Genet. Sel. Evol. 39 (2007) 319-340
DOI: 10.1051/gse:2007006

Genetic diversity and population structure inferred from the partially duplicated genome of domesticated carp, Cyprinus carpio L.

Lior David^{a, b}, Noah A. Rosenberg^c, Uri Lavi^d, Marcus W. Feldman^b and Jossi Hillel<sup>e

a</sup>  Department of Animal Sciences, Faculty of Agricultural, Food and Environmental Quality Sciences, The Hebrew University of Jerusalem, P.O. Box 12, Rehovot, 76100, Israel
^b  Department of Biological Sciences, Stanford University, Stanford, CA 94305, USA
^c  Department of Human Genetics, Bioinformatics Program, and the Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109-2218, USA
^d  Institute of Horticulture, ARO-Volcani Center, P.O. Box 6, Bet-Dagan, 50250, Israel
^e  The Robert H. Smith Institute of Plant Sciences & Genetics, Faculty of Agricultural, Food and Environmental Quality Sciences, The Hebrew University of Jerusalem, P.O. Box 12, Rehovot, 76100, Israel

(Received 10 May 2006; accepted 8 December 2006; published online 14 April 2007)

Abstract - Genetic relationships among eight populations of domesticated carp (Cyprinus carpio L.), a species with a partially duplicated genome, were studied using 12 microsatellites and 505 AFLP bands. The populations included three aquacultured carp strains and five ornamental carp (koi) variants. Grass carp (Ctenopharyngodon idella) was used as an outgroup. AFLP-based gene diversity varied from 5% (grass carp) to 32% (koi) and reflected the reasonably well understood histories and breeding practices of the populations. A large fraction of the molecular variance was due to differences between aquacultured and ornamental carps. Further analyses based on microsatellite data, including cluster analysis and neighbor-joining trees, supported the genetic distinctiveness of aquacultured and ornamental carps, despite the recent divergence of the two groups. In contrast to what was observed for AFLP-based diversity, the frequency of heterozygotes based on microsatellites was comparable among all populations. This discrepancy can potentially be explained by duplication of some loci in Cyprinus carpio L., and a model that shows how duplication can increase heterozygosity estimates for microsatellites but not for AFLP loci is discussed. Our analyses in carp can help in understanding the consequences of genotyping duplicated loci and in interpreting discrepancies between dominant and co-dominant markers in species with recent genome duplication.

Key words: genetic structure / C. carpio / AFLP / genome duplication

Correspondence and reprints: davidl@agri.huji.ac.il

© INRA, EDP Sciences 2007