1) The genetic basis of leaf succulence in the desert tomato Solanum pennellii: Building on the use of morphometric techniques to measure the genetic basis of leaf shape in tomato, we have begun studying the genetic basis of leaf succulence. To what degree leaf shape is adaptive and in what contexts remains understudied, but leaf thickness is associated with arid environments. As a desert species, S. pennellii possesses a number of desert-adapted features, including reduced stomatal density, a relatively impermeable cuticle layer, and thicker leaves. Most importantly, a set of near-isogenic S. pennellii introgression lines (ILs) enable identifying QTL underlying natural variation among tomato species. We have identified leaf shape and thickness QTL using the ILs and are currently mapping these loci and combining them to create succulent tomato lines. Once identified, the underlying genes will be used to study the developmental mechanisms underlying leaf thickness and its physiological consequences.
2) Graft transmissible effects of rootstocks on grapevine shoots: We are collaborating on a project analyzing the phenotypic effects of rootstocks on scions (the shoot) in grafted grapevines and the long-term environmental consequences of this interaction in a changing climate. The project seeks to analyze the effects of different rootstock combinations on common scions using transcriptomic, morphometric, ionomic, and physiological measures. Vineyards with different rootstocks in a common garden design, transects of vineyards in California, and clones of a segregating population planted in multiple locations will be studied. A novel aspect of the work is repeated measures on the same vines across years, monitoring plant responses to year-to-year changes in climate.
3) Morphology in a single cell: Previously, we created an intra-cellular transcriptomic atlas of the world's largest single-celled organism, the green algae (and plant) Caulerpa taxifolia. We observed the enrichment of RNA pol II, chromatin, and DNA replication and repair transcripts in the stolon and holdfast. We are exploring the possibility of long distance movement of molecules in this giant coenocyte. We will be comparing nascent to standing transcript accumulation patterns, examining the possibility of small RNA movement, and test hypotheses of active and inactive nuclear populations using methylation profiling.
4) Persistent homology and a universal theory of plant morphology: Together with the lab of Chris Topp, we are exploring the use of a mathematical topology-based method called persistent homology to create a universal theory of plant morphology to be applied to all organs and all species of plants. We are currently applying the method to 2D leaf shapes and developing statistics to compare disparate morphologies within a single plant, but eventually we hope to apply the approach to 3D objects and plants growing over time.