Progress 08/15/11 to 02/14/14
Outputs
Target Audience: There are three general groups that were targeted in this project. The first group comprises research scientists who study abiotic stress response. This community was served (and will continue to be served) through the dissemination of primary research conducted during the funding period of this grant. This group was reached through publications in the primary scientific literature, and through talks presented at domestic and international research conferences. The specific products for this output is listed below under “Other Products/ Outputs.” The second group targeted by this project were practicing plant breeders, agronomists and students engaged in research-oriented graduate programs. This community was served by lectures and lab courses presented by the PD through his role as a lecturer in the Plant Breeding for Drought tolerance course offered by the Colorado State University. The PD taught in this course in June 2012, and will teach again in the June 2014 course. The third group targeted by this project were undergraduate students at The University of Texas at Austin who served as research assistants during data collection funded by the grant. Working alone or in teams, these students aided in all aspects of planting, growing, harvesting, and data analysis. The students were collaborative members of a research team, and some developed novel methods for data collection. Over the course of the funding period, five undergraduates participated in data collection. Among these were two women and two under-represented minorities. One of these students is currently pursuing a PhD in plant sciences, one is attending medical school, and one is pursuing a career in the biotechnology sector. Changes/Problems: No major problems were encountered during the data collection phase of this project. The experiment described in Objective 1 was delayed by six months while the PD bulked seeds; this resulted in our request to extend the project by 6 months via a no-cost extension. The extra six months allowed us to complete RNASequencing. As described above, we elected to focus sequencing effort on the 37 inbred line experiment, rather than on the QTL experiment. These data represent a much greater resource for the Brachypodium community than the eQTL data would have been. In total, this project generated considerably more data than was feasible to analyze, interpret and publish in the funded 2.5 years. The PD has recently begun an independent position at the Arnold Arboretum of Harvard University, and is devoting the majority of his time in 2014 towards analysis and publication of these data. What opportunities for training and professional development has the project provided? Practicing plant breeders, agronomists and students engaged in research-oriented graduate programs. This community was served by lectures and lab courses presented by the PD through his role as a lecturer in the Plant Breeding for Drought tolerance course offered by the Colorado State University. The PD taught in this course in June 2012, and will teach again in the June 2014 course. Undergraduate students at The University of Texas at Austin who served as research assistants during data collection funded by the grant. Working alone or in teams, these students aided in all aspects of planting, growing, harvesting, and data analysis. The students were collaborative members of a research team, and some developed novel methods for data collection. Over the course of the funding period, five undergraduates participated in data collection. Among these were two women and two under-represented minorities. One of these students is currently pursuing a PhD in plant sciences, one is attending medical school, and one is pursuing a career in the biotechnology sector. How have the results been disseminated to communities of interest? Dissemination of research results has been via papers in the primary literature (reported under "Products," and to include at least 4 additional manuscripts in the coming months), and through a presentation given by the PD at The 1st International Brachypodium Conference in Modena, Italy in June, 2013. What do you plan to do during the next reporting period to accomplish the goals?
Nothing Reported
Impacts
What was accomplished under these goals?
