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Phenotype Curation in Gramene

Phenotype Curation in Gramene. Susan R. McCouch Junjian Ni Noel Yap. Why Is Phenotype Important?. Desired by breeders and geneticists doing forward genetics phenotype  genotype Entry point for gene discovery Critical dimension of comparative genomics Novel area for genome databases.

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Phenotype Curation in Gramene

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  1. Phenotype Curation in Gramene Susan R. McCouch Junjian Ni Noel Yap

  2. Why Is Phenotype Important? • Desired by breeders and geneticists doing forward genetics • phenotype  genotype • Entry point for gene discovery • Critical dimension of comparative genomics • Novel area for genome databases

  3. Challenges • Complex and heterogeneous datasets • Curation not easily automated • Raw data generally not available • Rapid evolution of the field with changing analytical techniques and expectations • No established standards for measurement and reporting of phenotypic variation • Vast amount of naturally occurring and highly variable germplasm of agricultural importance

  4. Phenotype Components Genotype Gramene Mutant Qualitative Trait loci (Mendelian trait loci, MTL ) Trait Gramene QTL Quantitative Trait loci (QTL ) Phenotype

  5. Updates for Rice Mutant Database • 1408 Genes Characterized by Phenotype • 424 Genes Fully Annotated with Info (562 references): • Phenotypic Description • Associations to Controlled Vocabularies (TO, PO, GO) • Map Position • Alleles, Phenotypic Study, Germplasm, Environment • Sequence and Gene Product • 984 Genes with Simple Version of Info: • Gene Name and Symbol; • Map Position • DBxref Link to Oryzabase if Feasible • 88 new genes from recent publications have been added

  6. Fully Annotated Mutant GeneAn Example

  7. Rice Phenotypes on Maps

  8. Three-Tiered Curation Core Info: Map Position, Trait, Reference and DBX References, Text Description, etc. LEVEL-1 Descriptions of Phenotypes Using Controlled Vocabularies; Phenotypic Assays and Environments; Alleles and Allelic Interactions; Genetic Materials (Mutants & Populations); Statistical Methods & Thresholds. LEVEL-2 Community Curation & Raw Data Submission LEVEL-3

  9. QTL Data Summary New species * Complete as of Aug 2004

  10. QTL by Trait Category

  11. QTL Map Sets • 93 total QTL map sets: • 36 new QTL map sets

  12. Environment Geographical location Schedule Trait Evaluation Analysis Method Linked Marker Mapping Population Statistics Allele Effect Ontology Associations: GO, PO, TO, EO QTL Phase-2

  13. QTL Curation SOP http://dev.gramene.org/internal/docs/qtl/phase-1/ • Data field specification • QTL, QTL interval • Map data for a particular QTL study • Trait symbol generation • Reuse of existing map sets or creation of new map set • Request map and marker position info from original authors • Upload tools • Quality checks

  14. Are there any putative homologs for Pi-ta in the rice genome that correlate with regions of known resistance?

  15. Rice blast resistance gene Pi-ta • Bryan et al. (2000) Plant Cell 12:2033-2046 • 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

  16. Gramene Protein Page

  17. Gramene BLAST Search

  18. Ensembl Genome Browser AC135644

  19. Gramene QTL Database Biotic stress

  20. QTL Trait Browser Biotic stress

  21. Blast disease resistance (BLRS)

  22. BLRS

  23. Xa21 Xa23 AC135644 BLRS Pi18 Pilm2 Pi1

  24. Region of disease resistance? • Possible cluster of disease resistance genes and QTL at the end of rice chromosome 11 • May or may not be the same gene

  25. Outreach and Ackowledgement • Distributed Annotation of Mutants • Toshiro Kinoshita - rice mutants - Hokkaido Univ. (Japan) • HeeJong Koh-rice mutants-Seoul National Univ. (Korea) • Distributed Annotation of QTL • Jonaliza Lanceras - drought-related QTLs in Rice - Kasetsart Univ. (Thailand) • Longxi Yu – drought-related QTLs in Maize • Contributed Map Position Info to Gramene: • H. W. Cai; Y. Fukuta; J. Leach; • H. Leung; Z. Li; M. Maheswaran; • D. Mackill; Adam Price; J. Xiao; • M. Yano; Q. Zhang; K. Zheng; • K. Devos; A. Doust; A. Patterson

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