Project 9. Deciphering the genetic basis of cell shape in plants: a computational and experimental approach  (S.O. Kotchoni , Biology), N. Bou Rabee, Mathematics)

Background. In plants, cell shape patterning and growth include a plethora of concerted and interchangeable trafficking pathways (Kotchoni et al 2009, Zhang et al., 2010). However, we lack a clear genetic and biochemical understanding of how cytoskeletal arrays (actin and microtubule) control cell shape and growth development in higher plants. This hinders our ability to fully harnessing the beneficial physico-chemical properties of plants. Understanding the genetic mechanism, by which plants take shape and cope with extreme environmental stress conditions, facilitates the production of next generation of superior plant genotypes for sustainable plant-derived. Computational and experimental approaches are needed to answer the following main scientific question: What are the groups of genes that control cell shape patterning in plants?

Research. In recent years, Dr Kotchoni’s lab used  computational and experimental approaches to pioneer a comparative functional genomics to identify novel genes controlling cell shape and growth development in Arabidopsis thaliana (Gachomo et al 2013, 2014a,b; Kotchoni et al., 2009, 2011; Zhang et al 2010, 2013). Despite intensive research, there are still several genes of the DISTORTED group, important regulators of growth, that are still uncharacterized in higher plants. We will use a MISTICS (Mutagenesis-Induced Specific Traits for Insights into Cell Shape) approach, a reverse genetic analysis of the entire genome using the Salk collection of Arabidopsis T-DNA knockout lines to gain insights into the mechanisms controlling cell morphogenesis in plants. In addition, computational models will be applied to generate mathematical predictions that will guide future experiments.

Student activities. Students will use a well design script, the PMF software, a search_engine.py and a nice data retrieving output to identify novel uncharacterized DISTORTED genes in Arabidopisis and perform a genotyping analysis of corresponding TDNA-knockout mutants using a simple, fast and hazardous-reagent free protocol developed in our lab (Kotchoni et al., 2011) to confirm/validate the phenotypes of identified mutants. They will then use a digitalized-microscope to screen and record cell shape patterns of trichomes in distorted mutants compared to the wild type. This information will be used to develop a mathematical prediction model that can be experimentally tested.