Advertisement

DNA Polymorphism and Genetic Diversity in Raphanus Accessions

Chapter
Part of the Compendium of Plant Genomes book series (CPG)

Abstract

Radish is an important vegetable crop that is widely distributed throughout the world. Because of the long cultivation history, radish is morphologically diverse and a large number of cultivars with widely varying morphology, especially in root shapes, sizes, skin, and flesh colors, are produced. According to the morphology of its edible root and its intended uses, cultivated radishes are classified into five main varieties. Radish has a wide range of genetic diversity which provides a tremendous scope for genetic improvement of economic traits. Studies on DNA polymorphisms and genetic diversity of radish help us to determine the genetic relationship between radish cultivars and to understand the origin and evolution of this species. In the past two decades, various molecular tools provide easy, less laborious means for identifying the DNA polymorphisms and genetic diversity of radish. Here, we review recent research on the DNA polymorphisms, including cytoplasmic and nuclear genomes, summarize the genetic relationship between wild and cultivated radishes, and discuss the origin and evolution of Raphanus according to their genetic diversity.

References

  1. Aoba T (1979) Varieties and breeding in Japanese radish. The Iden 33:55–60 (in Japanese)Google Scholar
  2. Arrieta-Montiel MP, Mackenzie SA (2011) Plant mitochondrial genomes and recombination. In: Kempken F (ed) Plant mitochondria. Springer, New York, pp 65–82CrossRefGoogle Scholar
  3. Bae KM, Sim SC, Hong JH, Choi KJ, Kim DH, Kwon YS (2015) Development of genomic SSR markers and genetic diversity analysis in cultivated radish (Raphanus sativus L.). Hortic Environ Biotechnol 56:216–224CrossRefGoogle Scholar
  4. Banga O (1976) Radish, Raphanus sativus (Cruciferae). In: Simmonds NW (ed) Evolution of crop plants. Longman, London, pp 60–62Google Scholar
  5. Becker C (1962) Rettish und radies (Raphanus sativus). Handbuch der Pflanzenzuchtung 6:23–78Google Scholar
  6. Chang S, Chen J, Wang Y, Gu B, He J, Chu P, Guan R (2013) A mitochondrial genome of Raphanus sativus and gene evolution of Cruciferous mitochondrial types. J Genet Genomics 40:117–126CrossRefPubMedGoogle Scholar
  7. Crisp P (1995) Radish–Raphanus sativus (Cruciferae). In: Smartt J, Simmonds NW (eds) Evolution of crop plants. Longman Scientific & Technical, Longman House, Harlow, pp 86–89Google Scholar
  8. Cui N, Qiu Y, Li X, Di Shen, Wang H, Song J (2012) Data mining for SSRs in EST rescources and EST-SSR markers development in radish. Acta Hortic Sinica 39:1303–1312 (in Chinese)Google Scholar
  9. Curtis IS (2011) Genetic engineering of radish: current achievements and future goals. Plant Cell Rep 30:733–744CrossRefPubMedGoogle Scholar
  10. George RAT, Evans DR (1981) A classification of winter radish cultivars. Euphytica 30:483–492CrossRefGoogle Scholar
  11. Hashida T, Nakatsuji R, Budahn O, Schrader O, Peterka H, Fujimura T, Kubo N, Hirai M (2013) Construction of a chromosome-assigned, sequence-tagged linkage map for the radish, Raphanus sativus L. and QTL analysis of morphological traits. Breed Sci 63:218–226CrossRefPubMedPubMedCentralGoogle Scholar
  12. Henslow G (1898) The history of the radish. Gard Chron 23:389Google Scholar
  13. Huh MK, Huh HW (2001) Genetic diversity of Raphanus sativus var. hortensis f. raphanistroides in Korea using AFLP markers. Korean J Genet 23:45–53Google Scholar
  14. Huh MK, Ohnishi O (2001) Allozyme diversity and population structure of Japanese and Korean populations of wild radish, Raphanus sativus var. hortensis f. raphanistroides (Brassicaceae). Genes Genet Syst 76:15–23CrossRefPubMedGoogle Scholar
  15. Huh MK, Ohnishi O (2002) Genetic diversity and genetic relationships of East Asian natural populations of wild radish revealed by AFLP. Breed Sci 52:79–88CrossRefGoogle Scholar
