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
http://www.gramene.org GRAMENE
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