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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
1. Understanding the genetic basis of heterotic groups for maize. Maize yield obtained by heterosis, where the hybrid line outperforms the parental lines, is the basis of the hybrid maize industry. However, the genetic basis of heterosis or the genetic changes that were required to form the major “heterotic groups” (parental lines used to generate hybrids) in maize are unknown. ARS scientists in Columbia, MO have examined the genetic changes that occurred during a 60 year yield selection experiment to understand the genetic response to selection. Results indicated that genetic drift (the random retention or loss of genetic variation) is a key factor in establishing genetic differentiation (distinct germplasm collections). The initial differentiation is subsequently reinforced by selection and fixation of large chromosomal regions within subsequent generations, defining emerging groups. This genetic fixation occurs in specific chromosomal regions with low recombination rates. Results indicated that the particular heterotic groups that form the foundation of commercial maize production have an “accidental” origin and that plant breeders can construct alternative groups. The results also illustrated that the problems breeders face in maize improvement are due to the limited recombination in a large fraction of the maize genome. These results are important in that they indicate a more open breeding structure may lead to enhance long-term corn yields.

2. The metabolic response of maize to drought. Droughts occurring in the U.S. and across the globe threaten food security and contribute to the growing problem of malnutrition and hunger. Understanding how plants respond to soil water deficits at the metabolic level is key to developing strategies for crop improvement for drought tolerance. ARS scientists in Columbia, MO examined the metabolic response of maize leaves, both fully formed and new, to a specific level of dehydration. The data obtained from this assessment was compared to that of leaves from a desiccation tolerant grass species at the same dehydration level so as to highlight what aspect of the metabolic response is involved in dehydration tolerance. They found a major metabolic deficiency in maize that relates to the accumulation of certain nitrogen rich compounds during dehydration. The ability to focus attention on specific metabolic deficiencies that relate to the dehydration sensitivity of maize will enable researchers to focus on specific gene targets for improving drought tolerance in maize. Progress in drought tolerance will ultimately improve food security and address yield stability in a changing climate.

3. High throughput genotyping in maize. Providing researchers with the ability to rapidly assess the genetic makeup (genotype) of the maize plants they are working with is a critical function of any large genome database. The ARS MaizeGDB scientist in Columbia, MO, transferred genetic and genomic data to MaizeGDB from a commercially available Single Nucleotide Polymorphism (SNP) microarray, a resource developed in collaboration with ARS scientists in Columbia, MO and Ithaca, NY and that allows researchers to assess the presence of over 56,000 genetic markers in a germplasm in one experiment. Apart from supporting high throughput genotyping of maize, this array assists researchers in linking regions on the genome sequence of maize to phenotypes of interest, such as oil content, drought response and flowering time. Markers on the array have been validated by many research groups, including ARS scientists in Columbia, MO and Ithaca, NY on germplasm adapted to the U.S., other regions of the Americas, Europe, China, and Africa, and also to wild relatives of maize. Making these data accessible at MaizeGDB transfers a relatively inexpensive technology to researchers and plant breeders for modern strategies in crop improvement and to deliver improved varieties to producers.

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: 05/24/2017
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