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United States Department of Agriculture

Agricultural Research Service


Location: Plant Genetics Research

2013 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:
Over the lifetime of the project this research addressed the application of genetics and genomics for the improvement of agronomic traits in maize. We evaluated teosinte near isogenic lines (NILs) to identify genes underlying agronomic traits and compared the allelic variation of teosinte to that of inbred maize. Progress was halted by the drought of 2012. However, our collected data allowed us to focus on kernel row number (KRN) and kernel weight (KWT) for current and future studies. We identified a large-effect quantitative trait locus (QTL), a region of the genome that explains much of the genetic variation in the trait, for KRN on chromosome 2, where one of the teosinte alleles is predicted to decrease row number by 4 rows. We validated these predicted allelic effects in summer and winter 2012/13, and planted fine mapping populations during spring 2013. We identified a number of KWT QTL and planted a validation trial spring 2013 in Missouri. Knowledge of the underlying genes for these yield components will enable mining for favorable alleles. We used recombinant chromosomes to fine-map the major regulator of DIMBOA (an insect/disease resistance metabolite) pathway to a defined region of chromosome 4 in the high DIMBOA line CI31A. We chose the inbred line CI31A for the donor allele because it has very high levels of DIMBOA at mid-whorl stage. Progress was prevented by hail in 2011 and the extreme drought of 2012. In the past three years we identified genes that are directly involved in dehydration tolerance of plants. We fully characterized the response of two sister species of grass, one desiccation tolerant the other desiccation sensitive, to reveal genes and gene networks associated with dehydration tolerance. To compliment this effort and to increase its discriminatory power, we fully characterized the metabolic responses of both roots and leaves from both grasses. We identified several aspects of the response for more detailed study and for transference to maize. Selected candidate genes are under assessment for use in drought tolerance improvement strategies. We continued our validation of transcription factors expressed in maize in response to specific water deficits and added a complete analysis of small ribonucleic acids (RNAs) [genetic control factors] in maize under drought conditions. In collaboration with members of the MaizeGDB team, we incorporated both gene expression and phenotype data for maize. We integrated a gene atlas for maize into MaizeGDB in an effort to make the database easier to use for all researchers. In the overall time frame of the project we described expressed phenotypes of maize using ontology (a formal shared vocabulary and concepts) standards that can be applied to all plants, and in harmony with standards under development for animal and microbial projects. It is expected that the same standard descriptions can be applied to agronomic traits for all crops. The goal is to allow greater interoperability of genome databases with phenotypic data from distinct species.

4. Accomplishments

Review Publications
Yobi, A., Wone, B., Xu, W., Alexander, D.C., Guo, L., Ryals, J.A., Oliver, M.J., Cushman, J.C. 2012. Comparative metabolic profiling between desiccation-sensitive and desiccation-tolerant species of Selaginella reveals insights into the resurrection trait. Plant Journal. 72:983-999.

Arighi, C.N., Carterette, B., Krallinger, M., Wilbur, J.W., Fey, P., Dodson, R., Cooper, L., Van Slyke, C.E., Dahdul, W., Mabee, P., Schaeffer, M.L., et al 2013. An overview of the biocreative 2012 workshop track III: Interactive text mining task. Database: The Journal of Biological Databases and Curation. 2012:1-18. Available:

Donald, P.A., Heinz, R., Bernard, E., Hershman, D., Hensley, D., Flint Garcia, S.A., Joost, R. 2012. Distribution host status and potential sources of resistance to Vittatidera zeaphila. Nematropica. 42:91-95.

Morohashi, K., Casas, M., Falcone-Ferreyra, L., Yilmaz, A., Pourcel, L., Guerra, M., McMullen, M.D., Grotewold, E. 2012. A genome-wide regulatory framework identifies maize Pericarp Color1 (P1) controlled genes. The Plant Cell. 24:2745-2764.

Voothuluru, P., Thompson, H.J., Flint Garcia, S.A., Sharp, R.E. 2013. Genetic variability of oxalate oxidase activity and elongation in water-stressed primary roots of diverse maize and rice lines. Plant Signaling and Behavior. 8:e23454. Available:

Peiffer, J.A., Flint Garcia, S.A., De Leon, N.N., McMullen, M.D., Kaeppler, S.M., Buckler IV, E.S. 2013. The genetic architecture of maize stalk strength. PLoS One. 8(6):e67066. Available:

Gasulla, F., Jain, R., Barrano, E., Guera, A., Balbuena, T., Thelen, J., Oliver, M.J. 2013. The response of Asterochloris erici (Ahmadjian) Skaloud et Peksa to desiccation: a proteomic approach. Plant Cell and Environment. 36:1363-1378.

Yobi, A., Wone, B., Xu, W., Alexander, D.C., Lining, G., Ryals, J.A., Oliver, M.J., Cushman, J.C. 2013. Metabolomic profiling in Selaginella lepidophylla at various hydration states provides new insights into the mechanistic basis of desiccation tolerance. Molecular Plant. 6(2):369-385.

Last Modified: 10/19/2017
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