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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: Rna-Seq Atlas of Glycine Max: a Guide to the Soybean Transcriptome

Authors
item Severin, Andrew -
item Woody, Jenna -
item Bolon, Yung Tsi
item Joseph, Bindu -
item Diers, Brian -
item Farmer, Andrew -
item Weeks, Nathan
item Muehlbauer, Gary -
item Nelson, Rex
item Grant, David
item Specht, James -
item Graham, Michelle
item Cannon, Steven
item May, Gregory -
item Vance, Carroll
item Shoemaker, Randy

Submitted to: Biomed Central (BMC) Plant Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: June 1, 2010
Publication Date: August 5, 2010
Repository URL: http://hdl.handle.net/10113/46582
Citation: Severin, A.J., Woody, J.L., Bolon, Y.E., Joseph, B., Diers, B.W., Farmer, A.D., Muehlbauer, G.J., Nelson, R., Grant, D.M., Specht, J.E., Graham, M.A., Cannon, S.B., May, G.D., Vance, C.P., Shoemaker, R.C. 2010. RNA-Seq Atlas of Glycine max: a guide to the soybean transcriptome. Biomed Central (BMC) Plant Biology. 10:610.

Interpretive Summary: Legumes are critical as sources of food and oil. They contribute to soil health and economic sustainability because they can produce their own nitrogen fertilizer through symbiotic nitrogen fixation. Soybean is the world's most valuable legume. The genome of soybean has been recently sequenced and we now know a great deal about where genes are located on the chromosome. However, we know much less about where the genes are expressed and what are the most highly expressed genes. To answer these questions about soybean gene expression, we performed massive high throughput sequencing of soybean gene expression. We evaluated 14 different organs at various developmental stages. Of the 46,430 known soybean genes, we found transcripts for 41,975 (90%). We also identified gene transcripts for 7,000 gene models that were previously unknown. Comparative analysis of genes expressed in various organs allowed us to identify organ-specific genes for each tissue evaluated. Our compilation of gene expression provides a global atlas of genes found in each organ. The data will be useful to any plant scientist interested in gene expression and organ function.

Technical Abstract: A first analysis of the Glycine max (L.) Merr. (soybean) transcriptome using next generation sequencing technology and RNA-Sequencing (RNA-Seq) is presented. This analysis will provide an important resource for understanding transcription and gene co-regulatory networks in soybean, the most economically important crop-legume globally. The RNA Seq-Atlas provides high-resolution gene expression in a diverse set of seven tissues and seven stages in seed development. Mining of these data suggested three clades of tissue (aerial, underground, and seed) that exhibited transcriptionally similar profiles. Furthermore, analysis of genes with preferential gene expression in seed revealed more than 177 genes with a significant increase in expression in late seed development. These genes have gene expression profiles similar to genes involved in nutrient reservoir activity, which may indicate functional roles that complement or aid in the economically important seed filling process. Additionally, the Seq-Atlas suggests legume-specific genes may have tissue-specific gene expression. The RNA-Seq Atlas reported here also provides a means of evaluating existing gene model annotations for the Glycine max genome.

Last Modified: 8/1/2014