Springer Nature is making SARS-CoV-2 and COVID-19 research free. View research | View latest news | Sign up for updates

Development of microsatellite markers in cultivated and wild species of sections Cepa and Phyllodolon in Allium

  • 305 Accesses

  • 17 Citations


The potential of microsatellite markers for use in genetic studies has been evaluated in Allium cultivated species (Allium cepa, A. fistulosum) and its allied species (A. altaicum, A. galanthum, A. roylei, A. vavilovii). A total of 77 polymerase chain reaction (PCR) primer pairs were employed, 76 of which amplified a single product or several products in either of the species. The 29 AMS primer pairs derived from A. cepa and 46 microsatellites primer pairs from A. fistulosum revealed a lot of polymorphic amplicons between seven Allium species. Some of the microsatellite markers were effective not only for identifying an intraspecific F1 hybrid between shallot and bulb onion but also for applying to segregation analyses in its F2 population. All of the microsatellite markers can be used for interspecific taxonomic analyses among two cultivated and four wild species of sections Cepa and Phyllodolon in Allium. Generally, our data support the results obtained from recently performed analyses using molecular and morphological markers. However, the phylogeny of A. roylei, a threatened species with several favorable genes, was still ambiguous due to its different positions in each dendrogram generated from the two primer sets originated from A. cepa and A. fistulosum.

This is a preview of subscription content, log in to check access.

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5


  1. Dubouzet JG, Etoh T, Arisumi KI, Yoshitake T (1996) A diagnostic test to confirm interspecific Allium hybrids using random amplified polymorphic DNA from crude leaf DNA extracts. J Jpn Soc Hortic Sci 65:321–326

  2. Felsenstein J (1989) PHYLIP—Phylogeny Inference Package (version 3.2). Cladistics 5:164–166

  3. Fischer D, Bachmann K (2000) Onion microsatellites for germplasm analysis and their use in assessing intra- and interspecific relatedness within the subgenus Rhizirideum. Theor Appl Genet 101:153–164

  4. Fritsch RM, Friesen N (2002) Evolution, domestication and taxonomy. In: Rabinowitch HD, Currah L (eds) Allium crop science: recent advances. CABI Publishing, Wallingford, pp 5–30

  5. Havey M (1995) Onion and other cultivated alliums. In: Smartt J, Simmonds NW (eds) Evolution of crop plants, 2nd edn. Longman Scientific and Technical, Burnt Mill, pp 344–350

  6. Havey M (2002) Genome organization in Allium. In: Rabinowitch HD, Currah L (eds) Allium crop science: recent advances. CABI Publishing, Wallingford, pp 59–80

  7. Jones RN, Rees H (1968) Nuclear DNA variation in Allium. Heredity 23:591–605

  8. Khrustaleva LI, De Melo PE, Van Heusden AW, Kik C (2005) The integration of recombination and physical maps in a large-genome monocot using haploid genome analysis in a trihybrid allium population. Genetics 169:1673–1685

  9. Kik C (2002) Exploitation of wild relatives for the breeding of cultivated Allium species. In: Rabinowitch HD, Currah L (eds) Allium crop science: recent advances. CABI Publishing, Wallingford, pp 81–100

  10. Kuhl JC, Cheung F, Yuan Q, Martin W, Zewdie Y, McCallum J, Catanach A, Rutherford P, Sink KC, Jenderek M, Prince JP, Town CD, Havey MJ (2004) A unique set of 11,008 onion expressed sequence tags reveals expressed sequence and genomic differences between the monocot orders Asparagales and Poales. Plant Cell 16:114–125

  11. Lacy ML, Lorbeer JW (2008) Botrytis leaf blight. In: Schwartz HF, Mohan SK (eds) Compendium of onion and garlic diseases and pests, 2nd edn. The American Phytopathological Society Press, Minnesota, pp 26–29

  12. Martin WJ, McCallum J, Shigyo M, Jakse J, Kuhl JC, Yamane N, Pither-Joyce M, Gokce AF, Sink KC, Town CD, Havey MJ (2005) Genetic mapping of expressed sequences in onion and in silico comparisons with rice show scant colinearity. Mol Genet Genomics 274:197–204

  13. Masuzaki S, Araki N, Yamauchi N, Yamane N, Wako T, Kojima A, Shigyo M (2006) Chromosomal locations of microsatellites in onion. HortScience 41:315–318

  14. McCallum J (2007) Onion. In: Kole C (ed) Genome mapping and molecular breeding in plants, vol 5: vegetables. Springer-Verlag, Berlin, pp 331–347

  15. Narayan RKJ (1988) Constraints upon the organisation and evolution of chromosomes in Allium. Theor Appl Genet 75:319–329

  16. Nei M, Li WH (1979) Mathematical model for studying genetic variation in terms of restriction endonucleases. Proc Natl Acad Sci USA 76:5269–5273

