A Comparative mapping resource

GRAMENEhttp://www.gramene.org

Doreen WareUSDA ARS

Cold Spring Harbor Laboratoryware@cshl.edu

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