  16. Huh MK, Ohnishi O (2003) Genetic diversity and relationships among natural and cultivated populations of radish in Korea revealed by RAPD. Korean J Genet 25:119–125Google Scholar
  17. Jiang L, Wang L, Liu L, Zhu X, Zhai L, Gong Y (2012) Development and characterization of cDNA library based novel EST-SSR marker in radish (Raphanus sativus L.). Sci Hortic 140:164–172CrossRefGoogle Scholar
  18. Johnston JS, Pepper AE, Hall AE, Chen ZJ, Hodnett G, Drabek J, Lopez R, Price HJ (2005) Evolution of genome size in Brassicaceae. Ann Bot 95:229–235CrossRefPubMedPubMedCentralGoogle Scholar
  19. Kaneko Y, Kimizuka-Takagi C, Bang SW, Matsuzawa Y (2007) Radish. In: Kole C (ed) Genome mapping and molecular breeding in plants. Springer, Berlin Heidelberg, pp 141–160Google Scholar
  20. Kim S, Lim H, Park S, Cho K, Sung S, Oh D, Kim K (2007) Identification of a novel mitochondrial genome type and development of molecular makers for cytoplasm classification in radish (Raphanus sativus L.). Theor Appl Genet 115:1137–1145CrossRefPubMedGoogle Scholar
  21. Kitamura S (1958) Varieties of radish and their transition. In: Nishiyama I (ed) Japanese radish. The Japan Science Society Press, Tokyo, pp 1–19Google Scholar
  22. Kitashiba H, Li F, Hirakawa H, Kawanabe T, Zou Z, Hasegawa Y, Tonosaki K, Shirasawa S, Fukushima A, Yokoi S, Takahata Y, Kakizaki T, Ishida M, Okamoto S, Sakamoto K, Shirasawa K, Tabata S, Nishio T (2014) Draft sequences of the radish (Raphanus sativus L.) genome. DNA Res 21:481–490CrossRefPubMedPubMedCentralGoogle Scholar
  23. Kobabe G (1959) Naturliche Einkreuzung von Hederich (Raphanus raphanistrum L.) in Radies (Raphanus sativus var. radicula DC.) und das Verhalten von Knollenform und Farbe in den nachfolgenden F-und R-Generationen. Zeitschrift fur Pflanzenzuchtung 42:1–10Google Scholar
  24. Kong Q, Li X, Xiang C, Wang H, Song J, Zhi H (2011) Genetic diversity of radish (Raphanus sativus L.) germplasm resources revealed by AFLP and RAPD markers. Plant Mol Biol Rep 29:217–223CrossRefGoogle Scholar
  25. Kumazawa S (1961) Horticulture, detailed discussion of crops. Tokyo, Yokendo, p 637 (in Japanese)Google Scholar
  26. Lawley YE, Weil RR, Teasdale JR (2011) Forage radish cover crop suppresses winter annual weeds in fall and before corn planting. Agron J 103(1):137–144CrossRefGoogle Scholar
  27. Lee Y, Kim S, Lim H, Ahn Y, Sung S (2009) Identification of mitochondrial genome rearrangements unique to novel cytoplasmic male sterility in radish (Raphanus sativus L.). Theor Appl Genet 118:719–728CrossRefPubMedGoogle Scholar
  28. Lewis-Jones LJ, Thorpe JP, Wallis GP (1982) Genetic divergence in four species of the genus Raphanus: Implications for the ancestry of the domestic radish R. sativus. Biol J Linn Soc 18:35–48CrossRefGoogle Scholar
  29. Li F, Hasegawa Y, Saito M, Shirasawa S, Fukushima A, Ito T, Fujii H, Kishitani S, Kitashiba H, Nishio T (2011) Extensive chromosome homoeology among Brassiceae species were revealed by comparative genetic mapping with high-density EST-based SNP markers in radish (Raphanus sativus L.). DNA Res 18:401–411CrossRefPubMedPubMedCentralGoogle Scholar
  30. Liu LW, Zhao LP, Gong YQ, Wang MX, Chen LM, Yang JL, Wang Y, Yu FM, Wang LZ (2008) DNA fingerprinting and genetic diversity analysis of late-bolting radish cultivars with RAPD, ISSR and SRAP markers. Sci Hortic 116:240–247CrossRefGoogle Scholar
  31. Lü N, Yamane K, Ohnishi O (2008) Genetic diversity of cultivated and wild radish and phylogenetic relationships among Raphanus and Brassica species revealed by the analysis of trnK/matK sequence. Breed Sci 58:15–22CrossRefGoogle Scholar
  32. Madhou P, Wells A, Pang ECK, Stevenson TW (2005) Genetic variation in populations of Western Australian wild radish. Aust J Agric Res 56:1079–1087CrossRefGoogle Scholar
  33. Makino T (1961) Makino’s new illustrated flora of Japan. Hokuryukan, Tokyo (in Japanese)Google Scholar
  34. Mitsui Y, Shimomura M, Komatsu K, Namiki N, Shibata-Hatta M, Imai M, Katayose Y, Mukai Y, Kanamori H, Kurita K, Kagami T, Wakatsuki A, Ohyanagi H, Ikawa H, Minaka N, Nakagawa K, Shiwa Y, Sasaki T (2015) The radish genome and comprehensive gene expression profile of tuberous root formation and development. Sci Rep 5:10835CrossRefPubMedPubMedCentralGoogle Scholar
