Abstract
Genetic variations including agronomic traits have been studied among landraces of Citrus depressa Hayata (common name, Shiikuwasha). In order to study nuclear variations, five SSR markers were developed with contigs created by de novo assembly of reads obtained by next generation sequencing. Genetic variations were high enough to allow identification of landraces. Chloroplast insertion/deletion (cpINDEL) markers were also developed through re-sequencing of whole chloroplast genome sequences of one wild accession, Oku. Four major maternal lineages were detected using this cpINDEL analysis. Maternal diversity was confirmed with SNPs extracted from whole cp sequences of three other Shiikuwasha landraces. A later-maturity landrace, MM2, had a cp genome distinct from the other Shiikuwasha landraces, being more similar to that of sweet orange. These nucleotide polymorphisms were applied to identify relationships among the local landraces Ishikata, Shima-kabuchi, Rokugatsu, Yukunibu, and Unzoki, which are all morphologically similar but differ from Shiikuwasha in size. Ishikata and Shima-kabuchi showed high similarity for all DNA markers; they had identical whole cp genome sequences and differed in two SNPs from MM2. Yukunib and Unzoki shared identical genotypes, which differed from those of Rokugatsu and Shiikuwasha.
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References
Bausher MG, Singh ND, Lee S-B, Jansen RK, Daniell H (2006) The complete chloroplast genome sequence of Citrus sinensis (L.) Osbeck var ‘Ridge Pineapple’: organization and phylogenetic relationships to other angiosperms. BMC Plant Biol 6:21
Hao Y, Akimoto M, Kaewcheenchai R, Sotowa M, Ishii T, Ishikawa R (2015) Inconsistent diversities between nuclear and plastid genomes of AA genome species in the genus Oryza. Genes Genet Syst 90:269–281
Ishikawa R (2016) Chapter 1. Wisdom in Shiikuwasha conserved in Oku ward. In: Onishi M, Miyagi K (eds) Wisdom in Shiikuwasha-Oku/Yanbaru, circulation among dialect, local community, life. Kyoto University Press, Kyoto, pp 33–66
Ishikawa R, Badenoch N, Miyagi K, Medoruma K, Osada T, Onishi M (2016) Multi-lineages of of Shiikuwasha (Citrus depressa Hayata) evaluated by using whole chloroplast genome sequences and its bio-diversity in Okinawa, Japan. Breed Sci 66:490–498
Kinjyo H (2007) About shiikuwasha in South-west archaeopelago. Studia Citologica 17:137–148
Kita M, Yonamine K, Tanahara N, Takeuchi M, Teruya M, Awaguni Y (2012) Exploration of Citrus genetic resources in Sakishima archipelago in Okinawa prefecture, Japan. Explore Introd Plant Genet Resour 28:89–103
Kita M, Yamamoto M, Inamori H, Sakaue H, Sekita T, Tahara A, Minoru H (2013) Exploration for Citrus genetic resources in Amami archipelago in Kagoshima prefecture, Japan. Explore Introd Plant Genet Resour 29:107–117
Middleton CP, Senerchia N, Stein N, Akhunov ED, Keller B, Wicker T, Kilian B (2014) Sequencing of chloroplast genomes from wheat, barley, rye and their relatives provides a detailed insight into the evolution of the Triticeae tribe. PLoS One 9:e85761
Nagano Y, Inafuku-Teramoto S, Hashimoto M, Mimura T, Matsumoto R, Yamamoto M (2014) Characterization of chloroplast matK sequences of Citrus tachibana and Citrus depressa, two indigenous species in Japan. Adv Hortic Sci 28:95–99
Nakano M, Nesumi H, Yoshida T (2001) Exploration for Citrus genetic resources on the Nansei archipelago. Ann Rep Explore Introd Plant Genet Resour 17:39–48
Omura M, Shimada T (2016) Citrus breeding, genetics and genomics in Japan. Breed Sci 66:3–17
Onishi M, Nathan B (2016) Link of dialect-living-organisms in Oku/Yanbaru. In: Onishi M, Miyagi K (eds) Wisdom of Shiikuwash. Kyoto University Press, Kyoto, pp 1–25