1. Determine physiological and life history response of diverse natural Brachypodium accessions to drought and heat stress and to their combination, and assess how these responses differ from individual stresses. This aspect of the project is complete and was very successful. I have demonstrated that drought and heat stress responses in Brachypodium are non-additive. Specifically, plants that are drought and heat stressed show responses that are not found in either drought-stressed or heat-stressed plants. These effects are seen at the level of gene expression, leaf-level physiology, development, and lifetime fitness. After several delays, owing to the very recent availability of complete genome sequences of the 37 diverse accessions used in this experiment, I am just now beginning to characterize gene expression responses in detail. A manuscript detailing the physiological, developmental, and fitness patterns is nearing draft form, and a second paper describing gene expression responses will follow later in the 2014 calendar year. 2. Determine the genetic architecture of physiological, life history and transcriptional traits in response to drought, heat, and their combination. This aspect of the project was only partially successful. As described above, we generated a new linkage map for a Brachypodium mapping population. This was used, in conjunction with a large greenhouse phenotyping experiment of RILs, to map QTL associated with drought stress response. Because of the considerable efforts that went into accomplishing the first objective, I elected not to perform a combined stress experiment and scaled the project back to a single experiment assessing drought stress response. Because of these changed plans, I focused all gene expression analysis (and a large portion of the budget!) towards the experiment described in the first objective. However, the RNASequence data which I generated will be used in a comparative expression QTL mapping framework as part of the collaborative project, described above under “Products,” making use of complete resquenced genomes. This analysis should allow me to identify the relative contribution of locally-acting (“cis-“) versus distantly-acting (“trans”) allelic effect on gene expression variation. These trans-acting loci will be pursued further as possible targets of applied breeding approaches (see below under Objective 4). 3. Compare abiotic stress responses at hierarchical levels of plant function. Using principal component analysis of the trait data collected under Objective 1, I have shown that many axes of variation in response are highly correlated. This suggests a modular nature of plant stress response, incorporating changes in biomass partitioning, leaf development, metabolite biosynthesis, gas exchange, and gene expression. Making explicit connections between the molecular level (gene expression) and higher-order traits (physiology and development) is possible now that we have completed the dataset for gene expression analysis. 4. Exploit the high level of synteny among grass genomes to identify homologous regions of the wheat and barley genomes. Unfortunately, this aspect of the project has not yet been accomplished using the data generated. As I move towards completing the gene expression analysis, I will identify homologous genes in cereal crop genomes to develop hypotheses about how master-regulatory loci change their contribution to plant responses under individual and combined stresses.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2013
Citation:
Des Marais, D. L., K. H. Hernandez and T. E. Juenger (2013). "Genotype-by-environment interaction and plasticity: exploring genomic responses of plants to the abiotic environment." Annual Review of Ecology, Evolution and Systematics 44: 5-29.
- Type:
Journal Articles
Status:
Accepted
Year Published:
2014
Citation:
Gordon, S., H. Priest, D. L. Des Marais, W. Schackwitz, M. Figueroa, J. Martin, J. Bragg, L. Tyler, C.-R. Lee, D. Bryant, W. Wang, J. Messing, A. Manzaneda, K. Barry, D. Garvin, H. Budak, M. Tuna, T. Mitchell-Olds, W. Pfender, T. Juenger, T. C. Mockler and J. Vogel (in press). "Genome Diversity in Brachypodium distachyon: Deep Sequencing of Highly Diverse Inbred Lines." The Plant Journal.
- Type:
Journal Articles
Status:
Published
Year Published:
2014
Citation:
Des Marais, D. L., L. C. Auchincloss, E. Sukamtoh, J. K. McKay, T. Logan, J. H. Richards and T. E. Juenger (2014). "Variation in MPK12 affects water use efficiency in Arabidopsis and reveals a pleiotropic link between guard cell size and ABA response." Proceedings of the National Academy of Sciences 111(7): 2836-2841.
|
Progress 08/15/12 to 08/14/13
Outputs
Target Audience: In June 2013, the PD was an invited speaker at the bi-annual International Brachypodium conference in Modena, Italy attended by cereal and forage crop breeders, molecular biologists, ecologists, bioenergy crop researchers and geneticists. The PD presented a seminar on the large multi-environment greenhouse experiment and developed several new collaborations with other Brachypodium researchers. Changes/Problems: The only substantive problem to report is that the library preparation for NextGen sequencing took longer than expected. This is the reason for the requested no cost extension. Progress since the extension has been excellent and I have every reason to believe that all data collection and most analyses should be done by the end of the extended funding period. What opportunities for training and professional development has the project provided? Emeline Sukamtoh, a recent graduate at UT-Austin, served as a