  17. Ohara T, Song YS, Tsukazaki H, Wako T, Nunome T, Kojima A (2005) Genetic mapping of AFLP markers in Japanese bunching onion (Allium fistulosum). Euphytica 144:255–263

  18. Ricroch A, Yockteng R, Brown SC, Nadot S (2005) Evolution of genome size across some cultivated Allium species. Genome 48:511–520

  19. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425

  20. Scholten OE, Van Heusden AW, Khrustaleva LI, Burger-Meijer K, Mank RA, Antonise RGC, Harrewijn JL, Van Haecke W, Oost EH, Peters RJ, Kik C (2007) The long and winding road leading to the successful introgression of downy mildew resistance into onion. Euphytica 156:345–353

  21. Schwartz HF (2008) Downy mildew. In: Schwartz HF, Mohan SK (eds) Compendium of onion and garlic diseases and pests, 2nd edn. The American Phytopathological Society Press, Minnesota, pp 32–35

  22. Sharma G, Gohil RN (2003) Cytology of Allium roylei Stearn. I. Meiosis in a population with complex interchanges. Cytologia 68:115–119

  23. Song YS, Suwabe K, Wako T, Ohara T, Nunome T, Kojima A (2004) Development of microsatellite markers in bunching onion (Allium fistulosum L.). Breed Sci 54:361–365

  24. Sulistyaningsih E, Tashiro Y, Shigyo M, Isshiki S (1997) Morphological and cytological characteristics of haploid shallot. Bull Fac Agric Saga Univ 82:7–15

  25. Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol Biol Evol 24:1596–1599

  26. Tsukazaki H, Fukuoka H, Song YS, Yamashita KI, Wako T, Kojima A (2006) Considerable heterogeneity in commercial F1 varieties of bunching onion (Allium fistulosum) and proposal of breeding scheme for conferring variety traceability using SSR markers. Breed Sci 56:321–326

  27. Tsukazaki H, Nunome T, Fukuoka H, Kanamori H, Kono I, Yamashita KI, Wako T, Kojima A (2007) Isolation of 1,796 SSR clones from SSR-enriched DNA libraries of bunching onion (Allium fistulosum). Euphytica 157:83–94

  28. Tsukazaki H, Yamashita KI, Yaguchi S, Masuzaki S, Fukuoka H, Yonemaru J, Kanamori H, Kono I, Hang TTM, Shigyo M, Kojima A, Wako T (2008) Construction of SSR-based chromosome map in bunching onion (Allium fistulosum). Theor Appl Genet 117:1213–1223

  29. Tsukazaki H, Yamashita KI, Kojima A, Wako T (2009) SSR-tagged breeding scheme for allogamous crops: a trial in bunching onion (Allium fistulosum). Euphytica 163:327–334

  30. van Heusden AW, van Ooijen JW, Vrielink-van Ginkel R, Verbeek WHJ, Wietsma WA, Kik C (2000) A genetic map of an interspecific cross in Allium based on amplified fragment length polymorphism (AFLP™) markers. Theor Appl Genet 100:118–126

  31. van Raamsdonk LWD, Smiech MP, Sandbrink JM (1997) Introgression explains incongruence between nuclear and chloroplast DNA-based phylogenies in Allium section Cepa. Bot J Linn Soc 123:91–108

  32. van Raamsdonk LWD, Ginkel MVV, Kik C (2000) Phylogeny reconstruction and hybrid analysis in Allium subgenus Rhizirideum. Theor Appl Genet 100:1000–1009

  33. Vvedensky A (1944) The genus Allium in the USSR. Herbertia 11:65–218

  34. Wako T, Ohara T, Song YS, Kojima A (2002) Development of SSR markers in bunching onion. Breed Res 4(Suppl 1):83 (in Japanese)

Download references


The authors wish to thank Misses N. Yamane, N. Matsubara, Y. Kousabara and M. Anraku (former students in Yamaguchi University) together with Messrs Y. Kosaka and S. Hasegawa (present students in YU) for their technical contributions to this study. The authors are grateful to Dr. C. Kik and Mr. W. Wietsma in PRI for the kind gift of wild species. The Polymorphic examinations were supported in part by a funding for ‘Research project for utilizing advanced technologies in agriculture, forestry and fisheries’ from the Ministry of Agriculture, Forestry and Fisheries of Japan, and segregation analyses by a Grant-in-Aid for Scientific Research (C) (No. 15580025) from the Ministry of Education, Science, Sports, and Culture of Japan.

Author information

Correspondence to Masayoshi Shigyo.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (DOC 275 kb)

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Araki, N., Masuzaki, S., Tsukazaki, H. et al. Development of microsatellite markers in cultivated and wild species of sections Cepa and Phyllodolon in Allium . Euphytica 173, 321–328 (2010).

Download citation


  • Allium
  • Microsatellite markers
  • DNA polymorphism