SNP discovery and development of genetic markers for mapping innate immune response genes in common carp (Cyprinus carpio)

Pawapol Kongchum, Yniv Palti*, Eric M. Hallerman, Gideon Hulata, Lior David

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

85 Scopus citations


Single nucleotide polymorphisms (SNPs) in immune response genes have been reported as markers for susceptibility to infectious diseases in human and livestock. A disease caused by cyprinid herpesvirus 3 (CyHV-3) is highly contagious and virulent in common carp (Cyprinus carpio). With the aim to develop molecular tools for breeding CyHV-3-resistant carp, we have amplified and sequenced 11 candidate genes for viral disease resistance including TLR2, TLR3, TLR4ba, TLR7, TLR9, TLR21, TLR22, MyD88, TRAF6, type I IFN and IL-1β. For each gene, we initially cloned and sequenced PCR amplicons from 8 to 12 fish (2-3 fish per strain) from the SNP discovery panel. We then identified and evaluated putative SNPs for their polymorphisms in the SNP discovery panel and validated their usefulness for linkage analysis in a full-sib family using the SNaPshot method. Our sequencing results and phylogenetic analyses suggested that TLR3, TLR7 and MyD88 genes are duplicated in the common carp genome. We, therefore, developed locus-specific PCR primers and SNP genotyping assays for the duplicated loci. A total of 48 SNP markers were developed from PCR fragments of the 13 loci (7 single-locus and 3 duplicated genes). Thirty-nine markers were polymorphic with estimated minor allele frequencies of more than 0.1. The utility of the SNP markers was evaluated in one full-sib family and revealed that 20 markers from 9 loci segregated in a disomic and Mendelian pattern and would be useful for linkage analysis.

Original languageAmerican English
Pages (from-to)356-361
Number of pages6
JournalFish and Shellfish Immunology
Issue number2
StatePublished - Aug 2010

Bibliographical note

Funding Information:
The authors thank Kristy Shewbridge, Roseanna Long and Brian Smith for their technical assistance and Dr. Sylvie Quiniou for her advice on how to design degenerate PCR primers. This work was funded by the US-Israel BARD Program grant no. IS-3997-07 . The Royal Thai Government is acknowledged for the provision of a scholarship to P.K. E.M.H. is partially supported by Virginia Agricultural Experimental Station through the USDA-CSREES Hatch Program.


  • Cyprinus carpio
  • Disease resistance
  • Genetic markers
  • Immune response genes
  • SNP


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