W092 Genome Diversity in Brachypodium distachyon: Deep Sequencing of Highly Diverse Natural Accessions

Date: Tuesday, January 17, 2012
Time: 11:00 AM
Room: Pacific Salon 2
Sean Gordon , USDA, ARS, WRRC, Albany, CA
Henry Priest , Donald Danforth Plant Science Center
Ludmila Tyler , University of California, Berkeley/USDA, Albany, CA
Doug Bryant , Donald Danforth Plant Science Center
Wendy Schackwitz , DOE Joint Genome Institute
Joel Martin , DOE Joint Genome Institute
Wenqin Wang , Waksman Institute, Rutgers University, Piscataway, NJ
Anna Lipzen , DOE Joint Genome Institute
Kerrie Barry , DOE Joint Genome Institute
Antonio Manzaneda , Universidad de Jaen
Christopher Schwartz , University of Wisconsin-Madison, Madison, WI
Richard Amasino , University of Wisconsin, Madison, WI
David Garvin , USDA-ARS PSRU, St. Paul, MN
Hikmet Budak , Sabanci University, Istanbul, Turkey
Joachim Messing , Rutgers University, Piscataway, NJ
Metin Tuna , Namik Kemal University, Tekirdag, Turkey
Thomas Mitchell-Olds , Duke University
Dan Rokhsar , DOE Joint Genome Institute, Walnut Creek, CA
Len Pennacchio , DOE Joint Genome Institute
Ana Caicedo , University of Massachusetts, Amherst, MA
Samuel Hazen , University of Massachusetts, Amherst, MA
Thomas Jeunger , University of Texas at Austin
Robert Hasterok , University of Silesia
John Doonan , John Innes Centre, Norwich, United Kingdom
Pilar Catalan , University of Zaragoza
Luis Mur , Aberystwyth University
Todd C. Mockler , Donald Danforth Plant Science Center
John Vogel , USDA, ARS, WRRC, Albany, CA
Natural variation is a powerful resource for studying the genetic basis of biological traits. Brachypodium distachyon (Brachypodium) is an excellent model grass with a large collection of inbred, diploid lines. These collections contain extensive phenotypic variation. To provide a genomic foundation for future studies, we are deep sequencing 56 diverse inbred natural accessions in collaboration with the US Department of Energy Joint Genome Institute. Analysis of the first six accessions shows tremendous genetic diversity with SNP frequencies ranging from every 200-600 base pairs. We have generated a set of 2,485,097 nonredundant, high confidence SNPs among these six accessions, including 152,920 SNPs in protein-coding regions. The SNP set in this study contains 96.6% (538 of 557) of SNPs previously used to produce a genetic linkage map, indicating a false negative rate of 3.4%. Deep sequencing also revealed numerous indels (61,582-163,776 small indels (1-30bp) and 2,064-8414 large indels and rearrangements (75bp - 20kbp) per accession), which we are confirming by other methods. In addition to comparing the resequenced reads to the reference genome to identify SNPs and structural variation, we are using de-novo assembly and targeted assembly approaches to identify sequences present in the resequenced genomes that are absent from the reference genome. Data and detailed analysis of these results will be made publicly available.