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ARS Home » Midwest Area » Madison, Wisconsin » Vegetable Crops Research » Research » Publications at this Location » Publication #168532
Title: EXPLOITING ESTS FOR COMPARATIVE MAPPING OF ONION AND RICE.

Author
item Martin, William
item CHEUNG, FOO - INST FOR GENOMIC RES-MD
item TOWN, CHRISTOPHER - INST FOR GENOMIC RES-MD
item Havey, Michael

Submitted to: Plant Genome Analysis Abstracts
Publication Type: Abstract Only
Publication Acceptance Date: 12/1/2003
Publication Date: 1/15/2004
Citation: Martin, W.J., Cheung, F., Town, C.D., Havey, M.J. 2004. Exploiting ests for comparative mapping of onion and rice.. Plant Genome Analysis Abstracts.

Interpretive Summary:

Technical Abstract: The Asparagales are a monophyletic order sister to the Poales and contain economically important plants such as asparagus, garlic, and onion. Genomic resources and syntenic relationships are well established for the Poales. However, the extent of synteny between the Asparagales and Poales is unknown. To assess these syntenic relationships, a comparative mapping project was initiated. Single pass sequencing from a normalized onion cDNA library revealed 11,008 unique ESTs. A sub-set of unique ESTs was selected based on high similarities to non-duplicated rice loci. Primers were designed from onion EST and rice EST/BAC alignments. Amplified onion genomic sequences were TA cloned and sequenced to confirm similarities between onion and rice and subsequently screened for SNPs, indels and microsatellites. The majority of detected polymorphisms were SNPs, of which 40 were added to the previously published onion map. A comparative linkage map of onion and rice was compiled and no obvious syntenic relationship on the recombinational level was found. The lack of synteny between onion and rice support the development of genomic resources for non-Poales monocots.