Shimizu T, Kitajima A, Nonaka K, Yoshioka T, Ohta S, Goto S, Toyoda A, Fujiyama A, Mochizuki T, Nagasaki H, Kaminuma E, Nakamura Y (2016) Hybrid origins of Citrus varieties inferred from DNA marker analysis of nuclear and organelle genomes. PLoS One 11:e0166969
Swingle WT (1943) The botany of Citrus and its wild relatives of the orange subfamily. In: Webber HJ, Batchelor LD (eds) The Citrus industry, vol I. University of California Press, USA, pp 129–474
Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28:2731–2739
Tanaka T (1954) Species problem in Citrus: a critical study of wild and cultivated units of Citrus, based upon field studies in their native homes (Revisio Aurantiacearum IX). Japanese Society for the Promotion of Science, Tokyo, pp 141–152
Tanaka T (1957) Citrus in Ryukyu. Department of Economics, Ryukyu, p 62
Tanaka T (1961) Further revision of Ryukyu Citrus (Revisio Aurantiacearum XIV). Bull Univ Osaka Prefect Ser B Agric Biol 11:11–15
Tanaka T (1969) Misunderstanding with regards Citrus classification and nomenclature. Bull Univ Osaka Prefect Ser B 21:139–145
Urasaki N, Yoshida K, Uehra T, Inoue H, Onda S, Kinjyo H, Kawano S (2005) Single nucleotide polymorphism in Shiikuwasha (Citurs depressa Hayata) Chloroplast DNA, trnL-trnF. Jpn J Trop Agric 49:246–251
Wambugu PW, Brozynska M, Furtado A, Waters DL, Henry RJ (2015) Relationships of wild and domesticated rices (Oryza AA genome species) based upon whole chloroplast genome sequences. Sci Rep 5:13957
Waters D, Nock CJ, Ishikawa R, Rice N, Henry RJ (2012) Chloroplast genome sequence confirms distinctiness of Australian and Asian wild rice. Ecol Evol 2:211–217
Wolfe KH, Li W-H, Sharp PM (1987) Rates of nucleotide substitutionvary greatly among plant mitochondrial, chloroplast, and nuclear DNAs. Proc Natl Acad Sci USA 84:9054–9058
Xu Q, Chen LL, Runan X, Chen D, Zhu A, Chen C, Bertland D, Jiao WB, Hao BH, Lyon MP et al (2013) The draft genome of sweet orange (Citrus sinensis). Nat Genet 45:59–68
Yamamoto M, Tominaga S (2005) Exploration and classification of Citrus genetic resources in Yoron island. Occas Pap 42:136–139
Yamamoto M, Matsuo Y, Kuniga T, Matsumoto R, Yamada Y (1998) Isozyme and RAPD analyses of Shiikuwashas (Citrus depressa Hayata). Bull Natl Inst Fruit Tree Sci 30(31):39–51
Yamamoto M, Matsushima K, Ijichi T, Uechi Y, Kwaguchi S, Nakano H, Nomura T, Tanimura O, Kubo T, Tominaga S (2006) Exploration and preservation of local Citrus germplasms in the Amami archipelago. Bull Exp Farm Agric Kagoshima Univ 29:5–11
Yamamoto M, Kubo T, Tominaga S (2008) Exploration of Citrus depressa Hayata germplasm in Okinoerabu island. Bull Exp Farm Agric Kagoshima Univ 30:15–17
Yamamoto M, Takakura A, Tanabe A, Teramoto S, Kita M (2017) Diversity of Citrus depressa Hayata (Shiikuwasha) revealed by DNA analysis. Genet Resour Crop Evol 64:805–814
Acknowledgements
We thank the local coordinators and farmers on Yoron and Okinawa islands. Many Ishikata accessions were donated by the townspeople of Yoron island. Accessions of local superior landraces in Oku Ward were kindly donated by local farmers, including Takahisa Shimada, Masaru Miyagi, Masakazu Shinjo, Eisho Sakihara and others. Shima-kabuchi, Yukunibu, Unzoki, and Rokougatsu were propagated by Takeshi Miyagi in Ogimi village. Other villagers in Kunigami and Ogimi also helped in this research, which was partly funded by the Churajima Foundation.
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Lam, D.T., Ishikawa, R. Molecular discrimination of landraces of Citrus species in the Okinawa, Japan. Genet Resour Crop Evol 66, 321–333 (2019). https://doi.org/10.1007/s10722-018-0710-x
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DOI: https://doi.org/10.1007/s10722-018-0710-x