Abstract
Medaka (comprising two species Oryzias latipes and Oryzias sakaizumii) is a small freshwater fish that is globally used as an experimental model organism. Wild Japanese medaka populations have been declining and their genetic diversity has been affected by extensive artificial introduction of non-native populations and ‘himedaka’, an orange-red variety derived from O. latipes, which is a commercially popular in Japan. To detect artificially caused genetic introgression in wild medaka populations, we developed a novel and effective nuclear markers. Sequencing analysis of a single-copy nuclear DNA (scnDNA) belonging to linkage group 21 (LG21b) was performed to identify specific haplotype in O. sakaizumii, nine genetically localized groups of O. latipes, and himedaka populations. A total of 28 haplotypes were identified from the 16 tested wild populations. Of the 28 haplotypes, 27 were considered specific to O. sakaizumii and to each genetically localized group of O. latipes; thus, these haplotypes could be used as diagnostic markers to detect artificially caused genetic introgression. Eight haplotypes were confirmed in himedaka, and four were considered specific to himedaka. Our tests involved direct sequencing of the 3′-sequence of the LG21b region as a diagnostic marker, which effectively detected artificially caused genetic introgression in wild populations. Analysis of the actual level of genetic introgression will be improved by incorporating the new scnDNA marker in combination with conventional DNA markers of medaka.
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Acknowledgements
We sincerely thank Dr. M. Kobayashi (ICU), Dr. M. Fukui (KESC), Dr. M. Maegata (KU), Dr. A. Munakata (MDU), Mr. T. Hagiwara (GEF), and other colleagues for helping with specimen collection. The samples in Yakushima Island were provided by Y. Kano (DSKU) under a fund “Development of mitigation and adaptation technologies to climate change in the sectors of agriculture, forestry, and fisheries” by the Ministry of Agriculture, Forestry and Fisheries, Japan. We are grateful to Dr. K. Hosoya, Dr. D. Hayasaka, Dr. M. Mori, Dr. T. Ito, and other members of our laboratory for their useful advice and helping with specimen sampling and fieldwork. We would like to thank Editage (www.editage.jp) for English language editing. This study complies with the current laws of Japan.
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Iguchi, Y., Nakao, R., Takata, K. et al. Development of a single-copy nuclear DNA sequence marker for the detection of artificially caused genetic introgressions in Japanese wild medaka populations. Conservation Genet Resour 12, 311–317 (2020). https://doi.org/10.1007/s12686-019-01106-x
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DOI: https://doi.org/10.1007/s12686-019-01106-x