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United States Department of Agriculture

Agricultural Research Service

Research Project: Utilization of Genomics for Improving Production Traits in Cool and Cold Water Aquaculture

Location: Cool and Cold Water Aquaculture Research

Title: Isolation of innate immune response genes, expression analysis, polymorphism identification and development of genetic marker for linkage analysis in common carp (Cyprinus carpio)

Authors
item Kongchum, Pawapol -
item Hallerman, Eric -
item Hulata, Gideon -
item David, Loir -
item Palti, Yniv

Submitted to: Plant and Animal Genome Conference
Publication Type: Abstract Only
Publication Acceptance Date: November 1, 2010
Publication Date: January 15, 2011
Citation: Kongchum, P., Hallerman, E., Hulata, G., David, L., Palti, Y. 2011. Isolation of innate immune response genes, expression analysis, polymorphism identification and development of genetic marker for linkage analysis in common carp (Cyprinus carpio). Plant and Animal Genome Conference. W053.

Technical Abstract: Common carp are economically important foodfish worldwide. Over the past few years, carp aquaculture has suffered from enormous losses to a disease caused by cyprinid herpesvirus 3 (CyHV-3). A recent study reported that common carp strains/crossbreds have differential resistance to CyHV-3, suggesting that genetic factors influence susceptibility to the disease. To develop molecular tools for breeding CyHV-3-resistant carp, we isolated innate antiviral immune response genes from common carp using degenerate primers. We then developed gene-specific primers to PCR-amplify gene fragments, and subsequently cloned and sequenced the amplified products to identify SNPs. Our sequence analyses showed that TLR3, TLR7, MyD88 and TRAF6 genes are duplicated in common carp. We identified SNPs in 14 genes and genotyped them using the SNaPshot method to evaluate their allele frequencies and Mendelian inheritance. Of 67 polymorphic markers, 23 from 12 genes were informative in an F2 mapping family. In a concurrent effort, these SNPs were analyzed with a set of approximately 300 microsatellites to generate a second generation genetic map and to identify QTL affecting resistance to CyHV-3. The ability of TLR9 to detect viral DNA and the important roles of MyD88 and TRAF6 in the TLR9 signaling pathway make them candidates for host antiviral response to CyHV-3. To further elucidate possible functions of these genes, we isolated full-length cDNA of the common carp (cc) TLR9, ccMyD88a/b and ccTRAF6a/b, and determined their mRNA expression in a panel of tissues. We found differential expression of the ccMyD88 and ccTRAF6 duplicates in red and white muscle tissues, suggesting that the paralogs of each gene have evolved and attained a new non-immune function.

Last Modified: 10/31/2014
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