Oryza SNP Project
The Oryza SNP Project is an international collaboration.
Researchers involved in the project include Ken McNally, Hei Leung and
Richard Bruksiewich from the International
Rice Research Institute in
the Philippines; Jan Leach's lab from Colorado
State University; Detlef
Weigel's lab from the Max
Planck Institute in Tubingen, Germany; Thomas
Bureau's lab from McGill
University in Quebec, Canada and Robin Buell's
group at Michigan State University.
The goal of the Oryza SNP Project was to resequence 100 Mb of the rice
genome from each of 20 diverse rice cultivars. The resequenced
cultivars include members from tropical and temperate japonica, indica,
deep water and aus rice. Resequencing was performed using a
hybridization-based method developed and performed by Perlegen
Sciences. Single-copy and low-copy regions of the genome were
targeted
for resequencing, and this necessarily included mostly gene-rich
regions within the genome.
Over 160,000 high quality SNPs have been identified in the rice genome.
The recall rate for SNP discovery was 10.7%, as determined by
Sanger-based sequencing of a portion of the sequences that were
resequenced by Perlegen's hybridization-based method. The false
positive rate for the high quality SNPs was 2.9%.
The Oryza SNP Project is more fully detailed at the OryzaSNP@MSU
website. Researchers who wish to view the data can do so by
either using the Oryza
SNP Genome Browser or by using any of several web-based search
pages at that site.
The OryzaSNP data are also mirrored at IRRI OryzaSNP
Consortium website.
