Theoretical and Applied Genetics

, Volume 122, Issue 3, pp 501–510 | Cite as

Direct determination of the chromosomal location of bunching onion and bulb onion markers using bunching onion–shallot monosomic additions and allotriploid-bunching onion single alien deletions

  • Hikaru Tsukazaki
  • Ken-ichiro Yamashita
  • Shigenori Yaguchi
  • Koichiro Yamashita
  • Takuya Hagihara
  • Masayoshi Shigyo
  • Akio Kojima
  • Tadayuki Wako
Original Paper


To determine the chromosomal location of bunching onion (Allium fistulosum L.) simple sequence repeats (SSRs) and bulb onion (A. cepa L.) expressed sequence tags (ESTs), we used a complete set of bunching onion–shallot monosomic addition lines and allotriploid bunching onion single alien deletion lines as testers. Of a total of 2,159 markers (1,198 bunching onion SSRs, 324 bulb onion EST–SSRs and 637 bulb onion EST-derived non-SSRs), chromosomal locations were identified for 406 markers in A. fistulosum and/or A. cepa. Most of the bunching onion SSRs with identified chromosomal locations showed polymorphism in bunching onion (89.5%) as well as bulb onion lines (66.1%). Using these markers, we constructed a bunching onion linkage map (1,261 cM), which consisted of 16 linkage groups with 228 markers, 106 of which were newly located. All linkage groups of this map were assigned to the eight basal Allium chromosomes. In this study, we assigned 513 markers to the eight chromosomes of A. fistulosum and A. cepa. Together with 254 markers previously located on a separate bunching onion map, we have identified chromosomal locations for 766 markers in total. These chromosome-specific markers will be useful for the intensive mapping of desirable genes or QTLs for agricultural traits, and to obtain DNA markers linked to these.


Allium cepa Allium fistulosum Chromosome identity Linkage map Monosomic addition lines Single alien deletion lines 



Expressed sequence tag




Single nucleotide polymorphism


Simple sequence repeat



We are grateful to Misses K. Tanaka and S. Negoro for the technical assistance. This work was supported by the project NARO Research Project No. 211 “Establishment of Integrated Basis for Development and Application of Advanced Tools for DNA Marker-Assisted Selection in Horticultural Crops”, National Institute of Vegetable and Tea Science Priority Research Program, and Grant-in-Aid for Young Scientists (B) (19780010), Japan Society for the Promotion of Science.

Supplementary material

122_2010_1464_MOESM1_ESM.xls (234 kb)
Suppl. Table 1 Primer sequences of 353 bunching onion SSR markers identified chromosome locations (XLS 234 kb)
122_2010_1464_MOESM2_ESM.xls (48 kb)
Suppl. Table 2 Primer sequences of 57 bulb onion EST-derived SSR markers identified chromosome locations (XLS 47 kb)
122_2010_1464_MOESM3_ESM.xls (100 kb)
Suppl. Table 3 Primer sequences of 160 bulb onion EST-derived non-SSR markers identified chromosome locations (XLS 100 kb)


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Copyright information

© Springer-Verlag 2010

Authors and Affiliations

  • Hikaru Tsukazaki
    • 1
  • Ken-ichiro Yamashita
    • 1
  • Shigenori Yaguchi
    • 2
    • 3
  • Koichiro Yamashita
    • 4
  • Takuya Hagihara
    • 4
  • Masayoshi Shigyo
    • 2
  • Akio Kojima
    • 1
  • Tadayuki Wako
    • 1
  1. 1.National Institute of Vegetable and Tea Science (NIVTS), NAROTsuJapan
  2. 2.Department of Biological and Environmental Science, Faculty of AgricultureYamaguchi UniversityYamaguchiJapan
  3. 3.Toricon Co., LtdOhnan, OhchiJapan
  4. 4.Hokuren Agricultural Research InstituteNaganumaJapan

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