jin, Yulin ; Tan, Suxu ; Wang, Wenwen ; Zhong, Xiaoxiao ; Qin, Guyu ; Geng, Xin ; Gao, Dongya ; Dunham, Rex ; Liu, Zhanjian "John". / Genome-wide association analysis of intra-specific QTL associated with the resistance for enteric septicemia of catfish. In: Molecular Genetics and Genomics. 2018 ; pp. 1-14.
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AU - Zhong, Xiaoxiao

AU - Qin, Guyu

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