Molecular Genetics and Genomics

, Volume 274, Issue 3, pp 197–204 | Cite as

Genetic mapping of expressed sequences in onion and in silico comparisons with rice show scant colinearity

  • William J. Martin
  • John McCallum
  • Masayoshi Shigyo
  • Jernej Jakse
  • Joseph C. Kuhl
  • Naoko Yamane
  • Meeghan Pither-Joyce
  • Ali Fuat Gokce
  • Kenneth C. Sink
  • Christopher D. Town
  • Michael J. Havey
Original Paper


The Poales (which include the grasses) and Asparagales [which include onion (Allium cepa L.) and other Allium species] are the two most economically important monocot orders. Enormous genomic resources have been developed for the grasses; however, their applicability to other major monocot groups, such as the Asparagales, is unclear. Expressed sequence tags (ESTs) from onion that showed significant similarities (80% similarity over at least 70% of the sequence) to single positions in the rice genome were selected. One hundred new genetic markers developed from these ESTs were added to the intraspecific map derived from the BYG15-23×AC43 segregating family, producing 14 linkage groups encompassing 1,907 cM at LOD 4. Onion linkage groups were assigned to chromosomes using alien addition lines of Allium fistulosum L. carrying single onion chromosomes. Visual comparisons of genetic linkage in onion with physical linkage in rice revealed scant colinearity; however, short regions of colinearity could be identified. Our results demonstrate that the grasses may not be appropriate genomic models for other major monocot groups such as the Asparagales; this will make it necessary to develop genomic resources for these important plants.


Expressed sequence tags (ESTs) Genetic markers Restriction fragment length polymorphisms (RFLPs) Simple sequence repeats (SSRs) Single nucleotide polymorphisms (SNPs) 



This work was completed in compliance with the current laws governing genetic experimentation in Japan, New Zealand, and USA and was supported by U.S. Department of Agriculture, Initiative for Future Agriculture and Food Systems Grant 2001-04434 and Grant-in-Aid for Young Scientists (No. 40314827) from the Ministry of Education, Culture, Sports, Science and Technology, Japan.

Disclaimer: Names are necessary to report factually on available data; however, the U.S. Department of Agriculture (USDA) neither guarantees nor warrants the standard of the product, and the use of the name by USDA implies no approval of the product to the exclusion of others that may also be suitable.

Supplementary material

438_2005_7_MOESM1_ESM.pdf (271 kb)
Supplementary material


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Copyright information

© Springer-Verlag 2005

Authors and Affiliations

  • William J. Martin
    • 1
  • John McCallum
    • 2
  • Masayoshi Shigyo
    • 3
  • Jernej Jakse
    • 4
  • Joseph C. Kuhl
    • 5
  • Naoko Yamane
    • 3
  • Meeghan Pither-Joyce
    • 2
  • Ali Fuat Gokce
    • 6
  • Kenneth C. Sink
    • 5
  • Christopher D. Town
    • 7
  • Michael J. Havey
    • 1
  1. 1.Agricultural Research Service, USDA, Department of HorticultureUniversity of WisconsinMadisonUSA
  2. 2.Crop and Food ResearchChristchurchNew Zealand
  3. 3.Faculty of AgricultureYamaguchi UniversityYamaguchiJapan
  4. 4.Department of HorticultureUniversity of WisconsinMadisonUSA
  5. 5.Department of HorticultureMichigan State University USA
  6. 6.Horticulture DepartmentUludag UniversityGorukleTurkey
  7. 7.The Institute for Genomic ResearchRockvilleUSA

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