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