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United States Department of Agriculture

Agricultural Research Service

Research Project: FUNCTIONAL AND STRUCTURAL GENETIC ANALYSIS OF SOYBEAN AND OTHER LEGUMES
2011 Annual Report


1a.Objectives (from AD-416)
Objective 1: Identify and evaluate genes important for agronomic performance (e.g., symbiosis/nitrogen fixation, nutrient uptake and utilization, yield, composition, etc.). Objective 2: Identify and evaluate genes useful for legume defense against pathogens, e.g., Asian Soybean Rust. Objective 3: Conduct comparative analyses of legume genes and genomes to place agronomically important genes in evolutionary and genome sequence context.


1b.Approach (from AD-416)
The project will define and characterize the organization and structure of the soybean genome and the genomes of other legumes with special emphasis on genes and gene families that underlie important agronomic and developmental traits. Hydroponics and global gene expression tools will be used to identify genes differentially expressed during iron stress conditions. Affymetrix GeneChips will be used to identify genes involved in yield, seed composition, and other important traits in soybean. Bioinformatics will be used to position these genes on the whole genome sequence and the genetic map. Bioinformatic and experimental approaches will be used to identify and map genes differentially expressed during defense response and to identify and map defensin-like genes. A set of comparative molecular-evolutionary protocols will be used to make systematic and integrated use of large amounts of new genomic and functional data. Analyses will include comparison of homeologous regions, phylogenetic comparisons, and annotation of specific genomic regions.


3.Progress Report
Viral induced gene silencing has been used to down-regulate genes thought to be involved in iron deficiency chlorosis. A beta helix-loop-helix transcription factor (gene regulator) was down regulated causing stunting in plants grown under hydroponic conditions. Additionally, a gene family associated with DNA replication was analyzed and it was determined that some members of the family are associated with iron deficiency chlorosis; probably as a repair mechanism after severe stress. The project combined soybean genetics and genomics with cutting-edge virus induced gene silencing (VIGS) technology to identify a single gene responsible for Rpp4-mediated resistance to Asian soybean rust. Using bioinformatic techniques ARS scientists from Ames, IA has examined the evolution of the Rpp4 gene cluster in soybean and other plant species. While the Rpp4 locus is conserved across a wide range of plant species, acquisition of resistance genes in this region has been relatively recent and is restricted to a small subset of legumes, including many crop legumes. Domestication of these species on separate continents has profoundly affected the evolution of this region and pathogen specificity. Understanding how Rpp4 evolved can help us find novel sources of resistance to Asian soybean rust. RNA-Seq technology was used to identify differentially expressed genes in iron efficient and iron inefficient genotypes, grown hydroponically in iron sufficient and iron insufficient conditions. Plants were assayed at 1 hour, 6 hour, and 24 hours after stress induction. RNA-Sequencing was conducted by collaborators at the National Center for Genome Resources, Santa Fe, New Mexico. Data is currently being analyzed to identify differentially expressed genes. A large collection of gene expression data (Gene Atlas) is continually being analyzed to determine in which tissues specific genes are expressed. These analyses contribute to the whole genome annotation of the soybean genome sequence.


4.Accomplishments
1. Soybean gene responsible for Asian soybean rust resistance identified. By combining soybean genetics and genomics with cutting-edge virus induced gene silencing (VIGS) technology, ARS scientists in Ames, Iowa, have identified a single gene (Rpp4) responsible for resistance to the rust pathogen. Asian soybean rust (ASR) is a devastating disease worldwide causing crushing losses in soybean production. Using bioinformatic techniques, the evolution of the Rpp4 gene cluster in soybean and other plant species was examined. Although the location on a chromosome where the resistance gene is found is present in a wide range of other plants, the resistance gene itself is only found in a small subset of plants. Thus, however the resistance gene was acquired, it seems it was acquired quite recently. Domestication of legumes on separate continents has profoundly affected the evolution of this region and pathogen specificity. Understanding how Rpp4 evolved can help us find novel sources of resistance to Asian soybean rust.

2. Soybean development genes decoded and characterized. ARS scientists at Ames, Iowa, have used 'next-generation' sequencing technology to decode and measure gene expression of all soybean genes expressed in 14 different environmental conditions. These ARS scientists, working with collaborators at the University of Minnesota and the National Center for Genome Resources in Santa Fe, New Mexico, used this information to uncover novel patterns of expression associated with certain physical attributes of chromosomes. They also created a novel and more precise method to pin-point the location of genes controlling key agronomic traits such as protein production and iron efficiency. All success in plant breeding is the result of altering gene combinations that result in changes in gene expression. These results are important for understanding crop adaptation to the environment and for understanding the regulation of gene expression critical to crop improvement.


Review Publications
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.

Severin, A.J., Peiffer, G., Xu, W.W., Hyten, D.L., Bucciarelli, B., O'Rourke, J.A., Bolon, Y.E., Grant, D.M., Farmer, A.D., May, G.D., Vance, C.P., Shoemaker, R.C., Stupar, R.M. 2010. An integrative approach to genomic introgression mapping. Plant Physiology. 154(1):3-12.

Pandey, A.K., Yang, C., Zhang, C., Graham, M.A., Horstman, H.D., Lee, Y., Zabotina, O.A., Hill, J.H., Pedley, K.F., Whitham, S.A. 2011. Functional analysis of the Asian soybean rust resistance pathway mediated by Rpp2. Molecular Plant-Microbe Interactions. Molecular Plant-Microbe Interactions. 24:194-206.

Woody, J.L., Severin, A., Bolon, Y.E., Joseph, B., Diers, B.W., Farmer, A.T., Weeks, N.T., 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. 2011. Gene expression patterns are correlated with genomic and genic structure in soybean. Genome. 54(1):10-18.

Last Modified: 12/21/2014
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