  35. Muminović J, Merz A, Melchinger AE (2005) Genetic structure and diversity among radish varieties as inferred from AFLP and ISSR analyses. J Am Soc Hortic Sci 130(1):79–87Google Scholar
  36. Nakatsuji R, Hashida T, Matsumoto N, Tsuro M, Kubo N, Hirai M (2011) Development of genomic and EST-SSR markers in radish (Raphanus sativus L.). Breed Sci 61:413–419CrossRefPubMedPubMedCentralGoogle Scholar
  37. Ogura H (1968) Studies on the new male-sterility in Japanese radish, with special reference to the utilization of this sterility towards the practical raising of hybrid seeds. Mem Fac Agric Kagoshima Univ 6:39–78Google Scholar
  38. Ohsako T, Hirai M, Yamabuki M (2010) Spatial structure of microsatellite variability within and among populations of wild radish Raphanus sativus L. var. hortensis Backer f. raphanistroides Makino (Brassicaceae) in Japan. Breed Sci 60:195–202CrossRefGoogle Scholar
  39. Park JY, Lee Y, Lee J, Choi B, Kim S, Yang T (2013) Complete mitochondrial genome sequence and identification of a candidate gene responsible for cytoplasmic male sterility in radish (Raphanus sativus L.) containing DCGMS cytoplasm. Theor Appl Genet 126:1763–1774CrossRefPubMedGoogle Scholar
  40. Plucknett DL, Smith NJH, Williams JT (1987) Gene bands and the world’s food. Princeton University Press, PrincetonGoogle Scholar
  41. Pradhan A, Yan G, Plummer JA (2004) Development of DNA fingerprinting keys for the identification of radish cultivars. Aust J Exp Agric 44:95–102CrossRefGoogle Scholar
  42. Rao VR, Hodgkin T (2002) Genetic diversity and conservation and utilization of plant genetic resources. Plant Cell Tissue Cult 68:1–19CrossRefGoogle Scholar
  43. Sahli HF, Conner JK, Shaw FH, Howe S, Lale A (2008a) Adaptive differentiation of quantitative traits in the globally distributed weed, wild radish (Raphanus raphanistrum). Genetics 180:945–955CrossRefPubMedPubMedCentralGoogle Scholar
  44. Salisbury PA (1987) Blacklet resistance in weedy crucifers. Crucif News 12:90Google Scholar
  45. Sahli HF, Conner JK, Shaw FH, Howe S, Lale A (2008b) Adaptive differentiation of quantitative traits in the globally distributed weeds, wild radish (Raphanus raphanistrum). Genetics 180:945–955CrossRefPubMedPubMedCentralGoogle Scholar
  46. Shen D, Sun H, Huang M, Zheng Y, Qiu Y, Li X, Fei Z (2013a) Comprehensive analysis of expressed sequence tags from cultivated and wild radish (Raphanus spp.). BMC Genom 14:721CrossRefGoogle Scholar
  47. Shen D, Sun H, Huang M, Zheng Y, Li X, Fei Z (2013b) RadishBase: a database for genomics and genetics of radish. Plant Cell Phys 54:e3CrossRefGoogle Scholar
  48. Shirasawa K, Oyama M, Hirakawa H, Sato S, Tabata S, Fujioka T, Kimizuka-Takagi C, Sasamoto S, Watanabe A, Kato M, Kishida Y, Kohara M, Takahashi C, Tsuruoka H, Wada T, Sakai T, Isobe S (2011) An EST-SSR linkage map of Raphanus sativus and comparative genomics of the Brassicaceae. DNA Res 18:221–232CrossRefPubMedPubMedCentralGoogle Scholar
  49. Streibig JC, Combellack JH, Pritchard GH, Richardson RG (1989) Estimation of thresholds for weed control in Australian cereals. Weed Res 29:117–126CrossRefGoogle Scholar
  50. Tanaka Y, Tsuda M, Yasumoto K, Yamagishi H, Terachi T (2012) A complete mitochondrial genome sequence of Ogura-type male sterile cytoplasm and its comparative analysis with that of normal cytoplasm in radish (Raphanus sativus L.). BMC Genom 13:352CrossRefGoogle Scholar
  51. Tang J, Zhang L, Peng C (2003) Study on mechanism of semen Raphanus in moving qi and removing food retention. Chin J Integr Tradit West Med Dig 11(5):287–289 (in Chinese)Google Scholar
  52. Terachi T, Yamaguchi K, Yamaguchi H (2001) Sequence analysis on the mitochondrial orfB locus in normal and Ogura malesterile cytoplasms from wild and cultivated radishes. Curr Genet 40:276–281CrossRefPubMedGoogle Scholar
