Progress 12/01/08 to 11/30/13
Outputs
Target Audience: Our research was published in scientific journals for a professional scientific audience. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided? Undergraduate student Megan Chang carried out the surface-shape equation fits and thus had training in data analysis. Graduate student Heather Manching analyzed field data. Graduate student Lauren Stutts carried out the multiple-stress field experiments and analyzed the data. PI Stapleton supervised the experiments and data analysis, trained the students, and wrote the manuscripts. How have the results been disseminated to communities of interest? We have disseminated our work via publication in scientific journals (listed above) and poster presentations at scientific meetings. Specifically, the following presentations were made: Simmons, Susan J., Borsay, Amy, White, Maria, Allery, Danielle, Chang, Megan M. Stapleton, Ann E. Genetics of Combined Abiotic Stress—Mapping Genes for Synergy Using Dose-Response Surfaces, Quantitative Genetics Gordon conference, Galveston, TX Feb 22-26 2013. Stutts, Lauren and Stapleton, Ann Presentation at the 55th Annual Maize Genetics Meeting March 2013. St. Charles, IL Manching, Heather, Stapleton, Ann E., Simmons, Susan J Leaf Epiphyte Function: How Abiotic Stress and Fungal Disease Organisms Interact with Community Structure Presentation at the 55th Annual Maize Genetics Meeting March 2013. St. Charles, IL What do you plan to do during the next reporting period to accomplish the goals?
Nothing Reported
Impacts
What was accomplished under these goals?
Our initial multiple stress mapping experiments informed us that genetic architecture of multiple stress responses is specific to each treatment mixture. To determine how stress combinations are sensed in combination, we carried out a multiple-stress dose-response mapping experiment, with five combined increasing levels of drought and nitrogen stress applied to the IBM maize mapping population. The experimental design was optimized with a cubic-centered face method, which is more efficient than factorial designs. Data analysis is complete and a manuscript is in preparation. We completed an extensive data analysis and submitted a manuscript titled “Genotype to phenotype maps: multiple input abiotic signals combine to produce growth effects via attenuating signaling interactions in maize”, by G. Buddhika Makumburage, H. Lee Richbourg, Kalindi D. LaTorre, , Andrew Capps, Cuixen Chen, and Ann E. Stapleton G3 December 2013 3:2195-2204; Early Online October 18, 2013, doi:10.1534/g3.113.008573. We completed and published a paper titled “Abiotic stress growth conditions induce different responses in kernel iron concentration across genotypically-distinct maize inbred varieties”, Front Plant Sci. 2013; 4: 488. Published online 2013 December 4. Prepublished online 2013 October 5. doi: 10.3389/fpls.2013.00488, PMCID: PMC3850239, Catherine B. Kandianis,1,† Abigail S. Michenfelder,2 Susan J. Simmons,2 Michael A. Grusak,1 and Ann E. Stapleton2,* on our analysis of single and multiple stress effects on maize nutritional traits, with a focus on seed micronutrient concentration and yield traits across diverse maize genotypes. We completed and submitted a manuscript titled “Bacterial phyllosphere diversity in maize is altered by fertilizer deprivation and fungal pathogen inoculation“, which is in review. We completed a field experiment in to map loci important for several combinations of multiple stresses, including both abiotic and biotic interactions in a factorial design. Data analysis and manuscript preparation is in progress. We completed a field experiment to test previously high and low lines for multiple stress and to determine if hormone and hormone-balance treatments could phenocopy multiple stress effects within those genotypes. Data analysis is underway and a manuscript is being drafted.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2013
Citation:
Genotype to phenotype maps: multiple input abiotic signals combine to produce growth effects via attenuating signaling interactions in maize , by G. Buddhika Makumburage, H. Lee Richbourg, Kalindi D. LaTorre, , Andrew Capps, Cuixen Chen, and Ann E. Stapleton G3 December 2013 3:2195-2204; Early Online October 18, 2013, doi:10.1534/g3.113.008573.