research assistant on all aspects of the funded research. She is currently a masters student in Northwestern University’s Biotechnology program. Ramsey Timmerman, an undergraduate student at UT-Austin, was funded during Spring 2013 as a research assistant on the project. Ramsey helped process samples from the greenhouse phenotyping experiment. The PD has committed to serve as a lecturer in the Plant Breeding for Drought Tolerance workshop in June 2014 at Colorado State University. The PD lectured on genomics and next-generation sequence technologies for crop improvement during the 2012 course. Participants in the 2012 course came from the United States, Africa, South America and Japan. How have the results been disseminated to communities of interest? In June 2013, the PD was an invited speaker at the bi-annual InternationalBrachypodiumconference in Modena, Italy, attended by a diverse group of cereal and forage breeders, molecular biologists, geneticists, ecologists, and bioenergy researchers. The PD presented a talk on the large multi-environment greenhouse experiment and developed several new collaborations with otherBrachypodiumresearchers. What do you plan to do during the next reporting period to accomplish the goals? I am currently writing two manuscripts describing work from the first two years of funding. The first should be submitted early in 2014 and describes results and analyses from the experiment completed during Year 2 of funding. The second describes work from Year 1 of funding and will be submitted during Spring 2014: Des Marais, David L. and Thomas E. Juenger. In prep. Temperature and water interact to impact fitness in diverse accessions of Brachypodium distachyon. To be submitted to New Phytologist. Des Marais, David L. Kyle Hernandez and Thomas E. Juenger. In prep. A new linkage map for Brachypodium distachyon allows identification of QTL for water use efficiency and biomass allocation in Bd21 x Bd3-1. To be submitted to Journal of Experimental Botany. I have completed library preparations of RNA samples from the greenhouse experiment to be run on Illumina HiSeq 2500. These libraries will be used to generate measures of differential gene expression under the imposed stresses among the diverse germplasm used in the experiment. During the no-cost extension period, I will process the resulting sequence libraries and perform statistical analyses to identify differentially expresses genes. I will also use these data to infer genetic regulatory networks to ask how these networks may differ between environments. I will also identify homologous transcripts in wheat and barley and compare my results in Brachypodium with published studies of these other species to ask whether gene expression responses are conserved in the Pooid grasses. I plan to submit a manuscript detailing this work to PLoS Genetics.
Impacts
What was accomplished under these goals?
Research during Year 2 focused on the central experiment of the funded project. I performed a large greenhouse experiment exposing 37 inbred genotypes of soil-grown Brachypodium distachyon to four environments: well-watered at moderate temperature, well-watered at elevated temperature, water-restricted at moderate temperature, and water-restricted at elevated temperature. There were several goals of this experiment. The first goal is to ask whether abiotic stress responses are additive in plants: is the response of plants to a hot dry environment simply the combination of responses to individual dry and heat stresses? The second goal was to identify specific physiological, developmental, and gene expression responses to drought and elevated temperature stress. I have completed analysis of the physiological and developmental data for this experiment and am currently preparing a manuscript for publication. The primary conclusion of the paper is that temperature and water stress are not additive, i.e. that the two stresses interact to shape adaptive plant responses and, ultimately, plant lifetime fitness/yield. During year 2 of funding I also extracted RNA from >300 samples from the greenhouse experiment. These RNA samples are being processed for whole genome measures of differential gene expression using RNASequencing, currently underway during the 3rd year no-cost extension of the funding period. A second effort during 2012-2013 was genotyping a B. distachyon recombinant inbred line population, Bd21 x Bd3-1, using RAD sequencing. This effort was a collaboration with another post-doctoral researcher in the host lab. The genetic map produced from these data has facilitated mapping quantitative trait loci describing variation in several phenotypes scored in an experiment conducted prior to the beginning of funding of the current grant. Specifically, we have identified several QTL which drive variation between the parental genotypes in water use efficiency, biomass acquisition, chlorophyll abundance, and metabolite accumulation. Some of these QTL describe inducible (plastic) responses to reduction in soil water content.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2013
Citation:
Des Marais, David L., Kyle Hernandez and Thomas E. Juenger. 2013. Genotype-by-environment interaction and plasticity: exploring genomic responses of plants to the abiotic environment. Annual Reviews in Ecology, Evolution and Systematics vol. 44.
- Type:
Journal Articles
Status:
Under Review
Year Published:
2013
Citation:
Gordon, Sean, Henry Priest, David L. Des Marais and 15 others. In Review. Genome Diversity in Brachypodium distachyon: Deep Sequencing of Highly Diverse Inbred Lines. Submitted to Plant Journal.
