Location: Cool and Cold Water Aquaculture ResearchTitle: SNP discovery and development of genetic markers for mapping immune response genes in common carp (Cyprinus carpio)) Author
Submitted to: Fish and Shellfish Immunology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/19/2010
Publication Date: 6/1/2010
Citation: Kongchum, P., Palti, Y., Hallerman, E., Hulata, G., David, L. 2010. SNP discovery and development of genetic markers for mapping immune response genes in common carp (Cyprinus carpio). Fish and Shellfish Immunology. 29:356-361. Interpretive Summary: Common carp is an economically important food fish that has the longest history of domestication and is cultured worldwide. Fancy carp or koi are members of a subgroup of this species and are an important component of the U.S. aquaculture industry. Over the past few years, common carp and koi production enterprises have suffered from enormous losses due to disease outbreaks caused by cyprinid herpes virus-3 (CyHV-3). Toll-like receptors (TLRs) are a family of transmembrane proteins that recognize conserved pathogen structures to induce innate immune effector molecules. In vertebrates, TLRs can also distinguish among classes of pathogens and serve an important role in orchestrating the appropriate adaptive immune responses. Detailed mapping and gene annotation of TLR genes in common carp and koi and the development of genetic markers for the different TLR genes will provide useful tools for genetic improvement of disease resistance in this economically important carp species.
Technical Abstract: 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 sequenced PCR fragments from 11 candidate genes for viral disease resistance and identified SNPs in 10 genes. Candidate genes that we screened for SNPs included TLR2, TLR3, TLR4a, TLR7, TLR9, TLR21, TLR22, MyD88, TRAF6, type I IFN and IL-1ß. For each gene, we initially screened a panel of common carp and koi strains for putative SNPs by PCR cloning and sequencing. We then evaluated putative SNPs for polymorphism and usefulness for linkage analysis in the SNP discovery panel and in a full-sib family using the SNaPshot method. Phylogenetic analyses of the coding sequences of TLR3 and TLR7 revealed that they likely are duplicated in the carp genome. In addition, intron size differences between two MyD88 gene fragments suggest that this locus is also duplicated in common carp. 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.