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A Comparative mapping resource
GRAMENEhttp://www.gramene.org
Doreen WareUSDA ARS
Cold Spring Harbor [email protected]
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A Resource for Comparative
Grass Genomics
An Overview
Image source: USGS and The American Phytopathological Society
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A genomes evolves over time
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… and space
Species A
Species B
X
X
X
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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
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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
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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
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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.
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Welcome to Gramenewww.gramene.org
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Find the location of your favorite sequenced gene/est on rice Genome
Genome Browser
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Find the best sequence match of your favorite sequenced gene/est/marker
SequenceBLAST search
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Find the inter species homeologies or do comparative mapping
CMap
Comparative map
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Find the QTL for your favorite plant trait
QTL
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Mutant
Find your favorite rice mutant gene
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Find your favorite protein
Protein
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Find your favorite reference
Literature
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Find everything about Gramene
Site Map
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Resources other than Gramene
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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.
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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
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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