Multi-lineages of Shiikuwasha (Citrus depressa Hayata) evaluated by using whole chloroplast genome sequences and its bio-diversity in Okinawa, Japan

Shiikuwasha (Citrus depressa Hayata) 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...

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Bibliographic Details
Published in:Breeding Science 2016, Vol.66(4), pp.490-498
Main Authors: Ishikawa, Ryuji, Badenoch, Nathan, Miyagi, Kunimasa, Medoruma, Kaname, Osada, Toshiki, Onishi, Masayuki
Format: Article
Language:English
Subjects:
Biodiversity
Chloroplasts
Citrus depressa
Citrus depressa Hayata
Citrus fruits
Citrus sinensis
Gene sequencing
Genetic diversity
Genomes
Genotyping
Markers
maternal lineage
Populations
re-sequencing
Research Paper
selection
Shiikuwasha
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Summary:Shiikuwasha (Citrus depressa Hayata) 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.
ISSN:1344-7610
1347-3735
DOI:10.1270/jsbbs.15151