Genetic Resources and Crop Evolution

, Volume 64, Issue 4, pp 805–814 | Cite as

Diversity of Citrus depressa Hayata (Shiikuwasha) revealed by DNA analysis

  • Masashi YamamotoEmail author
  • Akiko Takakura
  • Aika Tanabe
  • Sayuri Teramoto
  • Masayuki Kita
Research Article


Citrus depressa Hayata is an indigenous mandarin species on the Ryukyu Islands located in the subtropical region of Japan. We deduced its phylogenetic relationships by evaluating accessions grown on various Ryukyu Islands via cleaved amplified polymorphic sequence analysis of cpDNA and sequence-related amplified polymorphism (SRAP). The cpDNA results indicated that C. depressa could be classified into two types. SRAP revealed patterns of diversity within C. depressa consistent with our cpDNA results. These results indicate that maternal origin may influence or is correlated with the constitution of the nuclear genome of C. depressa. Another Japanese mandarin species, Citrus tachibana (Makino) Tanaka was distinguished from C. depressa by SRAP markers. Moreover, both C. depressa and C. tachibana could be distinguished from other Citrus species. Our results suggest that Japanese mandarin possesses a characteristic genome with the genus Citrus.


Citrus depressa cpDNA Mandarin Ryukyu Islands SRAP Tachibana 


  1. Asadi Abkenar A, Isshiki S, Tashiro Y (2004) Phylogenic relationships in the “true citrus fruit trees” revealed by PCR-RFLP analysis of cpDNA. Sci Hortic 102:233–242CrossRefGoogle Scholar
  2. Arnold M, Bucker LCM, Robinson JJ (1991) Pollen-mediated introgression and hybrid speciation in Louisiana irises. Proc Natl Acad Sci (USA) 88:1398–1402CrossRefGoogle Scholar
  3. Barkley NA, Roose ML, Krueger RR, Federici CT (2006) Assessing genetic diversity and population structure in a citrus germplasm collection utilizing simple sequence repeat markers (SSRs). Theor Appl Genet 112:1519–1531CrossRefPubMedGoogle Scholar
  4. Bayer RJ, Mabberley DJ, Morton C, Miller CH, Sharma IK, Pfeil BE, Rich S, Hitchcock R, Sykes S (2009) A molecular phylogeny of the orange subfamily (Rutaceae: Aurantioideae) using nine cpDNA sequences. Am J Bot 96:668–685CrossRefPubMedGoogle Scholar
  5. Dice LR (1945) Measures of the amount of ecologic association between species. Ecology 26:297–302CrossRefGoogle Scholar
  6. Dumolin-Lapegue S, Pemonge MH, Petit RJ (1997) An enlarged set of consensus primers for the study of organelle DNA in plants. Mol Ecol 6:393–397CrossRefPubMedGoogle Scholar
  7. Federici CT, Fang DQ, Scora RW, Roose ML (1998) Phylogenetic relationships within the genus Citrus (Rutaceae) and related genera as revealed by RFLP and RAPD analysis. Theor Appl Genet 96:812–822CrossRefGoogle Scholar
  8. Froelicher Y, Mouhaya W, Bassene J-B, Costantino G, Kamiri M, Luro F, Morillon R, Ollitraultet P (2011) New universal mitochondrial PCR markers reveal new information on maternal citrus phylogeny. Tree Genet Genomes 7:49–61CrossRefGoogle Scholar
  9. Hirai M, Kozaki I, Kajiura I (1986) Isozyme analysis and phylogenic relationship of citrus. Jpn J Breed 36:377–389CrossRefGoogle Scholar
  10. Hirai M, Mitsue S, Kita K, Kajiura I (1990) A survey and isozyme analysis of wild mandarin, tachibana (Citrus tachibana (Mak.) Tanaka) growing in Japan. J Jpn Soc Hortic Sci 59:1–7CrossRefGoogle Scholar
  11. Hodgeson RW (1967) Horticultural varieties of citrus. In: Reuther W, Webber HJ, Batchelor LD (eds) The citrus industry, vol 1. University of California, Berkeley, pp 431–588Google Scholar
  12. Inafuku-Teramoto S, Yamamoto M, Kinjo H, Kitajima A, Wada K, Kawamitsu Y (2010) Local citrus genetic resources and their polymethoxyflavones content in northern part of Okinawa Island. Hortic Res (Jpn) 9:263–271CrossRefGoogle Scholar
  13. Kinjo H (2007) Acid citrus “Shiikuwasha” in Ryukyu island. Stud Citrol 17:137–148Google Scholar
  14. 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. Annu Rep Explor Introd Plant Genet Resour 29:107–117Google Scholar
  15. Li G, Quiros CF (2001) Sequence-related amplified polymorphism (SRAP), a new marker system based on a simple PCR reaction: its application to mapping and gene tagging in Brassica. Theor Appl Genet 103:455–461CrossRefGoogle Scholar
