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United States Department of Agriculture

Agricultural Research Service


Location: Plant Genetics Research

2011 Annual Report

1a. Objectives (from AD-416)
Objective 1: Determine if altering expression of genes that exhibit evidence of past selection during maize domestication and improvement, modifies the expression of currently relevant agronomic traits. Objective 2: Develop strategies and mechanisms for improving drought-stress tolerance of maize. Objective 3: Conduct an analysis of the role of transcription factors in controlling agronomic traits in maize. Objective 4: Integrate new maize genetic and genomic data into the database (MaizeGDB).

1b. Approach (from AD-416)
Identify and verify selected genes. Make teosinte NIL and use to characterize phenotypic effect of teosinte alleles of selected genes. Identify genes central to drought-tolerance in plants for maize improvement. Use transgenic maize line to test candidate genes for drought tolerance. Identify transcription factors exhibiting specific transcription responses to drought treatments. Analysis the role of MYB transcription factors in controlling agronomic trait expression.

3. Progress Report
Progress of this research addresses the application of genetics and genomics to the improvement of agronomic traits of a major crop, maize. ARS scientists in Columbia, MO continued to evaluate teosinte near isogenic lines (NILs) to identify genes underlying agronomic traits and to compare the allelic variation of teosinte to that of inbreds. We measured flowering time, plant height, kernel row number, and kernel weight from multiple locations, and analyzed kernel composition (starch, protein, and oil content). We collected similar data in 2010 for 2500 diverse inbred lines from the USDA-ARS Plant Introduction Station in Ames, IA. A subset of these 2500 diverse inbreds was evaluated as hybrids in summer 2011, and data were collected for flowering time, plant height, and numerous other traits. The genetic and molecular basis underlying the steady yield gains in maize is unknown. The maize BSSS and BSCB1 selection populations are the most studied maize improvement populations and the source of many inbred lines of historic importance to corn production. Thirty-six individuals of the founders and of cycles 0, 4, 8, 12, and 16 of selection of each population were genotyped with a 55,000 assay maize single nucleotide polymorphism (SNP) array. These data allow the first analysis the importance of selection versus genetic drift and the identification of the most important regions of the maize genome to yield gains within a maize breeding program. This study will also allow us to form a testable hypothesis about the genetic basis of heterosis in maize. In collaboration with USDA-ARS colleagues, the nested association mapping (NAM) population continues to increase in its importance as the central biological resource for the maize community. Deciphering both putative and confirmed functionality of the B73 reference maize genome sequence is a major goal of the maize research community. This year, Maize Genome Database (MaizeGDB) began the integration of whole genome expression data, including from next generation technologies. Both maize-specific and plant-wide terms of the Plant Ontology project are employed in the data integration, so that these data can be transferred to other crop and model plant species. Progress is ongoing in the integration of experimentally confirmed functions to the computationally defined gene models viewed on the MaizeGDB genome browser. We completed our analysis of the Sporobolus transcriptome and established that approximately 2700 genes respond to dehydration and rehydration. We identified several clusters of genes that have identical expression profiles suggesting key regulatory programs that relate to dehydration tolerance. We are currently identifying candidate genes for homolog searches in maize. We completed Sporobolus metabolome data and have added hormone profiling to the analysis. We identified a key process that links dehydration tolerance, reactive oxygen species (ROS) protection, and nitrogen remobilization and extended these studies to maize. We completed our initial analysis of maize root miRNAs.

4. Accomplishments
1. Metabolic processes important for dehydration and drought tolerance in plants. Droughts in the U.S. and across the globe threaten food security and contribute to the growing problem of malnutrition and hunger. Understanding how plants tolerate dehydration stress during a drought is key to developing strategies for crop improvement for drought tolerance. ARS scientists in Columbia, MO utilized a closely related pair of grass species, one tolerant and one sensitive to dehydration of their vegetative tissues, to elucidate which metabolic processes contribute to dehydration tolerance. We found, along with accumulation of sugars and a change in membrane components, that a metabolic junction between pathways central to protection from plant cells from oxidative damage (associated with drought stress) and those involved in the movement of nitrogen within shoots is central to the response of the plant to dehydration. The identification of such a key metabolic response to dehydration allows us to take a focused approach to manipulating drought tolerance in corn, our target crop. The ability to focus attention to a specific process will enable breeders to develop novel genetic strategies for improving drought tolerance in maize and which will ultimately improve food security and address yield stability in a changing climate.

2. Teosinte, the ancestor of maize (corn), harbors wider genetic variation than modern maize for flowering time. Domestication of maize from its wild ancestor, teosinte, has resulted in a decrease in genetic diversity in modern maize. ARS scientists in Columbia, MO, hypothesized that there has been a corresponding decrease in phenotypic (measurable traits) diversity in maize relative to teosinte. ARS scientists in Columbia, MO, evaluated ten teosinte introgression populations (nearly genetically identical individual maize lines, each containing ~3% of the teosinte genome in a corn genetic background) for flowering time in seven environments previously grown between 2009 and 2010. We found that teosinte genes exhibit a greater range of effects for genomic regions previously shown to control flowering time in maize. These results confirm our hypothesis, and suggest that teosinte likely harbors large effect genes for many other agronomic traits. The populations developed by ARS scientists in Columbia, Mo, are currently used by breeders interested in obtaining new genes for disease resistance in maize. Ultimately, teosinte can be utilized as a source for useful variation to improve corn for producers and consumers, as well as many industrial applications.

