• campus:  a to z index
• map
• directory
• calendar

Search:

Richard M. Clark

Assistant Professor of Biology

B.A. Kenyon College

Ph.D. Stanford University

Research

References

clark@biology.utah.edu

Richard Clark's Lab Page

Richard Clark's PubMed Literature Search

Research

We are interested in understanding the effect of genotype and environment on phenotypic variation at both molecular and whole organism scales. To do this, we employ the reference plant, Arabidopsis thaliana (thale cress). Arabidopsis is an excellent choice for our studies, as exceptional molecular-genetic resources are available. Moreover, thousands of wild inbred strains have been collected, and harbor extensive phenotypic variation for traits of relevance to both medicine and agriculture (e.g., DNA methylation and flowering time, respectively).

As a first step to understand the genetic contribution to phenotype, as well as the genotype by environment interaction, I began work as a postdoc to systematically describe the complement of common sequence polymorphisms in the Arabidopsis population. Working with colleagues at the Max Planck Institute in Tuebingen, Germany, I identified over 1 million single nucleotide polymorphisms (SNPs), as well as thousands of deletions, in a global Arabidopsis population sample. This dense polymorphism data, collected with microarray methods, has become the basis for establishing a haplotype map (HapMap) resource for the species. An end goal of creating this resource is to enable the application of whole genome association (WGA) studies to quickly describe quantitative trait variation in the species. Beyond establishing the resource, we identified families of genes and sequence types that show extreme variation, potentially as a result of selection. As for human, such genes were enriched for those involved in response to pathogens.

Despite the large number of polymorphisms we discovered in our array studies, we identified only a fraction of all polymorphisms in given strains. To extend this work, I am now using so-called “second-generation” sequencing techniques (e.g., the Illumina/Solexa method) to more fully describe variation in Arabidopsis and other genomes. These ongoing studies will be expanded in future to characterize the effect of sequence variation on gene expression, and to understand how both genotype and environment alter regulatory networks to lead to phenotypic differences between strains and individuals.

Since we address fundamental questions about the relationships between sequence variation, complex traits, and evolution, our work should generalize well to other species. A long-term goal is the transfer of detailed methodology and biological insights from Arabidopsis to plant or animal species of environmental and economic importance.

 

References