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.
Highlights
The common carp (Cyprinus carpio L.) is an important freshwater food fish, produced in temperate climatic regions around the world
Using microsatellite markers, we found that paralogous fragments can frequently be amplified by the same primer-pair, and we estimated that about 60% of the carp genome remains duplicated [4]
An albino mutant of the grass carp (Ctenopharyngodon idella) was chosen as an outgroup population, because it is one of the few species that can hybridize with common carp, and because microsatellite markers in common carp have previously been shown to have a high rate of crossamplification in grass carp [3]
Summary
The common carp (Cyprinus carpio L.) is an important freshwater food fish, produced in temperate climatic regions around the world. Previous cytological [23] and molecular [15] studies have suggested that the common carp recently experienced whole-genome duplication. Accumulating data suggest that copy number variations and variability within and between duplicated regions have important functional consequences, including in human diseases For eight carp populations and a grass carp outgroup, using amplified fragment length polymorphism (AFLP) patterns and microsatellite loci that we have developed [3], we study levels of genetic variability and genetic relationships among groups. We discuss how different marker types perform in assaying these two aspects of genetic variation in the context of the recent whole-genome duplication of the common carp and the breeding histories of the populations
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