Open Access

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

  • Lior David1, 4Email author,
  • Noah A. Rosenberg2,
  • Uri Lavi3,
  • Marcus W. Feldman4 and
  • Jossi Hillel5
Genetics Selection Evolution200739:319

https://doi.org/10.1186/1297-9686-39-3-319

Received: 10 May 2006

Accepted: 8 December 2006

Published: 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.

Keywords

genetic structure C. carpio AFLPgenome duplication

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Authors’ Affiliations

(1)
Department of Animal Sciences, Faculty of Agricultural, Food and Environmental Quality Sciences, The Hebrew University of Jerusalem
(2)
Department of Human Genetics, Bioinformatics Program, and the Life Sciences Institute, University of Michigan
(3)
Institute of Horticulture, ARO-Volcani Center
(4)
Department of Biological Sciences, Stanford University
(5)
The Robert H. Smith Institute of Plant Sciences & Genetics, Faculty of Agricultural, Food and Environmental Quality Sciences, The Hebrew University of Jerusalem

Copyright

© INRA, EDP Sciences 2007

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