- Type:
Journal Articles
Status:
Published
Year Published:
2013
Citation:
Abiotic stress growth conditions induce different responses in kernel iron concentration across genotypically-distinct maize inbred varieties, Front Plant Sci. 2013; 4: 488. Published online 2013 December 4. Prepublished online 2013 October 5. doi: 10.3389/fpls.2013.00488, PMCID: PMC3850239, Catherine B. Kandianis, Abigail S. Michenfelder, Susan J. Simmons, Michael A. Grusak, and Ann E. Stapleton
- Type:
Theses/Dissertations
Status:
Other
Year Published:
2013
Citation:
LEAF EPIPHYTE FUNCTION: HOW ABIOTIC STRESS AND FUNGAL DISEASE
ORGANISMS INTERACT WITH COMMUNITY STRUCTURE, Heather C. Manching, 2013, Department of Biology and Marine Biology, UNCW
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Progress 12/01/11 to 11/30/12
Outputs
OUTPUTS: Our initial multiple stress mapping experiments informed us that genetic architecture of multiple stress responses is specific to each treatment mixture. To determine how stress combinations are sensed in combination, we carried out a multiple-stress dose-response mapping experiment, with five combined increasing levels of drought and nitrogen stress applied to the IBM maize mapping population. The experimental design was optimized with a cubic-centered face method, which is more efficient than factorial designs. Data analysis is complete and a manuscript is in preparation. We completed an extensive data analysis and submitted a manuscript titled "Genotype to phenotype maps: multiple input environmental signals combine to produce growth effects via negative signaling interactions in maize, which is in review. We completed and submitted a manuscript titled "Abiotic stress growth conditions induce different responses in kernel iron concentration across genotypically-distinct maize inbred varieties" on our analysis of single and multiple stress effects on maize nutritional traits, with a focus on seed micronutrient concentration and yield traits across diverse maize genotypes. We completed a field experiment in Summer 2012 to map loci important for several combinations of multiple stresses, including both abiotic and biotic interactions in a factorial design. Data analysis is in progress. PARTICIPANTS: Undergraduate student M. Chang carried out the MAPLE plotting of dose-response curves for each QTL group, and thus had training in data analysis. Graduate student H. Manching designed and carrier out the field factorial experiment and collected the trait data. Secondary education graduate student D. Allery managed seed stocks, collected data, and genotyped the mapping lines. Graduate student D. B. Moore developed and tested SAS code and ran the data analysis on the ARC UNCW high-performance research computing resource. Faculty statistics collaborator S. J. Simmons assisted with dose-response experimental design and designed the curve-fitting statistical model for dose-response experiment data analysis. PI Stapleton supervised the experiments and data analysis, trained the students, and wrote the manuscripts. TARGET AUDIENCES: Not relevant to this project. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.
Impacts
The statistics graduate student, the statistician researcher and the PI developed a procedure for mapping of loci for dose-response mapping experiments. Results were presented at the Maize Genetics Meeting in March 2012.
Publications
- Stapleton, A., Borsay, A., White, M., Allery, D., Chang, M., Simmons, S. J., 2012 Genetics of Combined Abiotic Stress Mapping Genes for Synergy Using Dose-Response Surfaces, 54th Annual Maize Genetics Meeting, Portland OR
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Progress 12/01/10 to 11/30/11
Outputs
OUTPUTS: Our initial multiple stress mapping experiments informed us that genetic architecture of multiple stress responses is specific to each treatment mixture. To determine how stress combinations are sensed in combination, we designed and carried out a multiple-stress dose-response mapping experiment, with five combined increasing levels of drought and nitrogen stress applied to the IBM maize mapping population. The experimental design was optimized with a cubic-centered face method, which is more efficient that factorial designs. Data analysis is in progress. We completed the data analysis from the NAM and IBM recombinant inbred population experiments (6,100 plants). There were four treatments (environments); control, ultraviolet radiation, drought, and UV plus drought. Five plant growth traits were included; three of the traits were non-destructive and were measured before and after treatment period, in order to adjust for variations in germination and non-treatment-related growth. Simulations were generated and mixed models run using SAS to determine thresholds for statistical significance for our data analysis. Statistical models were constructed in SAS using the thresholds, and all the recombinant inbred line data were analyzed using these optimized mixed models. The IBM94 population and the NAM population were analyzed separately using models constructed for each population's specific features. PARTICIPANTS: Undergraduate students Danielle Allery, Amy Borsay, Megan Chang, Maria White and Rachel Glenn carried out the dose-response experiment; they measured traits, entered trait data into spreadsheets, and worked with statistics graduate student G. Buddhika Makumburage on statistical analysis. They thus had training in data collection and data analysis. Graduate student G. B. Makumburage developed and tested the SAS mixed models and ran the data analysis on the ARC UNCW high-performance research computing resource. Faculty statistics collaborator Susan J. Simmons assisted with dose-response experimental design and designed the curve-fitting statistical model for dose-response experiment data analysis. TARGET AUDIENCES: Not relevant to this project. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.
Impacts
The statistics advisory board, the statistics graduate student, the statistician researcher and the PI developed a procedure for mapping of loci for UV-water factorial mapping experiments. The priority was effect estimation for treatments/treatment combinations. Results were presented at the Keystone Abiotic Stress and Global Agriculture meeting in February 2011, at the Genetics and Genomics Gordon Conference in February 2011, and at the USDA CSREES PD's meeting in May 2011. Results of uniformity analyses of previous field multiple-stress experiments were published in Frontiers in Plant Genetics and Genomics, and results of QTL mapping for nitrate reductase activity (with data analysis using methods developed in this project) were published in Physiologia Plantarum.
