2. A Comparative mapping resource GRAMENE http://www.gramene.org Doreen Ware USDA ARS Cold Spring Harbor Laboratory ware@cshl.edu

3. A Resource for Comparative Grass Genomics An Overview Image source: USGS and The American Phytopathological Society

4. A genomes evolves over time

5. … and space Species A Species B X X X

6. Grass genomes share syntenic regions MD Gale & KM Devos PNAS 1998 95(5):1971-4 Markers, QTL, and Genes are found in Similar Positions 11,315 MBOat 2240 MBMaize 780 MBSorghum 430 MBRice Genome sizes 15,996 MBWheat

7. Grass genomes vary in size Yet present a wealth of genetic information J Messing & V Llaca, PNAS 1998 95(5):2017-20 37.22Wheat 11.4Barley 5.81Maize 1.74Sorghum 0.34Arabidopsis National Plant Genome Initiative, Final Report 1998 Relative to Rice genome

8. Some thoughts on cereal genomics Cereal crops economically critical Sequencing of sorghum, wheat, maize, oats hindered by their large genomes Rice has emerged as genomics model for crop plants –430 Mb genome –Extensive genetic & comparative maps –Thousands of genes/QTLs mapped –Large mutant & germplasm collections –Diverse ploidy levels

9. Things you can do using Gramene Rice genomic information anchoring sequences from other cereals gives an overview of genomic diversity in the Poaceae (cereal) family. Genetic, Physical and Sequence maps from various grass species allow comparative mapping studies Rice functional information on phenotypes (mutants & QTL) and proteins acts as an anchor to find functional homologs from other cereals.

10. Welcome to Gramene www.gramene.org

11. Find the location of your favorite sequenced gene/est on rice Genome Genome Browser

12. Find the best sequence match of your favorite sequenced gene/est/marker Sequence BLAST search

13. Find the inter species homeologies or do comparative mapping CMap Comparative map

14. Find the QTL for your favorite plant trait QTL

15. Mutant Find your favorite rice mutant gene

16. Find your favorite protein Protein

17. Find your favorite reference Literature

18. Find everything about Gramene Site Map

19. Resources other than Gramene

20. A generic search in any one or all of Gramene database Last but not the least ! Please send us your valuable “Feedback” by clicking on the button.

21. Collaborations Sequence Map –Rice - TIGR Physical Maps –Rice - Rod Wing & Cari Soderland –Maize - Mary Polacco & Ed Coe –Sorghum - Patricia Klein ESTs –Sorghum - Andrew Paterson –Maize - Mary Polacco & Ed Coe –Triticeae - Dave Matthews & Olin Anderson –Gene indices - Robin Buell & John Quackenbush Genetic Maps –Maize - Mary Polacco & Ed Coe –Triticeae - Dave Matthews & Olin Anderson –Sorghum - John Mullet Protein Database –EBI & Swissprot Controlled Vocabulary –Lenore Reisner - TAIR –Richard Bruskeiwich - IRRI –Leszek Vincent - MaizeDB –Michael Ashburner - GOC Phenotypes - Mutants & QTL –Toshiro Kinoshita - RGN –Atutshi Yoshimura & Yukiko Yamazaki – OryzaBase –HeeJong Koh-Seoul National Univ. –Mary Polacco & Ed Coe - MaizeDB –Ed Buckler - ARS References –Cornell Library, Agricola, PubMed Numerous authors and institutions for sharing their data and resources

22. Credits  CSHL  Lincoln Stein (PI)  Ken Clark  Wei Zhao  Steve Schmidt  Liya Ren  Kiran Kumar  Shuly Avraham  Peter van Buren  Lenny Teytelman  Xiaokang Pan  USDA-ARS  Doreen Ware (Co-PI)  Cornell  Susan McCouch (Co-PI)  Pankaj Jaiswal (Co-PI)  Junjian Ni  Immanuel Yap  Molly Fogleman (Outreach)  Mauricio La Rota  Kuan Chang  USDA-ARS  Ed Buckler (Co-PI)  Sam Cartinhour (Co-PI)  Funding  USDA, IFAFS and NSF www.gramene.org