Maloof Lab:Jose M. Jimenez-Gomez

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Room 2115
Section of Plant Biology
1002 Life Sciences, One Shields Ave.
University of California Davis
Davis, CA 95616


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Jose M Jimenez-Gomez, PhD.


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I am a Postdoctoral fellow in Julin Maloof's lab in the Section of Plant Biology at the University of California Davis.

In 2005, I completed my PhD. in JM Martinez-Zapater's lab at the CNB (National Center for Biotechnology) in Madrid, Spain, where I performed a quantitative genetic analysis of flowering time in tomato.

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 grew replicated individual RILs in environments simulating shade and sun conditions and measured them for a number of traits characteristic of the shade avoidance response syndrome. For the QTL analysis I modeled this phenotipic data to calculate a shade avoidance response index and used an available map that includes more than 500 markers.

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LOD score graph for several of the traits measured

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 microarray experiments, colocalization with expression QTLs (West at el. 07), functional categorization and presence of polymorphisms (Clark et al. 07).

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Fragment of a gene network

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 behaviours. I will soon test if the variation in light responses between these plants are due to particular amino-acid changes in this photoreceptor.

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amino-acid changes in a fragment of the PHYB gene in 8 speceis, red and black bars indicate non conserverd/ conserved amino-acid changes respectively