Progress 12/15/15 to 12/14/16
What opportunities for training and professional development has the project provided?
How have the results been disseminated to communities of interest?The PDs and personell supported by this grant participated in an open house day at the Morrell Hall Museum of Natural History on on campus titled"Why Plants Don't Wear Sweaters" which sought to educate children about the diversity of grass species and careers in molecular and computational biology. A number of different hands on activity stations were run by us and members of our labs. Attendance:61 adults, 45 youth, 4 UNL students What do you plan to do during the next reporting period to accomplish the goals?1. Complete generation of the initial lipid data(wild species grow more slowly than domesticated ones), analyze the data and identify specific target changes in lipid metabolism which are unique to freeze tolerant species and those unique to cold tolerant species. Generate time course RNA-seq for theadditional five species for which we have samples collected, and collect samples for the remaining two species. 2. A postdoc will start on this project in year two who will focus on integrating the kmeans and GLMM based methods for analyzingsyntenic gene expression across multiple species and identifyng specific gene candidates. They will also start work on the integration of gene expression and lipid data types, although we do not anticipate this being completed in year 2. 3. An undergraduate is currently being trained in RNA extraction and controlled cold stress treatments and should begin working on this grant in Year 2. We anticipate havinghave reported cold and freezing test assessments for at least 32species in year 2. 4. Using data from #1 & 2 above, begin growing plants for specific time point tissue collection to enable generating this data in year 3.
What was accomplished under these goals?
1. We have generated lipid composition data for 8 of the 10 target species thus far. While working with a statistician to better control for between growth trial variation across species, our current statistical approaches have already identified a set of lipid head group abundance and fatty acid composition changes induced by prolonged cold stress which areunique to cold tolerant species across the panel of 8 as well as other changes which are shared across all the grasses in our panel. Detailed time course RNA-seq data has been sequenced and analyzed for 3/10 species. Detailed time course RNA samples have been collected for an additional 5 species, with library construction to start in the near future. 2. As described in the grant we have been employing k-means based clustering to identify groups of genes which react in the same way across multiple species. In addition, we have developed a new approach based upon a generalized linear mixed model, which allows us to identify genes where we have strong statistical evidence for changes in gene regulation across species. A manuscript describing this approach and the findings when applied to our existing data (changes in the transcriptional regulation of cold responsive gene regulation are far more common than would have been anticipated, even between closely related species with the same phenotype) is currently in review, with the support from this grant properly acknowledged. 3. Work on this goal is currently starting. 4. We anticipate completing data generation for this goal in years 2 & 3, after we have as much data from the RNA-seq and lipid assays as possible so we can pick the most informative timepoints.