Salk Arabidopsis
          1,001 Genomes
NSF Award 0929402  

Arabidopsis 2010 - 1,001 Genomes :

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 Arabidops is 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.

News:

[2013.8.22] SNP data of 345 strains from Monsanto-MPI are added.

[2012.9.10] SNP of Nd-1 from CeBiT is added.

[2012.4.02] SNPs for 1 accession from SALK have been added into the GE browser 3.0.

[2012.3.26] SNPs for over 46 accessions from SALK have been added into the GE browser 3.0.

[2011.11.21] New SNP data of 18 accessions from WTCHG have been added into the GE browser 3.0 now.

[2011.11.21] New SNP data of 8 accessions from JGI have been added into the GE browser 3.0 now.

[2011.11.2] New Unsequenced regions of 180 accessions from GMI have been added into the GE browser 3.0 now.

[2011.10.18] The phylogeny of 441 A. thaliana genomes is generated. This clustering linkage is generated by using multidendrograms-2.1.0 and its complete linkage clustering algorithm basing on the SNP matrix (polymorphisms per million base pairs) of 441 strains. Then the image is re-drawn by Trex-Online's Newick Viewer.

[2011.9.16] Unsequenced regions of 176 accessions from Salk and of 80 accessions from MPI have been added into the GE browser 3.0.

[2011.9.15] SNPs for over 180 accessions from GMI have been added into the GE browser 3.0.

[2011.6.9] SNPs for over 171 accessions have been added into the GE browser 3.0.

[2011.5.19] SNPs for over 168 accessions have been added into the GE browser 3.0.

[2011.5.17] SNPs for over 171 accessions have been added into the GE browser 3.0.

[2011.5.16] SNPs for over 166 accessions have been added into the GE browser 3.0.

[2011.5.13] SNPs for over 154 accessions have been added into the GE browser 3.0.

[2011.4.29] SNPs for over 150 accessions have been added into the GE browser 3.0.

[2011.4.21] SNPs for over 147 accessions have been added into the GE browser 3.0.

[2011.4.19] SNPs for over 136 accessions have been added into the GE browser 3.0.

[2011.4.11] SNPs for over 128 accessions have been added into the GE browser 3.0.

[2011.3.4~2011.4.8] SNPs for over 121 accessions have been added into the GE browser 3.0.

[2010.11.24]The TAIR has upgraded the Arabidopsis genome annotation to version 10. We have upgraded our database and genome browser to display TAIR10 too.

[2010.07.26] SNPs of six accessions (Kro-0, C24, Ler-1 from MPI, Eil-0, Lc-0, Sav-0 from UNIL) added into the GE browser 3.0.

[2010.06.16] The Genome Express Browser Version 3.0 is now open for testing.
what's new in this release:
1. The User-friendly tracktrees options.
2. The TAIR9 annotations added.
3. The Google 3D Earth map of the resources.

[2010.04.16] The Genome Express Browser Version 2.0 [2.0/gebrowser.php] is now available for publics and set as the default browser.

[2010.03.21] The Genome Express Browser Version 1.0 (gebv1) in PHP for the 1,001 genomes is now released. The link is /atg1001/gebv1.php.

[2010.03.18] The new PHP scripted pages for Salk 1,001 genomes project are released.