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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 Title: Transcriptome of common bean (Phaseolus vulgaris) through RNA-seq: nodulation, symbiotic nitrogen fixation, transcription factors

Authors
item Hernandez, Georgina -
item Iniguez, Luis -
item O'Rourke, Jamie
item Mcclean, Phillip -
item Shoemaker, Randy
item Jackson, Scott -
item Vance, Carroll

Submitted to: Plant and Animal Genome Conference
Publication Type: Abstract Only
Publication Acceptance Date: September 14, 2011
Publication Date: January 10, 2012
Citation: Hernandez, G., Iniguez, L.P., O'Rourke, J.A., McClean, P., Shoemaker, R.C., Jackson, S., Vance, C.P. 2012. Transcriptome of common bean (Phaseolus vulgaris) through RNA-seq: nodulation, symbiotic nitrogen fixation, transcription factors [abstract]. Plant and Animal Genome XX Conference, January 14-18, 2012, San Diego, California. Available: http://pag.confex.com/pag/xx/webprogram/Paper1559.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 have performed next generation sequencing (RNA-seq) of different plant tissues from Phaseolus vulgaris cv. Negro Jamapa. RNA-seq of 24 RNA libraries from common bean seeds, pods, leaves, roots, and nodules at different stages of development generated 25 million 36-bp reads per sample. From these, 80,462 transcripts were assembled and 50,000 were annotated. Our libraries included: nitrogen-fixing nodules, non-fixing nodules (elicited by an inefficient rhizobia), and roots associated with the nodules. A total of seven RNA samples were collected at two distinct stages of nodule development: 5 and 21 days post inoculation. A sample of non-inoculated roots was used as a control. These samples allow a comprehensive transcriptomic study of symbiotic nitrogen fixation (SNF) in common bean and the role of Rhizobium etli in nodule formation. Comparative analyses of the expression profiles has allowed the identification of genes specific for nodulation, nitrogen fixation, and changes induced in root tissues due to SNF. Our common bean transcriptome revealed 3,567 transcripts annotated as transcription factors (TF) belonging to 52 gene families. Utilizing our expression profiles, we have identified TFs specifically involved in nodulation and SNF signaling and regulation.

Last Modified: 10/22/2014
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