Maloof Lab:Jose M. Jimenez-Gomez

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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.  
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 <i>Arabidopsis thaliana</i>: Bayreuth, originary from the German low altitude fallow lands, and Shahdara, from the high mountains of Tadjikistan (Loudet et al. 02).<br>
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 <i>Arabidopsis thaliana</i>: Bayreuth, originary from the German low altitude fallow lands, and Shahdara, from the high mountains of Tadjikistan (Loudet et al. 02).<br>
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We 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 we modeled this phenotipic data to calculate a response index and used an available map that includes more than 500 markers.<br>
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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 response index and used an available map that includes more than 500 markers.<br>
[[Image:QTL_analysis.jpg]]
[[Image:QTL_analysis.jpg]]
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We are 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 we employ traditional genetic approaches as well as genomic and network analysis. We are developing a protocol to construct gene networks that will help us 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).
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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).
[[Image:Network_fragment.jpg]]
[[Image:Network_fragment.jpg]]
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<h3><font style="color:#F8B603;">Single Nuncleotide Polymorphism discovery between wild Tomato species</font></h3>
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My main interests include genomics, bioinformatics and plant genetics, as tools for studying natural variation and evolution.
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I am currently involved in the study of the evolution of plants responses to different light environments.<br>
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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.
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My research focuses in the changes produced at the molecular level during evolution. In order to do so, I analyze the vast variation in light responses existing in nature, as well as the effect that domestication has in the way that plants perceive and respond to light.<br/>
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A more detailed explanation on plant adaptation, responses to light and molecular evolution can be found at the [[Maloof_Lab |Maloof lab]] webpage.
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Revision as of 01:24, 24 November 2007

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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 response index and used an available map that includes more than 500 markers.

Image:QTL_analysis.jpg

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).

Image:Network_fragment.jpg

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.


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