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Development of nuclear DNA markers to characterize genetically diverse groups of Misgurnus anguillicaudatus and its closely related species

Abstract

Repetitive DNA sequences, ManDra and ManBgl, were isolated from the DraI and BglII digests of the genomic DNA of Misgurnus anguillicaudatus, respectively. A primer set of ManDra distinguished two genetically different groups (A and B) of M. anguillicaudatus by specific electrophoretograms. A primer set of ManBgl amplified the DNA of M. anguillicaudatus and M. mizolepis. The individuals of M. anguillicaudatus were divided into two groups depending on the fragment sizes, in which the groups A and B (B-1 and B-2) showed 400 and 460 bp, respectively. M. mizolepis was distinguished by a different pattern (400-, 460-, and 510-bp fragments). PCR–RFLP analyses of recombination activating gene 1 gave a clear difference between A or B-2 (443-bp fragment) and B-1 groups (296- and 147-bp fragments). Clonal lineages and hybrids between B-1 and B-2 groups could be identified by appearance of three fragments (443, 296, and 147 bp). The combined analyses using the above three nuclear markers discriminated among nuclear genomes of genetic groups (A, B-1 and B-2) of M. anguillicaudatus and M. mizolepis. In several localities, natural hybridizations between the group B-1 and B-2 loaches and introgressions of clonal mitochondrial genomes into the group B-1 loaches were detected.

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Acknowledgements

This work was supported in part by JSPS KAKENHI Grant Numbers 21380114 and 15H02457. We thank the staff of the Ishikawa Prefecture Fisheries Research Center for sampling loaches in the Ishikawa Prefecture. We also thank Dr. H Matsubara, Faculty of Bio-industry, Tokyo University of Agriculture, for sampling loaches in the eastern part of Hokkaido Prefecture.

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Correspondence to Takafumi Fujimoto.

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Fujimoto, T., Yamada, A., Kodo, Y. et al. Development of nuclear DNA markers to characterize genetically diverse groups of Misgurnus anguillicaudatus and its closely related species. Fish Sci 83, 743–756 (2017). https://doi.org/10.1007/s12562-017-1108-y

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Keywords

  • Repetitive DNA sequence
  • RFLP
  • Hybrid
  • Species identification
  • Cobitidae