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United States Department of Agriculture

Agricultural Research Service

Title: Expressed Sequence Tags of Onion for Comparative Mapping of the Asparagales

Authors
item Havey, Michael
item Jenderek, Maria
item Sink, Ken - MICHIGAN STATE UNIV
item Cheung, Foo - INST FOR GENOME RESEARCH
item Town, Chris - INST FOR GENOME RESEARCH

Submitted to: Plant Genome Conference Proceedings
Publication Type: Abstract Only
Publication Acceptance Date: December 1, 2002
Publication Date: December 1, 2002
Citation: Havey, M.J., Jenderek, M.M., Sink, K., Cheung, F., Town, C. 2002. Expressed sequence tags of onion for comparative mapping of the asparagales. Plant Genome Conference Proceedings.

Technical Abstract: Enormous genomic resources are being developed for model plants such as Arabidopsis thaliana and rice. However, it is not clear how broadly these genomic resources can be applied to the genetic improvement of related crops. Onion (Allium cepa) is the most economically important member of the monocot order Asparagales, followed by garlic (A. sativum), and asparagus (Asparagus officinalis). The Asparagales and Poales (contains the grass family) represent two distinct monophyletic groups in the monocots comprising the Lilianae and Commelinanae, respectively. A salient question is whether the genomic resources developed for rice or other members of the Poales will be applicable to the Asparagales. To address this question, we synthesized a normalized cDNA library of onion from equal molar amounts of mRNA from callus, immature bulbs, and roots. The frequency of beta-tubulin cDNAs was reduced from 0.28% to 0.004% by the normalization process, a 70-fold reduction. So far, 14,102 single pass sequencing reactions have yielded 12,308 good sequences that assembled into 2,296 clusters and 6,015 singletons for a total of 8,311 distinct sequences, at least twice the number expected from a non-normalized library. Over 5,000 showed highly significant homologies to rice ESTs. These significant homologies between ESTs from onion and rice will be used for comparative mapping of the Poales and Asparagales.

Last Modified: 10/21/2014
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