Exploring Rice Phenotypes Using Gramene

A Comparative Mapping Resource

GRAMENE

http://www.gramene.org GRAMENE

What is Gramene?

• Comparative mapping resource for cereals

• Rice genome browser• Genetic and physical maps for rice and

other cereals• Rice mutant phenotypes, QTL and

proteins• Literature• Ontology

http://www.gramene.org GRAMENE

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http://www.gramene.org GRAMENE

Gramene Modules

• Genome Browser• BLAST• CMap• Proteins• Mutants• QTL• Ontology• Literature

• Markers• Germplasm• Environment• Diversity

http://www.gramene.org GRAMENE

Rice blast resistance gene Pi-ta

• Bryan et al. (2000) Plant Cell 12:2003-2045

• Mediates gene-for-gene resistance against strains of the fungus Magnaporthe grisea that express avirulent alleles of AVR-Pita

• 928-aa cytoplasmic receptor with centrally localized nucleotide binding site (NBS)

• Mapped to centromeric region of rice chromosome 12

Are there any putative homologs for Pi-ta in the

rice genome?

http://www.gramene.org GRAMENE

Gramene Literature Page

Q9AY26

http://www.gramene.org GRAMENE

Gramene Protein Page

http://www.gramene.org GRAMENE

http://www.gramene.org GRAMENE

Gramene Protein Page

http://www.gramene.org GRAMENE

Gramene BLAST Search

http://www.gramene.org GRAMENE

http://www.gramene.org GRAMENE

Ensembl Protein Report

http://www.gramene.org GRAMENE

Ensembl Gene Report

AC135644

http://www.gramene.org GRAMENE

Ensembl Genome Browser

http://www.gramene.org GRAMENE

Gramene QTL Database

• 7,738 quantitative trait loci• Rice, maize, barley, oat, pearl millet,

foxtail millet, wild rice (Zizania)• Literature curated from 1994-Aug.

2004

Biotic stressBiotic stress

http://www.gramene.org GRAMENE

QTL Trait Browser

Trait Categories• Abiotic stress• Anatomy• Biochemical• Biotic stress• Development• Quality• Sterility or

fertility• Vigor

Biotic stress

http://www.gramene.org GRAMENE

QTL Text Search

blast*resistance

http://www.gramene.org GRAMENE

Blast disease resistance (BLRS)

QTL Data Fields•Species name•Trait name•Trait synonyms•Linkage group•Trait category•Trait symbol•Published symbol•QTL Accession ID

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CMap Comparative Map Viewer

http://www.gramene.org GRAMENE

AC135644

BLRS

Xa21

Xa23

Pi18

Pilm2

Pi1

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Millet in Gramene

SpeciesGenetic maps

QTL maps

QTL

Pearl millet 4 5 284

Foxtail millet

1 65

Sorghum 2

http://www.gramene.org GRAMENE

Millet QTL

Category Foxtail millet

Pearl millet

Abiotic stress 17

Anatomy 31

Biotic stress 24

Development 35

Vigor 65 15

Yield 162

http://www.gramene.org GRAMENE

The Gramene Team

• Susan McCouch• Pankaj Jaiswal• Junjian Ni• Molly Fogleman• Noel Yap

• Lincoln Stein• Doreen Ware• Ken Clark• Kiran Ratnapu• Liya Ren• Wei Zhao• Steve Schmidt• Shuly Avraham