- Type:
Journal Articles
Status:
Under Review
Year Published:
2013
Citation:
Des Marais, David L., John K. McKay, James H. Richards, Tierney Wayne and Thomas E. Juenger. In Revision. Variation in MPK12 affects water use efficiency in Arabidopsis and reveals a pleiotropic link between guard cell size and ABA response. Submitted to PNAS.
|
Progress 08/15/11 to 08/14/12
Outputs
OUTPUTS: Research during Year 1 of funding focused on three experiments. First, I performed an experiment in which I subjected 7 natural accessions of Brachypodium distachyon to soil drying and contrasted transcriptome responses of these lines using RNASequencing on the SOLiD platform. I quantified differential expression of 15,000 genes in these lines, identifying transcripts which varied due to genotypic differences, treatment differences, and the interaction of genotype and treatment. The transcript sequences generated in this experiment were provided to Dr. John Vogel of USDA-ARS in Albany, CA for use in annotating novel genes in 6 Brachypodium genomes that were recently resequenced by the Joint Genome Institute. This work is currently being prepared for publication in collaboration with Dr. Vogel and other members of the Brachypodium resequencing team. The second experiment involved a detailed physiological assessment of plant response to a progressive soil water deficit with and without a high temperature treatment. This experiment was performed in two B. distachyon genotypes which serve as the parents in a RIL mapping population, and aimed to identify a level of drought and heat stress which resulted in a significant change in plant water status and a leaf-level physiological response. The results of this experiment will be presented at the 2013 Plant and Animal Genome Conference. The third major effort this year was to assemble and bulk seed for 40 genotypes of B. distachyon that will be used in a large experiment during FY2012-2013 that constitutes the core of the project funded by NIFA. Finally, I served as an instructor at the USDA-NIFA-funded Plant Breeding for Drought Tolerance workshop at Colorado State University in June 2012. I lectured on genomic and transcriptomic approaches for plant breeding and led a computer workshop on the analysis of next-generation sequence data for plant breeding. I also presented a paper on my earlier primary research as part of the workshop's capstone Symposium. PARTICIPANTS: Project Director: David L. Des Marais, UT-Austin. Collaborators and contacts: Dr. John Vogel and Dr. Sean Gordon (USDA-ARS Albany) are collaborating on this project. They are heading the genome analysis of JGI's effort to resequence natural accessions of Brachypodium distachyon. Data generated by the PD are being used by Vogel and Gordon to annotate resequenced genomes, and the resequenced genomes serve as reference genomes necessary for mapping RNASeq transcripts for the current project. Dr. Thomas Juenger is the host lab mentor at UT-Austin and a collaborator on all aspects of the funded research. Training and professional development: Emeline Sukamtoh, an undergraduate at UT-Austin, is serving as a research assistant on all aspects of the funded research. She is preparing for a career in science in the private sector. The PD also served as a lecturer in the Plant Breeding for Drought Tolerance workshop, educating academics and professional breeders about new developments in the use of next-generation sequence technologies for crop improvement. TARGET AUDIENCES: The PD served as a lecturer in the Plant Breeding for Drought Tolerance workshop, educating academics and professional breeders about new developments in the use of next-generation sequence technologies for crop improvement. Participants in the 2012 class came from the United States, Africa, South America and Japan. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.
Impacts
I have begun to make progress on the stated goals of the Project to identify the functional basis of grass response to abiotic stress. Most outcomes fall under the NIFA outcome "Change in Knowledge." Referring to the three experiments described in the "Outputs" section: In the first experiment, we have identified transcripts that show genotype by environment interaction (GxE) for drought stress. By combining these transcriptional analyses with analysis of the resequencing data generated by JGI, we have identified cases where these GxE effects are apparently mediated by segregating gene deletions as well as cases where GxE is possibly mediated by promoter variation. Such transcripts are of interest because they represent allelic variation in genes that may be manipulated in a breeding context to improve plant response to stressful environments. We have also now developed statistical methodologies and bioinformatic pipelines that will be essential for the FY2012-2013 stage of the project in which we look at combined drought and heat stress responses in a much larger panel of genotypes. In the second experiment, we identified the treatment levels that will be imposed in the large experiment. We have learned that the two studied genotypes respond differently to combined drought and heat stress, and that variation in abscisic acid signaling may drive these differences. These differences center largely around how the plants adjust their osmotic potentials in response to drought in the presence or absence of heat stress.
Publications
- No publications reported this period
|