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United States Department of Agriculture

Agricultural Research Service

Research Project: ALLIUM, CUCUMIS, AND DAUCUS GERMPLASM ENHANCEMENT, GENETICS, AND BIOCHEMISTRY Title: Developing genomic resources for the apiaceae

Authors
item Bowman, Megan -
item Matvienko, Marta -
item Van Deynze, Allen -
item Simon, Philipp
item Senalik, Douglas

Submitted to: Plant and Animal Genome Conference
Publication Type: Abstract Only
Publication Acceptance Date: November 12, 2009
Publication Date: January 9, 2010
Citation: Bowman, M., Matvienko, M., Van Deynze, A., Simon, P.W., Senalik, D.A. 2010. Developing genomic resources for the apiaceae [abstract]. Plant and Animal Genome Conference. P. 037.

Technical Abstract: The Apiaceae family includes carrot, celery, cilantro, dill, fennel and numerous other spice and medicinal crops. Carrot is the most economically important member of the Apiaceae with an annual value of $600 M in the United States alone. There are few genomic resources for carrot or other Apiaceae, with 3600 genomic or EST sequences available in GenBank for carrot (October, 2009). To expand the sequence database for carrot, an EST database using Sanger sequencing was developed from carrot mapping parent, B493, and using Illumina sequencing of two additional mapping inbreds, B6274 and B7262YC, and pooled tissue of 4 F4 families derived from the B493 × QAL (wild carrot) mapping population. Normalized cDNA libraries were constructed from storage and fibrous root, and leaf tissue with insert sizes ranging from 0.5 kb to > 2kb. 18,044 Sanger sequences were assembled to 7285 unigenes using CAP3. Of these, 720 sequences contained one or more SSRs, of which 677 could have primers designed. Illumina sequencing of the three additional samples generated 153 million reads up to 61 bp and from 35 to 39 million reads of 40 bp or longer from each genotype. Twenty seven million have been aligned with Sanger-derived unigenes thus far, and SNPs identified. De novo assembly was done by ABySS or Velvet in conjunction with CAP3. Further analysis of Illumina runs is in progress. Illumina reads have been mapped to the reference unigenes to identify SNPs. A subsample of SNP markers will be validated and evaluated for segregation.

Last Modified: 12/22/2014
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