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 (Loudet et al. 02).
I am focusing now in a chromosomal region containing about 200 genes to fine map and identify the gene responsible for the differential response to shade between the two natural populations. To do this I employ traditional genetic approaches as well as genomic and network analysis. I am developing a protocol to construct gene networks that will help me consider candidate genes based on coexpression with other genes across all microarray experiments performed in Arabidopsis, colocalization with expression QTLs (West at el. 07), functional categorization and presence of polymorphisms (Clark et al. 07).
Single Nuncleotide Polymorphism discovery between wild Tomato species
I use a bioinformatic approach to scrutinize the available sequences from wild tomato species and detect Single Nucleotide Polymorphisms. This will allow me to estimate the philogenetic distance between these species, and calculate the effectiveness of the high throughput genomic methods that are and will be available soon for these species.