  16. Mabberley DJ (1997) A classification for edible Citrus (Rutaceae). Telopea 7:167–172CrossRefGoogle Scholar
  17. 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 28:95–99Google Scholar
  18. Nicolosi E, Deng ZN, Gentile A, La Malfa S, Continella G, Tribulato E (2000) Citrus phylogeny and genetic origin of important species as investigated by molecular markers. Theor Appl Genet 100:1155–1166CrossRefGoogle Scholar
  19. Swingle WT, Reece PC (1967) The botany of citrus and its wild relatives. In: Reuther W, Webber HJ, Batchelor LD (eds) The citrus industry, vol 1. University of California, Berkeley, pp 190–430Google Scholar
  20. Taberlet P, Gielly L, Pautou G, Bouvet J (1991) Universal primers for amplification of three non-coding regions of chloroplast DNA. Plant Mol Biol 17:1105–1109CrossRefPubMedGoogle Scholar
  21. Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol Biol Evol 24:1596–1599CrossRefPubMedGoogle Scholar
  22. Tanaka T (1926) Wild Citri of the Japanese territories. Bul Sci Fak Kjusu Imp Univ 2:51–58Google Scholar
  23. Tanaka T (1969) Misunderstanding with regards citrus classification and nomenclature. Bull Univ Osaka Prefect B21:139–145Google Scholar
  24. Tanaka T (1977) Fundamental discussion of citrus classification. Stud Citrol 14:1–5Google Scholar
  25. Tanaka Y (1948) An iconography of Japanese citrus fruits, vol 2. Yokendo, Tokyo (in Japanese)Google Scholar
  26. Ueno I, Iwamasa M, Nishiura M (1967) Embryo number of various varieties of citrus and its relatives. Bull Hortic Res Sta Jpn B7:11–21Google Scholar
  27. Urasaki N, Yoshida K, Uehara T, Inoue H, Onda S, Kinjyo H, Kawano S (2005) Single nucleotide polymorphism in shiikuwasha (Citrus depressa Hayata) chloroplast DNA, trnL-trnF. Jpn J Trop Agric 49:246–251Google Scholar
  28. Uzun A, Yesiloglu T, Aka-Kacar Y, Tuzcu O, Gulsen O (2009) Genetic diversity and relationships within Citrus and related genera based on sequence related amplified polymorphism markers (SRAPs). Sci Hortic 121:306–312CrossRefGoogle Scholar
  29. Yamamoto M, Tominaga S (2003) High chromosomal variability of mandarin (Citrus spp.) revealed by CMA banding. Euphytica 129:267–274CrossRefGoogle Scholar
  30. 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 30/31:39–51Google Scholar
  31. Yamamoto M, Kubo T, Tominaga S (2006a) Self- and cross-incompatibility of various Citrus accessions. J Jpn Soc Hortic Sci 75:372–378CrossRefGoogle Scholar
  32. Yamamoto M, Matsushima K, Ijichi T, Uechi Y, Kawaguchi S, Nakano H, Nomura T, Tanimura O, Kubo T, Tominaga S (2006b) Exploration and preservation of local citrus germplasms in the Amami archipelago. Bull Exp Farm Fac Agric Kagoshima Univ 29:5–11Google Scholar
  33. Yamamoto M, Kubo T, Tominaga S (2008) Exploration of local citrus Citrus depressa Hayata germplasms in Okinoerabu Island. Bull Exp Farm Fac Agric Kagoshima Univ 30:15–17Google Scholar
  34. Yamamoto M, Fukuda M, Koga T, Kubo T, Tominaga S (2010) Examination of the origin of Keraji (Citrus keraji), local citrus of Kikaijima Island, Kagoshima Prefecture. Hortic Res (Jpn) 9:7–12CrossRefGoogle Scholar
  35. Yamamoto M, Tsuchimochi Y, Ninomiya T, Koga T, Kitajima A, Yamasaki A, Inafuku-Teramoto S, Yang X, Yang X, Zhong G, Nasir N, Kubo T, Tominaga S (2013) Diversity of chloroplast DNA in various mandarins (Citrus spp.) and other citrus demonstrated by CAPS analysis. J Jpn Soc Hortic Sci 82:106–113CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media Dordrecht 2016

Authors and Affiliations

  • Masashi Yamamoto
    • 1
    Email author
  • Akiko Takakura
    • 1
  • Aika Tanabe
    • 1
  • Sayuri Teramoto
    • 2
    • 4
  • Masayuki Kita
    • 3
  1. 1.Faculty of AgricultureKagoshima UniversityKagoshimaJapan
  2. 2.Faculty of AgricultureUniversity of the RyukyusNakagami-gunJapan
  3. 3.Okitsu Citrus Research StationNARO Institute of Fruit Tree ScienceOkitsunakacho, ShimizuJapan
  4. 4.JICA Ethiopia OfficeAddis AbabaEthiopia

Personalised recommendations