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

• Published in: Genetics selection evolution (Paris) Vol. 39; no. 3; pp. 319 - 340
• Main Authors: DAVID, Lior, ROSENBERG, Noah A, LAVI, Uri, FELDMAN, Marcus W, HILLEL, Jossi
• Format: Journal Article
• Language: English
• Published: Les Ulis EDP Sciences 14.04.2007; BioMed Central Ltd; BioMed Central; BMC
• Subjects: AFLP; Alleles; Animal genetics; Animals; Biological and medical sciences; Breeding; C. carpio; Carps - genetics; Chromosome Banding; Chromosomes; Crosses, Genetic; DNA - genetics; Fundamental and applied biological sciences. Psychology; Gene Frequency; Genetic Markers; genetic structure; Genetic Variation; Genetics; Genetics of eukaryotes. Biological and molecular evolution; Genetics, Population; Genome; genome duplication; Genotype; Heterozygote; Life Sciences; Microsatellite Repeats; Models, Genetic; Polymorphism, Restriction Fragment Length; Population genetics, reproduction patterns; Vertebrata; Yugoslavia; Europe; Edible fish; Genome organization; Ornamental fish; Genomics; genetic structure; Molecular marker; Biodiversity; Population genetics; Freshwater environment; C. carpio; Pisces; Microsatellite DNA; Domestic animal; genome duplication; Cyprinus carpio; Intraspecific comparison; Animal population; Ctenopharyngodon idella; Farming animal; Carp; Breeds (animals); Interspecific comparison; Animal sciences; Population structure; Genetic diversity; Vertebrata; Pisciculture; AFLP; Gene duplication; Molecular biology; Genome; Amplified fragment length polymorphism marker
• ISSN: 0999-193X; 1297-9686; 1297-9686
• DOI: 10.1186/1297-9686-39-3-319

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.