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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

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Abstract

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.

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Abbreviations

EST:

Expressed sequence tag

InDel:

Insertion–deletion

SNP:

Single nucleotide polymorphism

SSR:

Simple sequence repeat

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Acknowledgments

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.

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Author notes

  1. Shigenori Yaguchi

    Present address: Toricon Co., Ltd, Nakano 3825-8, Ohnan, Ohchi, Shimane, 696-0102, Japan

Authors and Affiliations

  1. National Institute of Vegetable and Tea Science (NIVTS), NARO, 360 Ano-Kusawa, Tsu, Mie, 514-2392, Japan

    Hikaru Tsukazaki, Ken-ichiro Yamashita, Akio Kojima & Tadayuki Wako

  2. Department of Biological and Environmental Science, Faculty of Agriculture, Yamaguchi University, 1677-1 Yoshida, Yamaguchi, Yamaguchi, 753-8515, Japan

    Shigenori Yaguchi & Masayoshi Shigyo

  3. Hokuren Agricultural Research Institute, Minami2, Higashi9, Naganuma, Hokkaido, 069-1316, Japan

    Koichiro Yamashita & Takuya Hagihara

Authors
  1. Hikaru Tsukazaki
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  2. Ken-ichiro Yamashita
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Corresponding author

Correspondence to Hikaru Tsukazaki.

Additional information

Communicated by M. Havey.

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Suppl. Table

 1 Primer sequences of 353 bunching onion SSR markers identified chromosome locations (XLS 234 kb)

Suppl. Table

 2 Primer sequences of 57 bulb onion EST-derived SSR markers identified chromosome locations (XLS 47 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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Tsukazaki, H., Yamashita, Ki., Yaguchi, S. et al. 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. Theor Appl Genet 122, 501–510 (2011). https://doi.org/10.1007/s00122-010-1464-9

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  • DOI: https://doi.org/10.1007/s00122-010-1464-9

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