Genomics-assisted introgression of viral resistance in commercial common carp strains

• Published in: Journal of animal science Vol. 94; pp. 170 - 171
• Main Authors: Tadmor-Levi, R, Asulin, E, David, L, Hulata, G
• Format: Journal Article
• Language: English
• Published: Champaign Oxford University Press 01-09-2016
• Subjects: Animal breeding; Aquaculture; Breeding; Breeding of animals; Carp; Cyprinus carpio; Fish; Fish diseases; Gene mapping; Gene sequencing; Genomics; Genotyping; Heritability; Immune response; Immune system; Markers; Progeny; Quantitative trait loci; Strains (organisms); Viruses; Zebrafish
• ISSN: 0021-8812; 1525-3163

Viral fish diseases pose a major global threat to aquaculture. Breeding resistant fish strains is the most sustainable solution to this problem. Cyprinid herpes virus-3 (CyHV-3/KHV) is a dsDNA virus that inflicts massive mortalities on commercial common carp (Cyprinus carpio L.) and Koi strains around the world. CyHV-3 resistance was identified in a feral carp strain that does not fit commercial aquaculture. Using a CyHV-3 disease model we established in the lab, we screened families of different strains and found considerable variation in susceptibility levels between families and strains. We progressed in family-based selection trials to continuously produce resistant and susceptible families for research and breeding purposes. Furthermore, we found good correspondence between the level of resistance in the family of the parent and that in its progeny, indicating resistance has good heritability. By analyzing viral loads, we found that resistant fish restrain the viral spread in their bodies better than susceptible fish, suggesting that in this case, resistance reflects a difference in the function of their immune response. To enhance the selection program and to understand the genetic basis of resistance, we identified quantitative trait loci (QTLs) associated with resistance. We adopted the genotyping-by-sequencing (GBS) approach to carp and genotyped individuals from two semiresistant families. From over 25,000 markers with Mendelian segregation, almost 9,000 were shared by both families. We constructed a high-density genetic map consisting of 48 linkage groups and spanning 5,142 cM, and mapped on it 192 resistance associated markers that were grouped into three QTLs. Two QTLs were shared by both families, and we are confirming these associations in several other families. Finding multiple QTLs validated our phenotypic results, implying that CyHV-3 resistance is a complex trait. Markers in validated QTLs will therefore assist future breeding. Due to the preliminary state of the common carp genome, we are using the GBS tag sequences for mapping the QTL regions to the scaffolds of the duplicated carp genome. Additionally, we are using comparative genomics to the closely related zebrafish to identify candidate genes in these QTLs. Our research will support breeding of resistant common carp strains and enhance our understanding of fish immunogenetics.