PCR-RFLP analysis of the mitochondrial ND-3/4 and ND-5/6 gene polymorphisms in the European and East Asian subspecies of common carp (Cyprinus carpio L.)
Abstract
Polymorphism within the mitochondrial NADH-3,4 dehydrogenase (ND-3/4) and NADH-5,6 dehydrogenase (ND-5/6) gene regions was studied by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis among common carp populations belonging to the European (two farmed strains and three wild populations) and East Asian (Amur wild carp, Vietnamese wild carp and Japanese Koi carp) subspecies, Cyprinus carpio carpio and C. c. haematopterus, respectively. Polymorphism was detected using eight and six restriction enzymes, respectively, and a total of seven composite haplotypes were identified. Both distance-based and maximum likelihood phylogenetic inference methods clustered the haplotypes into four distinct groups-the European (two haplotypes), Amur (two haplotypes), Vietnamese (two haplotypes) and Koi (one haplotype), and their distributions strictly follow the geographic origin of populations. The populations are clustered into two highly divergent groups (average net nucleotide divergence, 2.4%), the European and the East Asian populations, suggesting an ancient separation. Six enzymes (HinfI, AluI, HpaII and TaqI at ND-3/4; Eco47I and BsuRI at ND-5/6) yielded diagnostic restriction sites for discriminating between the European and East Asian maternal lineages that can be applied to monitoring of genetic purity of the European farmed strains.
- Publication:
-
Aquaculture
- Pub Date:
- 2002
- DOI:
- 10.1016/S0044-8486(01)00836-5
- Bibcode:
- 2002Aquac.204..507G
- Keywords:
-
- Mitochondrial DNA;
- Polymorphism;
- Phylogeography;
- Cyprinus carpio