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

Construction of SSR-based chromosome map in bunching onion (Allium fistulosum)

  • 628 Accesses

  • 33 Citations


We have constructed a linkage map of bunching onion (Allium fistulosum L., 2= 16) using an F2 population of 225 plants. The map consists of 17 linkage groups with 212 bunching onion SSR markers and 42 bulb onion (A. cepa L.) SSR, InDel, CAPS or dCAPS markers, covering 2,069 cM. This is the first report of a linkage map mainly based on SSR markers in the genus Allium. With the 103 anchor markers [81 bunching onion SSRs, 11 bulb onion SSRs and 11 bulb onion non-SSRs (1 InDel, 9 CAPSs and 1 dCAPS)] whose chromosome assignments were identified in A. cepa and/or A. fistulosum, via the use of several kinds of Allium alien addition lines, 16 of the 17 linkage groups were connected to the 8 basic chromosomes of A. cepa.

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

Fig. 1
Fig. 2
Fig. 3
Fig. 4


  1. 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

  2. Ford-Lloyd BV, Armstrong SJ (1993) Welsh onion Allium fistulosum L. In: Kalloo G, Bergh BO (eds) Genetic improvement of vegetable crops, Pergamon Press, pp 51–58

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

  4. Fukuoka H, Nunome T, Minamiyama Y, Kono I, Namiki N, Kojima A (2005) read2Marker: a data processing tool for microsatellite marker development from a large data set. BioTechniques 39:472–476

  5. Gökçe AF, McCallum J, Sato Y, Havey MJ (2002) Molecular tagging of the Ms locus in onion. J Amer Soc Hort Sci 127:576–582

  6. Hang TTM, Shigyo M, Yamauchi N, Tashiro Y (2004) Production and characterization of alien chromosome additions in shallot (Allium cepa L. Aggregatum group) carrying extra chromosome(s) of Japanese bunching onion (A. fistulosum L.). Genes Genet Syst 79:263–269

  7. Jones CJ, Edwards KJ, Castaglione S, Winfield MO, Sala F, van de Wiel C, Bredemeijer G, Vosman B, Matthes M, Daly A, Brettschneider R, Bettini P, Buiatti M, Maestri E, Malcevschi A, Marmiroli N, Aert R, Volckaert G, Rueda J, Linacero R, Vazquez A, Karp A (1997) Reproducibility testing of RAPD, AFLP and SSR markers in plants by a network of European laboratories. Mol Breed 3:381–390

  8. King JJ, Bradeen JM, Bark O, McCallum JA, Havey MJ (1998) A low-density map of onion reveals a role for tandem duplication in the evolution of an extremely large diploid genome. Theor Appl Genet 96:52–62

  9. Kosambi D (1944) The estimation of map distance from recombination values. Ann Eugen 12:172–175

  10. Kuhl JC, Cheung F, Yuan Q, Martin W, Zewdie Y, MaCallum J, Catanach A, Rutherford P, Sink KC, Jenderk 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. Kumazawa S, Katsumata H (1965) Negi (Japanese bunching onion). In: Kumazawa S (ed) Sosai-engei kakuron (vegetable crops), Yokendo Press, Tokyo, pp 280–289 (in Japanese)

  12. Lander E, Green P, Abrahamson J, Barlow A, Daly M, Lincoln S, Newburg L (1987) MAPMAKER: an interactive computer package for constructing primary genetic linkage maps of experimental and natural populations. Genomics 1:174–181

  13. MAFF (2005) Nousanbutsu-Sanshutsugaku no Jun-I (The ranking of vegetables for annual output in Japan). In: Pocket nourinsuisan toukei, 2005 (in Japanese).

  14. Martin WJ, McCallum J, Shigyo M, Jakše J, Kuhl JC, Yamane N, Pither-Joyce M, Gökçe 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 Gen Genomics 274:197–204

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

  16. McCallum J, Leite D, Pither-Joyce M, Havey MJ (2001) Expressed sequence markers for genetic analysis of bulb onion (Allium cepa L.). Theor Appl Genet 103:979–991

  17. Neff MM, Turk E, Kalishman M (2002) Web-based primer design for single nucleotide polymorphism analysis. Trends Genet 18:613–615

  18. Ohara T, Song YS, Tsukazaki H, Wako T, Nunome T, Kojima A (2005) Construction of a genetic linkage map of Japanese bunching onion (Allium fistulosum) based on AFLP and SSR markers. Euphytica 144:255–263

  19. Peffley EB (1986) Evidence for chromosomal differentiation of Allium fistulosum and A. cepa. J Amer Soc Hort Sci 111:126–129

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

  21. Rozen S, Skaletsky HJ (2000) Primer 3 on the WWW for general users and for biologist programmers. In: Krawetz S, Misener S (eds) Bioinformatics methods and protocols: methods in molecular biology. Humana Press, Totowa, pp 365–386

  22. Shigyo M, Tashiro Y, Issiki S, Miyazaki S (1996) Establishments of a series of alien monosomic addition lines of Japanese bunching onion (Allium fistulosum L.) with extra chromosomes from shallot (A. cepa L. Aggregatum group). Genes Genet Syst 71:363–371

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

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

  25. Tsukazaki H, Nunome T, Fukuoka H, Kanamori H, Kono I, Yamashita K, 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

  26. Wako T, Ohara T, Song YS, Kojima A (2002a) Development of SSR markers in bunching onion. Breed Sci 4(suppl 1):83 (in Japanese)

  27. Wako T, Shigyo M, Tashiro Y, Kataoka S, Ohara T, Kojima A (2002b) Development of chromosome-specific CAPS markers in shallot. J Jpn Soc Hort Sci 71(suppl 1):348 (in Japanese)

  28. Yaguchi S, Hang TTM, Tsukazaki H, Vu QH, Masuzaki S, Wako T, Masamura N, Onodera S, Shiomi N, Yamauchi N, Shigyo M (2008) Molecular and biochemical identification of alien chromosome additions in shallot (Allium cepa L. Aggregatum group) carrying extra chromosome(s) of bunching onion (A. fistulosum L.). Genes Genet Syst (submitted)

Download references


We are grateful to Ms. K. Tanaka, K. Wakita and S. Negoro for the technical assistance. This work was supported by the project “Green Technology Project (DM-1604)”, Ministry of Agriculture, Forestry and Fisheries, Japan and Grant-in-Aid for Young Scientists (B) (19780010), Japan Society for the Promotion of Science. The authors wish to thank Ms. N. Matsubara, Y. Kousabara and M. Anraku (former students in Yamaguchi University) for their contributions to this study.

Author information

Correspondence to Tadayuki Wako.

Additional information

Communicated by M. Xu.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary Tables (PDF 97.3 kb)

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Tsukazaki, H., Yamashita, K., Yaguchi, S. et al. Construction of SSR-based chromosome map in bunching onion (Allium fistulosum). Theor Appl Genet 117, 1213 (2008).

Download citation


  • Linkage Group
  • Simple Sequence Repeat Marker
  • Cleave Amplify Polymorphic Sequence
  • Bulb Onion
  • Cleave Amplify Polymorphic Sequence Marker