• Update on group research progress - summary of meeting in San Diego January 2019

    This was the fifth annual meeting of the Sorghum Systems research team. In 2015 we met at the Danforth Center in St. Louis, in 2016 the meeting was held in Fort Collins, in 2017 the meeting was held in Walnut Creek, in 2018 the meeting was held in St. Louis and in 2019 the meeting was held in La Jolla, California.   In 2019 the meeting was held at the Scripps Oceanography Institute in a great setting on the ocean.  In person attendees included: Becky Bart, Zach Brenton (Kresovich Lab), Ismail Dweikat, Bryan Emmett (Harrison Lab), Andrea Eveland, Stephanie Futrell (Schachtman Lab), Kyle Hartmen (Tringe Lab), Todd Mockler, Daniel Schachtman, Amy Sheflin (Prenni Lab), Bala Sonawane (Cousins Lab), and Susannah Tringe were in attendance.  The members of the team on the zoom video conference included: Jeffrey Berry (Bart Lab), Asaph Cousins, Maria Harrison, Peng Liu, Emily Goren, Phil Ozersky (Mockler Lab), Jessica Prenni, Ranjev, Max  Mingsheng.   This was by far the most exciting meeting of the grant group to date. All the groups reported excellent progress on the initial aims of the grant and additional progress on new research topics.  Many members of the group across different geographies are working together on different aspects of the project which was gratifying given the aim of the original grant was to bring develop a system’s understanding of biofuel feedstock production on marginal land. The meeting started with an exciting talk from Todd Mockler about his sorghum genome research efforts to develop a PanGenome understanding of the species. This was followed by Phil Ozersky and Jeff Berry talking about the database that is being created to store and access the teams data. Bryan Emmett from the Harrison lab then described the development of methods to analyze field samples for mycorrhizal colonization and also work that’s developed more recently on studying the bacteria associated with mycorrhizal hyphae. Susannah Tringe and Kyle Hartman talked about their work that’s focused on the dissection of the Pseudomonas strain that seemingly dominated the early sampling in 2015 and the initial analysis of the 2017 field data set. The 2015 data set is being dissected with the help of new methods from Loop Genomics and the 2017 data set showed both treatment and genotype effects from the field studies. Becky Bart followed showing the extensive work that her lab has done with microbial cocktails using the Danforth phenotyper.  Their third experiment and a follow up greenhouse trial showed that the microbial cocktails assisted in enhancing growth under drought stressed conditions possibly by enhancing plant water content. Amy Sheflin then reviewed the metabolomics data from 2016 with a quick glimpse at some of the some of the 2017 data.  Interesting trends were identified related to specific sorghum genotypes.  Amy has also been using the 2016 data for modeling biomass yields and show some stunning correlations between leaf metabolites and yield which may be used in future as predictors of yield at an early stage of plant development leading to more rapid genetic gain in future. Andrea Eveland then showed data from a preliminary greenhouse and a large Nebraska Phenotyper experiment.  Andrea is working to unravel more of the molecular details of response to low nitrogen and drought in sorghum using ATACseq and transcriptional profiling.  The large data set and molecular analysis of the NE phenotyper data set is underway with more exciting results to come. Next Bala Sonawane discussed their physiological experiments on leakiness in sorghum and the underlying mechanisms behind traits that may be responsible for water use efficiency. Bala also showed their carbon isotope discrimination data and wrapped up with a small greenhouse experiment they did to try to begin to understand how nitrogen isotope discrimination may relate to nitrogen use efficiency. Daniel Schachtman followed up with a summary of the difficult 2018 field season in which the Grassl X RIO recombinant inbred line population and the bioenergy association panel under drought stress conditions.  Both fields had different problems and so the summer was used developing assays for traits that could be mapped and may be related to nitrogen and water use efficiency. Zach Brenton representing the Kresovich lab went into more detail about the difficulty in mapping traits and the need for adequate heritability in order to map.  The low heritability of genotype X microbiome traits make the mapping of these traits unlikely to be successful.  Zach also showed an example of the mapping of an unknown gene in RIO as compared to BTx623 related to carbohydrate production. Emily Goren from Peng Liu’s lab went into detail about three projects in which the lab was working on computational methods for three interesting questions including: which microbes have an effect on an outcome adjusting for treatment effect; What microbes are impacted by treatment (N or water stress); Which rhizosphere microbes mediate the effect of N treatment on specific metabolites. In addition to this world Peng’s lab is also contributing to other areas of the project by providing expert advice and assistance in the statistical analysis of different data sets. The meeting was wrapped up by Ismail Dweikat who is doing work on developing new genetic material in sorghum for both drought and nitrogen use efficiency.    Overall several members of the group agreed with Daniel’s comment about this being the best meeting of the group to date with the most exciting results from the project. Several members of the group will meet up again in February at the DOE contractor’s meeting in Washington DC
  • SorghumSysBio is live

    Welcome to the SorghumSysBio website.  The goal of this site is to disseminate data produced by this multi-facetted project.