Submitted to: Plant Physiology
Publication Type: Peer reviewed journal
Publication Acceptance Date: 3/15/2005
Publication Date: 4/1/2005
Citation: Ramirez, M., Graham, M.A., Blanco-Lopez, L., Silvente, S., Medrano-Soto, A., Blair, M.W., Hernandez, G., Vance, C.P., Lara, M. 2005. Sequencing and analysis of common bean ESTs. Building a foundation for functional genomics. Plant Physiology. 137:1211-1227. Interpretive Summary: Common bean (Phaseolus vulgaris) is a primary source of protein throughout the world. While concerted efforts on model crops like rice, corn, soybean, and wheat have determined sequences of thousands of genes that may prove useful in improving nutritional content and tolerance to diseases and other stresses, comparable information is not available for common bean. In this report we document the sequence of some 20,000 genes from various organs of bean including roots, leaves, pods, seeds, and nitrogen-fixing root nodules. Because we sequenced genes from two different cultivars of bean, we were able to isolate gene markers for more than 300 genes. Due to the importance of symbiotic nitrogen fixation to bean production and quality, we evaluated the expression of 3,000 genes found in symbiotic root nodules. The data showed that the types of genes expressed in common bean symbiotic root nodules are very different than those expressed in alfalfa, pea, and soybean symbiotic root nodules. Results reported in this manuscript are important for several reasons: 1) they provide new genetic resources that will be useful in improving common bean through both conventional breeding and biotechnology; 2) new findings about genes involved in symbiotic nitrogen fixation lay the foundation for improving this critical process; and 3) the diversity of genes found in legume symbiotic root nodules shows that while these organs have a common function (nitrogen fixation), they accomplish it through genes unique to each species. Resources developed in this project provide genetic and genomic tools for an international consortium devoted to bean improvement.
Technical Abstract: Although common bean (Phaseolus vulgaris L.) is the most important grain legume in the developing world for human consumption, few genomic resources exist for this species. The objectives of this research were to develop EST resources for common bean and assess nodule gene expression through high-density macroarrays. We sequenced a total of 21,026 ESTs derived from five different cDNA libraries including: nitrogen-fixing root 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%), and 15 sub-categories within these. Comparison to other legume ESTs 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 root 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 an international consortium devoted to bean improvement.