Research in the lab is unified in our goal to characterize and utilize RNA-based mechanisms by which plants respond to changes in their environment in order to improve agronomic traits in crop species. Projects of focus over the past year can be divided into three main foci: functional and evolutionary analysis of long non-coding RNAs (lncRNAs; I), Post-transcriptional RNA modifications as conserved plant stress response regulators (II), and the identification of novel targets for crop improvement (III).

Plant lncRNA Biology:

Long non-coding RNAs (lncRNAs) are key transcriptional regulators in plants, with several well-characterized examples. However, even in the most well-studied plant system, Arabidopsis, thousands of lncRNAs remain functionally unannotated. Over the past few years, my lab has been using genetic, comparative transcriptomic, and evolutionary approaches to assign lncRNAs across plants into functional archetypes. In short, we are 1) assessing functional conservation using transcriptional and k-mer based features to assess conservation across long evolutionary distances, 2) determining how antisense lncRNAs evolve in plants, particularly after whole genome duplication events, and 3) better defining the distinction between lncRNAs and those with cryptic short open reading frames (sORFs).

Post-transcriptional RNA modifications as conserved plant stress response regulators:

RNA covalent modifications (RCMs) represent a diverse and pervasive layer of co- and post-transcriptional gene regulation in eukaryotes, affecting a myriad of RNA-related processes, including stability, translation, localization, and protein interactions. More than 170 distinct RCMs have been identified on all classes of RNA across the eukaryotic tree of life, with most of these modifications occurring on ribosomal RNAs and transfer RNAs. Improvements in transcriptome-wide detection of RCMs over the past decade have revealed that a diverse cadre of RCMs are found on eukaryotic mRNAs. My group has been using a number of cutting-edge transcriptome-wide techniques to better understand the complexity of mRNA-associated RCMs in plants, and to better understand the mechanisms by which they influence abiotic stress responses.

Identification of novel targets for crop improvement:

The wealth of sequenced plant genomes and the tools to edit them have currently failed to surpass traditional breeding approaches in developing crops that maintain yield under unfavorable environmental conditions. To address these gaps in knowledge, my group has been developing field-focused, population-level comparative transcriptomic approaches to not only identify trait regulators but also better understand how they are regulated in the plant under abiotic stress conditions. We have utilized these approaches in a number of crop systems: cotton, sorghum, guayule, and tepary bean.