Publications
- Makumburage G. B.,Stapleton A. E. (2011) Phenotype uniformity in combined-stress environments has a different genetic architecture than in single-stress treatments. Frontiers in Plant Science 2 http://www.frontiersin.org/Journal/Abstract.aspxs=905&name=plant_gen etics_and_genomics&ART_DOI=10.3389/fpls.2011.00012
- Morrison, Kristin M., Simmons, Susan J., Stapleton, Ann E. (2010) Loci controlling nitrate reductase activity in maize: ultraviolet-B signaling in aerial tissues increases nitrate reductase activity in leaf and root when responsive alleles are present. Physiologia Plantarum 140(4):1399-3054 http://dx.doi.org/10.1111/j.1399-3054.2010.01406.x DOI 10.1111/j.1399-3054.2010.01406.x
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Progress 12/01/09 to 11/30/10
Outputs
OUTPUTS: We analyzed data from the NAM and IBM recombinant inbred population experiments (6,100 plants). There were four treatments (environments); control, ultraviolet radiation, drought, and UV plus drought. Five plant growth traits were measured and data entered into spreadsheets; three of the traits were non-destructive and were measured before and after treatment period, in order to adjust for variations in germination and non-treatment-related growth. Simulations were generated and mixed models run using SAS to determine thresholds for statistical significance for our data analysis. Statistical models were constructed in SAS using the thresholds, and all the recombinant inbred line data were analyzed using these optimized mixed models. The IBM94 population and the NAM population were analyzed separately using models constructed for each population's specific features. PARTICIPANTS: Undergraduate honors students Abigail Michenfelder and Myles Fenske carried out the dose-response experiment, measured traits, entered trait data into spreadsheets, and worked with statistics graduate student G. Buddhika Makumburage on statistical analysis; they thus had training in data collection and data analysis. Graduate student G. B. Makumburage developed and tested the SAS mixed models and ran the data analysis on the ARC UNCW high-performance research computing resource. Researcher Cuixen Chen wrote the R code for simulations and ran SAS mixed models on simulated data to select thresholds for data analysis. TARGET AUDIENCES: Not relevant to this project. PROJECT MODIFICATIONS: Not relevant to this project.
Impacts
The statistics advisory board, the statistics graduate student, the statistician researcher and the PI developed a procedure for mapping of loci. The priority was effect estimation for treatments/treatment combinations. Data analysis of preliminary data from IBM mapping population was completed and presented at the Maize Genetics meeting in March 2010 and at the USDA CSREES PD's meeting in May 2010.
Publications
- P182 Combining two stresses creates a joint-stress environment that has a different genetic architecture (submitted by Ann Stapleton ) Richbourg, H. Lee; Blum, James E.; Chen, Cuixian; Capps, Andrew; LaTorre, Kalindi; Stapleton, Ann E. 52nd Annual Maize Genetics Conference, March 18-21, 2010 http://www.maizegdb.org/maize_meeting/
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Progress 12/01/08 to 11/30/09
Outputs
OUTPUTS: A statistical advisory board meeting was held Spring 2009, to prioritize for most power to detect QTL effect differences in the NAM mapping population. We set up two replicates of the mapping experiment in summer 2009, and collected phenotype data on more than 5000 samples. There were four treatments (environments): control, ultraviolet radiation, drought, and UV plus drought. Five plant growth traits were measured; three of the traits were non-destructive and were measured before and after the treatment period, in order to adjust for variations in germination and non-treatment-related growth. Laser scanning for 3D growth analysis completed (using a new commercial system) on checks under four environments. PARTICIPANTS: Undergraduate honors student K. LaTorre carried out the dose-response surface experiment, measured traits, and worked with statistics faculty member Dr. Susan Simmons on 3D curve fitting and statistical analysis; she thus had training in experimental design and data analysis. Graduate student A. Capps developed methods for 3D laser scanning and representation of check plants and measured 3D growth rates under control and stress conditions in checks. He thus had training on 3D phenotyping. The students and the PI together carried out large-scale phenotyping of control and stress-treatment plants, included training in management of large experiments and sample tracking for the students. TARGET AUDIENCES: PI Stapleton presented data on the genetic architecture of multiple stress responses in the IBM RIL population at the Genetics and Genomics Gordon Conference in Galveston, TX. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.
Impacts
The statistics advisory board and the PI developed an experimental design for mapping of loci using the maize NAM population. The priority was effect estimation for treatments/treatment combinations. Data analysis of preliminary data from the IBM mapping population was completed and presented at the Gordon conference on Genetics and Genomics. A dose-response surface experiment for two genotypes exposed to 36 combinations of stress intensity was completed, and data analysis was carried out using 3D curve fits. The results were used to select doses and dose combinations for the large-scale mapping experiment.
Publications
- No publications reported this period
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