title: A genome-wide association study in catfish reveals the presence of functional hubs of related genes within QTLs for columnaris disease resistance.
abstract: BACKGROUND
  Columnaris causes severe mortalities among many different wild and cultured freshwater fish species, but understanding of host resistance is lacking. Catfish, the primary aquaculture species in the United States, serves as a great model for the analysis of host resistance against columnaris disease. Channel catfish in general is highly resistant to the disease while blue catfish is highly susceptible. F2 generation of hybrids can be produced where phenotypes and genotypes are segregating, providing a useful system for QTL analysis. To identify genes associated with columnaris resistance, we performed a genome-wide association study (GWAS) using the catfish 250 K SNP array with 340 backcross progenies derived from crossing female channel catfish (Ictalurus punctatus) with male F1 hybrid catfish (female channel catfish I. punctatus × male blue catfish I. furcatus).
  
  
  RESULTS
  A genomic region on linkage group 7 was found to be significantly associated with columnaris resistance. Within this region, five have known functions in immunity, including pik3r3b, cyld-like, adcyap1r1, adcyap1r1-like, and mast2. In addition, 3 additional suggestively associated QTL regions were identified on linkage groups 7, 12, and 14. The resistant genotypes on the QTLs of linkage groups 7 and 12 were found to be homozygous with both alleles being derived from channel catfish. The paralogs of the candidate genes in the suggestively associated QTL of linkage group 12 were found on the QTLs of linkage group 7. Many candidate genes on the four associated regions are involved in PI3K pathway that is known to be required by many bacteria for efficient entry into the host.
  
  
  CONCLUSIONS
  The GWAS revealed four QTLs associated with columnaris resistance in catfish. Strikingly, the candidate genes may be arranged as functional hubs; the candidate genes within the associated QTLs on linkage groups 7 and 12 are not only co-localized, but also functionally related, with many of them being involved in the PI3K signal transduction pathway, suggesting its importance for columnaris resistance.
authors.affiliation: 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, Auburn, AL, 36849, USA. xzg0008@auburn.edu.
authors.forename: Xin
authors.initials: X
authors.lastname: Geng
authors.affiliation: Department of Biostatistics, University of Alabama at Birmingham, Birmingham, AL, 35294, USA. jsha@uab.edu.
authors.forename: Jin
authors.initials: J
authors.lastname: Sha
authors.affiliation: 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, Auburn, AL, 36849, USA. szl0021@auburn.edu.
authors.forename: Shikai
authors.initials: S
authors.lastname: Liu
authors.affiliation: 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, Auburn, AL, 36849, USA. lzb0021@auburn.edu.
authors.forename: Lisui
authors.initials: L
authors.lastname: Bao
authors.affiliation: 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, Auburn, AL, 36849, USA. jzz0007@auburn.edu.
authors.forename: Jiaren
authors.initials: J
authors.lastname: Zhang
authors.affiliation: 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, Auburn, AL, 36849, USA. rzw0010@auburn.edu.
authors.forename: Ruijia
authors.initials: R
authors.lastname: Wang
authors.affiliation: 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, Auburn, AL, 36849, USA. jzy0026@auburn.edu.
authors.forename: Jun
authors.initials: J
authors.lastname: Yao
authors.affiliation: 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, Auburn, AL, 36849, USA. czl0020@auburn.edu.
authors.forename: Chao
authors.initials: C
authors.lastname: Li
authors.affiliation: 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, Auburn, AL, 36849, USA. jbfeng@shou.edu.cn.
authors.forename: Jianbin
authors.initials: J
authors.lastname: Feng
authors.affiliation: 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, Auburn, AL, 36849, USA. fzs0005@auburn.edu.
authors.forename: Fanyue
authors.initials: F
authors.lastname: Sun
authors.affiliation: 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, Auburn, AL, 36849, USA. lzs0023@auburn.edu.
authors.forename: Luyang
authors.initials: L
authors.lastname: Sun
authors.affiliation: 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, Auburn, AL, 36849, USA. czj0017@auburn.edu.
authors.forename: Chen
authors.initials: C
authors.lastname: Jiang
authors.affiliation: 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, Auburn, AL, 36849, USA. yzz0016@auburn.edu.
authors.forename: Yu
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: 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, Auburn, AL, 36849, USA. azc0028@auburn.edu.
authors.forename: Ailu
authors.initials: A
authors.lastname: Chen
authors.affiliation: 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, Auburn, AL, 36849, USA. dunhara@auburn.edu.
authors.forename: Rex
authors.initials: R
authors.lastname: Dunham
authors.affiliation: Department of Biostatistics, University of Alabama at Birmingham, Birmingham, AL, 35294, USA. dzhi@uab.edu.
authors.forename: Degui
authors.initials: D
authors.lastname: Zhi
authors.affiliation: 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, Auburn, AL, 36849, USA. liuzhan@auburn.edu.
authors.forename: Zhanjiang
authors.initials: Z
authors.lastname: Liu
mesh_terms: D000818:Animals; D002397:Catfishes / Q000235:genetics*; D060467:Disease Resistance / Q000235:genetics*; D005260:Female; D056726:Genetic Association Studies; D008040:Genetic Linkage; D055106:Genome-Wide Association Study; D023281:Genomics; D015810:Linkage Disequilibrium; D008297:Male; D009026:Mortality; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci