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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

2012 Annual Report


1a.Objectives (from AD-416):
Objective 1: Use discoveries from Medicago truncatula, a model legume, root and root nodule genomics to characterize and improve the biological efficiency of symbiotic nitrogen (N2) fixation in alfalfa. Objective 2: Develop and employ RNA interference (i) -mediated gene silencing to identify the functional role of genes involved in phosphorus and nitrogen acquisition and metabolism in root tissues of legumes such as common bean, pea, and lentil. Objective 3: Determine genes regulating protein and oil accumulation in soybean through whole genome transcript analysis and functionally characterize gene candidates.


1b.Approach (from AD-416):
Alfalfa genes important in nitrogen fixation will be identified from the Medicago EST and genome sequencing projects. The sequence of 5'-promoter regions of selected genes will be identified from both alfalfa and M. truncatula. The expression of selected root nodule genes will be silenced through RNA interference. Nodules from plants containing RNA interference will be characterized for nitrogen fixation and nodule development. The Medicago truncatula gene chip will be used to assess global gene expression in alfalfa.


3.Progress Report:
High-throughput RNA-seq data from phosphorus-stressed lupin leaves and roots, 16 common bean tissues, and 12 alfalfa tissues were analyzed. In lupin, suites of genes involved in plant hormone signaling, one carbon metabolism, glyoxylate cycle, and organic acid synthesis were found to respond to low phosphorus. In alfalfa, genes specific to nodules, stems, roots, leaves, and flowers were identified. Using the common bean RNA-seq data, we found several thousand genes in soybean that evolved different expression patterns. Fifty new soybean fast neutron mutants were identified. These mutants were found through root phenotype screens. We found fibrous root, small root, no tap-root, and ineffective nodule mutants.


4.Accomplishments
1. Understanding genetic regulation of soybean growth and development. A major objective for the legume community is to develop genomic tools to understand soybean growth, development, and quality. In order to understand genetic regulation of soybean, ARS researchers at St. Paul, Minnesota, in collaboration with State colleagues developed a large population of soybean mutants generated through mutagenesis. Root visual phenotype was evaluated on 5,000 individual mutagenized plants. To date we have found 50 mutants exhibiting altered root phenotypes. The plants exhibiting altered root phenotypes will enable new discoveries of the genetic control of soybean productivity.

2. Phosphorus stress in legumes. Although phosphorus (P) is abundant in soils, it is largely unavailable for uptake by plants and is frequently the most limiting nutrient for plant growth and development. ARS researchers in St. Paul, Minnesota, in collaboration with University of Minnesota cooperators conducted next generation high-throughput RNA sequencing on leaves and roots of P-stressed white lupin. A white lupin gene index was developed from the RNA-seq data. Plant gene acclimation to P deficiency was assessed by comparing RNA transcripts expressed in P-sufficient versus P-deficient tissue. A novel plant growth signaling pattern involving gibberillic acid was found to be responsive to P-deficiency and mediate root architecture. The discovery of growth hormone signaling to be important in acclimation to P deficiency offers strategies for management of root architecture to improve crop adaptation to abiotic stress.

3. Sugars are required for plant response to abiotic stress. Sugars from photosynthesis have been shown to be integrally involved in the expression of genes that respond to phosphorus, iron, and sulfur deficiency. ARS scientists at St. Paul, Minnesota, have discovered a mutant Arabidopsis plant having extremely high expression of a gene designated sucrose transporter 2 (SUC2). Plants having high expression of SUC2 show a phenomenal increase in growth. Gene constructs were made to recapitulate the SUC2 phenotype (increased vigor and growth). Discovery of the SUC2 growth response will improve the partitioning of photosynthate to seeds and fruits.

4. Plant transporters are required for symbiotic nitrogen fixation and legume seed development. Legumes are important for agriculture because they can symbiotically fix atmospheric nitrogen, thus requiring no nitrogen fertilizer, and because their seeds are rich sources of protein and oil. ARS scientists at St. Paul, Minnesota, in collaboration with colleagues at the University of Minnesota conducted whole genome high-throughput RNA-sequencing on root nodules and developing seed of soybean and common bean. Plant genes expressed only in nodules and seeds were identified and expression levels calculated. Selected genes identified as being crucial to symbiosis and/or seed development can be utilized to increase symbiotic nitrogen fixation and seed nitrogen content.


Review Publications
Bolon, Y.E., Vance, C.P. 2012. Characterization of the Linkage Group I seed protein QTL in soybean. In: Wilson, R.F., editor. Designing Soybeans for 21st Century Markets. Urbana, Illinois: American Oil Chemists' Society. p. 175-195.

Last Modified: 4/19/2014
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