  53. Wang LZ, He QW (2005) Chinese radish. Scientific and Technical Document Publishing House, Beijing (in Chinese)Google Scholar
  54. Wang N, Hu J, Ohsawa R, Ohta M, Fujimura T (2007) Identification and characterization of microsatellite markers derived from expressed sequence tags (ESTs) of radish (Raphanus sativus L.). Mol Ecol Notes 7:503–506CrossRefGoogle Scholar
  55. Wang N, Kitamoto N, Ohsawa R, Fujimure T (2008) Genetic diversity of radish (Raphanus sativus) germplasms and relationships among worldwide accessions analyzed with AFLP markers. Breed Sci 58:107–112CrossRefGoogle Scholar
  56. Wang QB, Zhang L, Zheng PJ (2015) Genetic diversity and evolutionary relationship analyses within and among Raphanus species using EST-SSR markers. Mol Breeding 35:62CrossRefGoogle Scholar
  57. Wang SF, Wang XF, He QW, Liu XX, Xu WL, Li LB, Gao JW, Wang FD (2012) Transcriptome analysis of the roots at early and late seedling stages using Illumina paired-end sequencing and development of EST-SSR markers in radish. Plant Cell Rep 31:1437–1447CrossRefPubMedGoogle Scholar
  58. Wang X, Wang H, Wang J, Sun R, Wu J, Liu S, Bai Y, Mun JH, Bancroft I, Cheng F et al (2011) The genome of the mesopolyploid crop species Brassica rapa. Nat Genet 43:1035–1139CrossRefPubMedGoogle Scholar
  59. Warwick SI (1993) Guide to the wild germplasm of Brassica and allied crops. Part IV. Wild species in the tribe Brassiceae (Cruciferae) as sources of agronomic traits. Tech Bull 17E:1–19Google Scholar
  60. Wolfe KH, Li WH, Sharp PM (1987) Rates of nucleotide substitution vary greatly among plant mitochondrial, chloroplast, and nuclear DNAs. Proc Natl Acad Sci 84:9054–9058CrossRefPubMedPubMedCentralGoogle Scholar
  61. Yamagishi H (2004) Assessment of cytoplasmic polymorphisms by PCR-RFLP of the mitochondrial orfB region in wild and cultivated radishes (Raphanus). Plant Breeding 123:141–144CrossRefGoogle Scholar
  62. Yamagishi H, Tateishi M, Terachi T, Murayama S (1998) Genetic relationships among Japanese wild radishes (Raphanus sativus f. raphanistroides Makino), cultivated radishes and R. raphanistrum revealed by RAPD analysis. J Jpn Soc Hortic Sci 67:526–531CrossRefGoogle Scholar
  63. Yamagishi H, Terach T (2003) Multiple origins of cultivated radishes as evidenced by a comparison of the structural variations in mitochondrial DNA of Raphanus. Genome 46:89–94CrossRefPubMedGoogle Scholar
  64. Yamaguchi H (1987) Latitudinal cline and intra populational differentiation in leaf shape of wild radish in Japan. Jpn J Breed 37:54–65 (in Japanese)CrossRefGoogle Scholar
  65. Yamane K, Lü N, Ohnishi O (2005) Chloroplast DNA variations of cultivated radish and its wild relatives. Plant Sci 168:627–634CrossRefGoogle Scholar
  66. Yamane K, Lü N, Ohnishi O (2009) Multiple origins and high genetic diversity of cultivated radish inferred from polymorphism in chloroplast simple sequence repeats. Breed Sci 59:55–65CrossRefGoogle Scholar
  67. Yasumoto K, Matsumoto Y, Terachi T, Yamagishi H (2008) Restricted distribution of orf687 as the pollen fertility restorer gene for Ogura male sterility in Japanese wild radish. Breed Sci 58:177–182CrossRefGoogle Scholar
  68. Zhai L, Xu L, Wang Y, Cheng H, Chen Y, Gong Y, Liu L (2013) Novel and useful genic-SSR markers from de novo transcriptome sequencing of radish (Raphanus sativus L.). Mol Breeding 33:611–624CrossRefGoogle Scholar
  69. Zou Z, Ishida M, Li F, Kakizaki T, Suzuki S, Kitashiba H, Nishio T (2013) QTL analysis using SNP markers developed by next-generation sequencing for identification of candidate genes controlling 4-methylthio-3-butenyl glucosinolate contents in roots of radish, Raphanus sativus L. PLoS One 8(1):e53541CrossRefPubMedPubMedCentralGoogle Scholar

Copyright information

© Springer International Publishing AG 2017

Authors and Affiliations

  1. 1.National Engineering Research Center for VegetablesBeijingPeople’s Republic of China
  2. 2.Beijing Vegetable Research CenterBeijing Academy of Agriculture and Forestry SciencesBeijingPeople’s Republic of China

Personalised recommendations