Plant biologists need many completely sequenced and functionally annotated genomes within each species in order to fully exploit the power of evolution to understand how an organism functions and adapts to its environment. Researchers interested in natural variation in Arabidopsis propose to generate genomic DNA sequences from over 1000 inbred strains, driving technology developments in both hardware for the DNA sequencing itself and in software development to make sense of the DNA sequence data. The goal of this research project is to record the genetic variation in the entire genome of many strains of the reference plant Arabidopsis thaliana. We will develop and apply cutting edge DNA sequencing approaches using the reference plant A. thaliana to address questions of fundamental importance about plant evolution and gene function. The complete genome sequences for 200 accessions, produced as a result of this project, will provide the first complete view of haplotype structure for Arabidopsis thaliana and will allow future studies of epigenetic variation among different individuals in a population or within a species, a potential source of phenotypic diversity. The patterns of sequence and structural variation will reveal important insights into the dynamics of genome change and pinpoint potentially functionally important sources of genetic and epigenetic variation. Moreover, these data will enable subsequent mechanistic studies through experimental manipulation of Arabidopsis strains.

The 1001 Arabidopsis Genomes Project will provide detailed genotyping data of wild strains that will complement the efforts of individual investigators to phenotype these same accessions for thousands of traits of interest. For example, this research has the potential for rapid advancement toward the mechanisms by which plants adapt to various climates, utilize soil nutrients and resist pathogen infection. The knowledgebase produced from the 1,001 Arabidopsis Genomes Project will yield direct and measurable outcomes for deployment of similar traits in economically important crops for a changing global environment.

Broader Impacts of the Proposed Research

The impact of this project will be in two broad areas. First, the completion of the planned research will result in important new resources for the plant biology community: large-scale information on genetic variation among closely related genotypes. The very limited availability of whole genome sequence variation information has negatively impacted a variety of research endeavors such as the understanding of adaptive evolution or the development of association mapping. All of the DNA sequence data will be made freely and easily accessible to the research community. The long-term impact of these enabling tools and technologies on agriculture and forestry is expected to be profound, providing fundamental knowledge for the construction of new plant varieties with superior agronomic traits. An equally important aspect of this program is training, which will be provided at a variety of levels, including outreach to high school and undergraduate students as well as postdoctoral mentoring.