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United States Department of Agriculture

Agricultural Research Service

Research Project: IDENTIFICATION AND CHARACTERIZATION OF GENES AFFECTING COOL AND COLD WATER AQUACULTURE PRODUCTION Title: SNP discovery and marker development for disease resistance candidate genes in common carp (Cyprinus carpio)

Authors
item Kongchum, Pawapol -
item Hallerman, Eric -
item David, Lior -
item Hulata, Gideon -
item Kotler, Moshe -
item Palti, Yniv

Submitted to: International Symposium on Genetics in Aquaculture
Publication Type: Abstract Only
Publication Acceptance Date: June 22, 2009
Publication Date: June 22, 2009
Citation: Kongchum, P., Hallerman, E., David, L., Hulata, G., Kotler, M., Palti, Y. 2009. SNP discovery and marker development for disease resistance candidate genes in common carp (Cyprinus carpio). International Symposium on Genetics in Aquaculture. Paper No. 001.

Technical Abstract: Single nucleotide polymorphisms (SNPs) in immune response genes have been reported as markers of susceptibility to infectious diseases in human and livestock. A disease caused by cyprinid herpes virus 3 (CyHV-3) is highly contagious and virulent in common carp. With the aim to investigate the genetic basis of CyHV-3 resistance and develop the molecular tools for breeding disease resistant broodstock, we have identified SNPs in candidate genes for viral disease resistance and developed SNP markers for genetic mapping of CyHV-3 resistance. The genes that we screened for SNPs included toll-like receptors (TLRs) 3, 7 and 9 and genes in the TLR signaling pathways such as TRAF6, I-IFN, TNFa and IL-1B. The SNP discovery panel was composed of fish from two domesticated strains and one wild population of common carp and from koi carp. Where possible, PCR primers were designed from publicly available carp gene sequences. For the other genes we used degenerate primers that we developed from conserved peptide sequences. PCR amplification, cloning and sequencing were carried out using genomic DNA of three samples from each strain. Putative SNPs were then genotyped in a larger panel (N = 29) using the SNaPshot method. The number of putative SNPs we identified per genes varied from 3 in 569 bp (I-IFN) to 65 in 975 bp (TLR7). The large number of SNPs in the latter suggests that it is duplicated in the carp genome which is thought to be allotetraploid. We are currently assessing analysis protocols to improve our ability to discriminate between paralogous and allelic sequence variation.

Last Modified: 10/20/2014
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