Maloof Lab:Jose M. Jimenez-Gomez
QTL analysis of the shade avoidance response in Arabidopsis
Plants exhibit phenotypic plasticity in response to different environmental light cues. For example, shade from neighboring plants sensed by the phytochrome photoreceptors causes increased petiole and stem elongation and early reproduction, collectively called the Shade Avoidance Response. Interestingly, the degree of plasticity varies among strains and species, and this variation can have adaptive value.
Plants form different environments exhibit different degrees of responsiveness to the same light stimulus. For example, when plants accommodated to sunny environments detect foliar shade from neighboring vegetation they respond increasing petiole and stem elongation and reducing the time to reproduction, a phenomenon called the "shade avoidance response". On the other hand, plants surrounded by tall vegetation, used to the shade and do not present this response.
To identify the molecular mechanisms underlying this differences we are performing QTL analysis using a previously developed, well characterized Recombinant Inbred Line set descent from two different natural populations of Arabidopsis thaliana: Bayreuth, originary from the German low altitude fallow lands, and Shahdara, from the high mountains of Tadjikistan .
Single Nuncleotide Polymorphism discovery between wild Tomato species
I use a bioinformatic approach to scrutinize the available tomato EST sequences and detect Single Nucleotide Polymorphisms. This will allow me to estimate the divergence between wild and cultivated tomato species, and will serve to have an idea of the effectiveness of the high throughput genomic methods that are and will be available soon for these species.
Molecular evolution of PHYTOCHROME B
PHYTOCHROME B (PHYB) is the main plant photoreceptor involved in the shade avoidance response. This gene has been reported to be under selective pressure, suggesting that plants with different shade avoidance responses may have different functional alleles of PHYB. Under these presumptions I am sequencing and cloning PHYB genes from a number of species with diverse shade avoidance behaviors. I will soon test if the variation in light responses between these plants are due to particular amino-acid changes in this photoreceptor.
Proteomics of light perception
When plants are exposed to light a number of changes occur that are controlled by complex signaling processes. Light perception includes interaction with flowering time pathways, the circadian clock and hormone pathways between others. Genetics and genomic analysis have so far allowed us to identify and understand part of how this signals occur at the gene expression level, but very little is known about the changes produced in the plant at protein level. The new advances in Proteomics make possible to identify small protein changes with high precision. In collaboration with the Proteomics Facility at the UC Davis Genome Center we are preparing a set of experiments that will allow us to determine the accuracy and power of the newest techniques in protein quantification and to better understand how the proteome is regulated by light.