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United States Department of Agriculture

Agricultural Research Service

Research Project: FUNCTIONAL GENOMICS FOR IMPROVING NUTRIENTS AND QUALITY IN ALFALFA AND SOYBEAN

Location: Plant Science Research

Title: The transcriptome of common bean: more than nodulation

Authors
item O'Rourke, Jamie
item Iniguez, Luis -
item BUCCIARELLI, BRUNA
item Woodey, Jenna -
item Mcclean, Phillip -
item Jackson, Scott -
item Shoemaker, Randy
item Hernandez, Georgina -
item VANCE, CARROLL

Submitted to: American Society of Plant Biologists Annual Meeting
Publication Type: Abstract Only
Publication Acceptance Date: April 7, 2011
Publication Date: August 6, 2011
Citation: O'Rourke, J.A., Iniguez, L.P., Bucciarelli, B., Woodey, J.L., McClean, P.E., Jackson, S.A., Shoemaker, R.C., Hernandez, G., Vance, C.P. 2011. The transcriptome of common bean: more than nodulation [abstract]. Plant Biology 2011, American Society of Plant Biologists Annual Meeting, August 6-10, 2011, Minneapolis, Minnesota. Available: http://abstracts.aspb.org/pb2011/public/M20/M2003.html.

Technical Abstract: Phaseolus vulgaris (common bean) is one of the most important grain legumes for direct human consumption. It comprises 50% of the grain legumes consumed worldwide and is important as a primary source of dietary protein in developing countries. We performed next generation sequencing (RNAseq) on five tissues (seeds, pods, leaves, roots, and nodules) of Phaseolus vulgaris cv. Jamapa at three stages of development generating 2.1 x 10**9 bp of sequence data. The sequences were used in a de-novo assembly to identify expressed transcripts. The study identified 102,179 transcript assemblies (greater than or equal to 100 bp) were expressed in seeds, 108,174 assemblies expressed in pods, 139,389 in leaves, 171,349 in roots, and 85,557 assemblies were expressed in nodules. This is the first whole plant transcriptome study of Phaseolus vulgaris. Comparative analysis of the expression profiles of the transcripts identified tissue-specific transcripts. The assemblies were also aligned to both the Phaseolus genome scaffolds and the soybean predicted genes to identify any changes in gene expression patterns potentially related to whole genome duplication. Additionally, we have identified potential alternative splice patterns within these assemblies and have examined their expression patterns to determine if expression is modified due to tissue or developmental specificity. A whole transcriptome analysis will be presented for root and nodule development.

Last Modified: 7/25/2014