3. Integration at Maize Genome Database (MaizeGDB) of a gene atlas for the maize genome. The maize genome sequence has been available several years, but remains largely anonymous with little information about what the various 35,000 genes actually do. One type of project to decipher the maize genome sequence defines the expression conditions of each and every gene. USDA-ARS MaizeGDB scientists at Columbia, Missouri, Ames, Iowa and Albany, California have designed and implemented the online display of data recently supplied by researchers at the University of Wisconsin, Madison, Wisconsin, and Michigan State University, East Lansing, Michigan, and reports expression for over 30,000 gene models in 60 tissues and developmental stages. ARS scientists have enhanced the utility of these data so that breeders and geneticists working with other crop plants, through use of generic plant anatomy and growth terms from the Plant Ontology project, make better decisions in their trials and experiments. Plant breeders and researchers make use of this data representation to find candidate genes important for improving both maize and related crops. Examples include genes critical to the response to environmental stresses, the development of varieties for niche markets, and the utility of maize as a biofuel, a target of the researchers that supplied the data.

Review Publications
Zhang, N., Gur, A., Gibbon, Y., Sulpice, R., Flint Garcia, S.A., Mcmullen, M.D., Stitt, M., Buckler IV, E.S. 2010. Genetic analysis of central carbon metabolism unveils an amino acid substitution that alters maize NAD-dependent isocitrate dehydrogenase activity. PLoS One. 5(4):e9991.

Koster, K.L., Balsamo, R.A., Catherine, E., Oliver, M.J. 2010. Desiccation sensitivity and tolerance in the moss Physcomitrella patens: assessing limits and damage. Plant Growth Regulation. 62:293-302.

Bottoms, C., Flint Garcia, S.A., McMullen, M.D. 2010. IView: Introgression library visualization and query tool. BMC Bioinformatics. 11(6):S28.

Zhao, Q., Weber, A., McMullen, M.D., Guill, K.E., Doebley, J. 2010. MADS-box genes in maize: Frequent targets of selection during domestication. Genetics Research. 93:65-75.

Tian, F., Bradbury, P., Brown, P., Sun, Q., Flint Garcia, S.A., Rocheford, T.R., McMullen, M.D., Holland, J.B., Buckler IV, E.S. 2011. Genome-wide association study of maize identifies genes affecting leaf architecture. Nature Genetics. 43:159-162.

Kump, K., Bradbury, P., Buckler IV, E.S., Belcher, A., Oropeza-Rosas, M., Wisser, R., Zwonitzer, J., Kresovich, S., McMullen, M.D., Ware, D., Balint Kurti, P.J., Holland, J.B. 2011. Genome-wide association study of quantitative resistance to southern leaf blight in the maize nested association mapping population. Nature Genetics. 43:163-168.

Oliver, M.J., Guo, L., Alexander, D.C., Ryals, J.A., Wone, B., Cushman, J.C. 2011. A sister group metabolomic contrast delineates the biochemical regulation underlying desiccation tolerance in Sporobolus stapfianus. The Plant Cell. 23(4):1231-1248.

Oliver, M.J., Jain, R., Balbuena, T.S., Agrawal, G.K., Gasulla, F., Thelen, J.J. 2010. Proteome analysis of leaves of the desiccation-tolerant grass, Sporobolus stapfianus, in response to desiccation. Phytochemistry. 72:1273-1284.

Green, J.M., Harnsomburana, J., Schaeffer, M.L., Lawrence, C.J., Shyu, C. 2011. Multi-source and ontology-based retrieval engine for maize mutant phenotypes. Database: The Journal of Biological Databases and Curation. 2011:Article ID bar012. Available:

Schaeffer, M.L., Harper, E.C., Gardiner, J.M., Andorf, C.M., Campbell, D.A., Cannon, E.K., Sen, T.Z., Lawrence, C.J. 2011. MaizeGDB: Curation and outreach go hand-in-hand. Database: The Journal of Biological Databases and Curation. 2011:Article bar022. Available:

Harper, E.C., Schaeffer, M.L., Thistle, J., Gardiner, J., Andorf, C.M., Campbell, D.A., Cannon, E.K., Braun, B.L., Birkett, S., Lawrence, C.J., Sen, T.Z. 2011. The MaizeGDB Genome Browser Tutorial: One example of database outreach to biologists via video. Database: The Journal of Biological Databases and Curation. DOI: 10.1093/database/bar016:1.

Last Modified: 06/26/2017
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