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A Comparative mapping resource

A Comparative mapping resource. GRAMENE. http://www.gramene.org. Doreen Ware USDA ARS Cold Spring Harbor Laboratory ware@cshl.edu. A Resource for Comparative Grass Genomics An Overview. Image source: USGS and The American Phytopathological Society. A genomes evolves over time.

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A Comparative mapping resource

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

  2. A Resource forComparative Grass Genomics An Overview Image source: USGS and The American Phytopathological Society

  3. A genomes evolves over time

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

  5. Genome sizes Rice 430 MB Sorghum 780 MB Maize 2240 MB Oat 11,315 MB Wheat 15,996 MB Grass genomes share syntenic regions Markers, QTL, and Genes are found in Similar Positions MD Gale & KM Devos PNAS 1998 95(5):1971-4

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

  7. 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

  8. 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.

  9. Welcome to Gramene www.gramene.org

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

  11. Find the best sequence match of your favorite sequenced gene/est/marker SequenceBLAST search

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

  13. Find the QTL for your favorite plant trait QTL

  14. Find your favorite rice mutant gene Mutant

  15. Find your favorite protein Protein

  16. Find your favorite reference Literature

  17. Find everything about Gramene Site Map

  18. Resources other than Gramene

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

  20. 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 Collaborations Numerous authors and institutions for sharing their data and resources

  21. 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

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