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United States Department of Agriculture

Agricultural Research Service

Title: Sequencing and Analysis of Phaseolus Vulgaris Ests: Building a Foundation for Functional Genomics

Authors
item Hernandez, G - UNAM, CUERNAVACA, MEXICO
item Ramirez, M - UNAM, CUERNAVACA, MEXICO
item Graham, M - UNIVERSITY OF MINNESOTA
item Blanco-Lopez, L - UNAM, CUERNAVACA, MEXICO
item Silvente, S - UNAM, CUERNAVACA, MEXICO
item Medrano-Soto, A - UNAM, CUERNAVACA, MEXICO
item Blair, M - CIAT-INT CTR TROP AGRIC
item Vance, Carroll
item Lara, M - UNAM, CUERNAVACA, MEXICO

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: June 5, 2005
Publication Date: June 5, 2005
Citation: Hernandez, G., Ramirez, M., Graham, M.A., Blanco-Lopez, L., Silvente, S., Medrano-Soto, A., Blair, M.W., Vance, C.P., Lara, M. 2005. Sequencing and analysis of Phaseolus vulgaris ESTs: building a foundation for functional genomics. 2005 Model Legume Congress, June 5-9, 2005, Pacific Grove, California. Paper No. S36, p. 47.

Technical Abstract: Common bean (Phaseolus vulgaris L.) is the most important grain legume for direct human consumption. It comprises 50% of the grain legume consumed worldwide. In several countries, such as Mexico and Brazil, common bean is very important nutritionally as a primary source of dietary proteins. Common bean is one of the most ancient crops in the Americas. Beans were domesticated separately to form two distinct gene pools, the Andean and the Mesoamerican. Despite the importance of common beans as crop legumes, few genomic resources exist for this species. The objectives of our research were to develop EST resources for common bean and assess nodule gene expression through high-density macroarrays. Our research has been performed within the framework of Phaseomics, the international consortium for Phaseolus genomics, devoted to bean improvement. We sequenced a total of 21,026 ESTs derived from 5 different cDNA libraries including: nitrogen-fixing nodules, phosphorus-deficient roots, developing pods, and leaves of the Mesoamerican genotype, Negro Jamapa 81. The fifth source of ESTs was a leaf cDNA library derived from the Andean genotype, G19833. Of the total high-quality sequences, 5,703 ESTs were classified as singletons, while 10,078 were assembled into 2,266 contigs producing a non-redundant set of 7,969 different transcripts. Sequences were grouped according to four main categories: metabolism (34%), cell cycle and plant development (11%), interaction with the environment (19%), and unknown function (36%). Comparison to other legume EST projects suggest that an entirely different repertoire of genes are expressed in Phaseolus vulgaris nodules. Phaseolus specific contigs, gene families, and single nucleotide polymorphisms (SNPs) were also identified from the EST collection. Functional aspects of individual bean organs were reflected by the 20 contigs from each library comprised of the most redundant ESTs. The abundance of transcripts corresponding to selected contigs was evaluated by RNA blots to determine whether gene expression determined by laboratory methods correlated with in silico expression. Evaluation of nodule gene expression by macroarrays and RNA blots showed that genes related to nitrogen and carbon metabolism are integrated for ureide production. Resources developed in this project provide genetic and genomic tools for Phaseomics.

Last Modified: 9/22/2014
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