title: Multi-lineages of Shiikuwasha (Citrus depressaHayata) evaluated by using whole chloroplast genome sequences and its bio-diversity in Okinawa, Japan.
abstract: Shiikuwasha (Citrus depressaHayata) is distributed from the South-west of the Japanese archipelago to Taiwan. In this study, re-sequencing against the orange (C. sinensis(L.) Osbeck) chloroplast genome was applied to one superior landrace of Shiikuwasha cultivated in Oku ward, Okinawa, Japan. The chloroplast genome of the landrace was estimated to comprise 160,118 bp, including 48 indels and 71 nucleotide substitutions against the reference genome. The presumptive chloroplast indels were confirmed by subsequent experiments, and these identified multiple maternal lineages among other landraces. Some of the orange SSR markers were available for genotyping of other superior landraces and were able to distinguish among them. These molecular markers were then applied for evaluation of genetic diversity among wild and cultivated Shiikuwasha accessions. Except for Oku ward, the cultivated populations were found to have lost their genetic diversity in comparison with wild populations. Groves in Oku ward maintained, or showed even higher genetic diversity than wild accessions in the surrounding areas by the force of villagers.
authors: Faculty of Agriculture and Life Science, Hirosaki University , Hirosaki, Aomori 036-8561 , Japan.
authors: Ryuji
authors: R
authors: Ishikawa
authors: Center for Southeast Asian Studies, Kyoto University , Kyoto, Kyoto 606-8501 , Japan.
authors: Nathan
authors: N
authors: Badenoch
authors: Association of Shishigaki Network , Naha, Okinawa 902-0071 , Japan.
authors: Kunimasa
authors: K
authors: Miyagi
authors: Okinawa prefectural Chūbu Agricultural Development Center, Department of Agriculture, Forestry and Fisheries, Okinawa Prefecture , Nago, Okinawa 904-2155 , Japan.
authors: Kaname
authors: K
authors: Medoruma
authors: Research Institute of Humanity and Nature , Kyoto, Kyoto 603-8047 , Japan.
authors: Toshiki
authors: T
authors: Osada
authors: Research Center for Knowledge Science in Cultural Heritage, Doshisha University , Kyoto, Kyoto 610-0394 , Japan.
authors: Masayuki
authors: M
authors: Onishi
keywords: Citrus depressa Hayata; Shiikuwasha; maternal lineage; re-sequencing; selection