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Title: Legume genomics: Understanding biology through DNA and RNA sequencing

item O`Rourke, Jamie
item BOLON, YUNG-TSI - University Of Minnesota
item Bucciarelli, Bruna
item VANCE, CARROLL - University Of Minnesota

Submitted to: Annals of Botany
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/26/2014
Publication Date: 9/24/2014
Citation: O'Rourke, J.A., Bolon, Y., Bucciarelli, B., Vance, C.P. 2014. Legume genomics: Understanding biology through DNA and RNA sequencing. Annals Of Botany. 113(7):1107-1120.

Interpretive Summary: The legume family (Leguminosae) consists of approximately 17,000 species. Two of these are important crop species in the US (soybean and alfalfa) while other members are important components of traditional diets, providing protein and carbohydrates for over 300 million people world-wide. Next-generation sequencing technologies have allowed individual researchers to assemble genome sequences, identify gene coding regions, and study gene expression patterns. We present an over-view of how researchers are using next-generation sequencing to study legume genomics and biological processes. To illustrate the power of these technologies we include an in-depth analysis on the gene expression profiles of oil seed development in soybean and changes in gene expression due to phosphate deficiency in white lupin.

Technical Abstract: Background. The legume family (Leguminosae) consists of approximately 17,000 species. A few of these species including, but not limited to; Phaseolus vulgaris, Cicer arietinum, and Cajanus cajan, are important dietary components, providing the dietary protein for approximately 300 million people worldwide. Additional species, including soybean, Glycine max; and alfalfa, Medicago sativa; are important crop species utilized mainly in animal feed. Additionally, legumes are important contributors to biological nitrogen, forming symbiotic relationships with rhizobia to fix atmospheric N2 and providing up to 30% of available N for the next season’s crops. The application of high throughput genomic technologies including genome sequencing projects, genome re-sequencing (DNA-seq), and transcriptome sequencing (RNA-seq) by the legume research community has provided major insights into genome evolution, genomic architecture, and domestication. Scope. In this article we present an over-view of the current state of legume genomics and explore the role next-generation sequencing technologies play in advancing legume genomics. The adoption of next-generation sequencing and implementation of associated bioinformatic tools has allowed researchers to turn each species of interest into their own model organism. To illustrate the power of next-generation sequencing, we provide an in-depth overview of the transcriptomes of both soybean and white lupin. The soybean transcriptome focuses on analyzing soybean seed development in two near-isogenic lines, examining the role of transporters, oil biosynthesis, and nitrogen utilization (Bolon et al., 2010, Severin et al., 2010b). The white lupin transcriptome analysis examines how phosphate deficiency alters gene expression patterns inducing the formation of cluster roots (O'Rourke et al., 2013). These studies illustrate the power of next-generation sequencing and bioinformatic analyses in elucidating the gene networks underlying biological processes.