Phenotype Curation

Susan R. McCouch

Department of Plant Breeding

Cornell University

QTL curation strategy for rice (Oryza sp.)

•Time

• Initiate with the current reports and work the backlog

•Traits

• Use of commonly accepted trait terms for clustering QTL phenotypes complementing the knowledge of breeders and geneticists

•Number

• Adopt a strategy that provides rapid processing of information on large number of QTLs followed by a deeper curation.

Three level curation strategy

• Level-1: A version with core features• Trait, map position, and citation.

• Develop tools for community curation and data mining

• Level-2: Deeper curation includes• Use of controlled vocabularies (PO, TO, GO and GEO),

defining the phenotypic assay and environment

• Genetic population structure and germplasms

• QTL analysis methodology, etc.

• Level-3: Populations and genotypes• Invite authors to submit raw data

• Train researchers to curate their own data

Demand for QTL curation

• Repeated requests from rice and other cereal research communities

• Thousands of QTLs reported in cereal crop literature

• Critical component of overall phenotype curation

• Continuity with previous versions of RiceGenes

• Critical links for breeders/geneticists looking for genes associated with agronomic traits

Comparison among cereals• Build and share data structure/schema required for useful

phenotypic/QTL comparison across cereal sp.

• Gramene is funded to curate QTL information for rice only, though working with cereal communities (e.g. maize and Triticeae).

• Contributions to a community based phenotype consortium of model organism databases through:

• Newly funded NSF initiatives

•POC (www.plantontology.org)

•Gramene RCN

•Phenotype Ontology initiatives of OBO (http://obo.sf.net)

QTL data in Gramene

• 3843 QTLs

• Rice (Oryza sp.): 3475

• Maize: 327

• Wild Rice (Zizania sp.): 41

• Curated references: 152

• Rice (Oryza sp.): 143 (2003-1999)

• Maize 8 (test cases on drought tolerance)

• Wild Rice (Zizania sp.): 1

• 57 QTL reference maps generated from different genetic populations such as DH, RIL, BC, F2 etc.

QTL traits clustered by trait categories

Trait Category Number of Traits Number of QTL

Abiotic stress 51 589

Biotic stress 8 256

Quality 30 200

Yield 24 773

Development 13 314

Anatomy 44 662

Sterility or fertility 9 38

Vigor 14 816

Biochemical 27 195

OPTION-1Search your query

QTL database search

Trait name. Links to all the QTLs in Gramene database, detected for this trait

Number of QTLs listed in Gramene database, detected for the given trait

Sort by any column heading

Found 30 traits under category “Quality”. Displayed 25 entries per page.

View Next 25 entries or type a page number and hit Page to go to that page

OPTION-2Browse by trait categoryBrowse QTL database

Trait assayed

QTL detected on linkage group. Links to all the QTLs listed in Gramene but mapped to this linkage group

Trait symbol. Links to all the QTLs detected for this trait listed in Gramene.

Trait category to which the trait belongs. Links to a trait browser displaying all the traits listed in Gramene belonging to this category.

QTL symbol assigned in the publication

Links to Gramene citation a published QTL reference.

Links to the QTL map on Gramene Comparative map viewer

QTL displayed on CMap

QTL always defined by linkage

• Population x marker set x phenotypic assay x statistical test of association

• Generally many phenotypes assayed for each population and multiple loci identified per phenotype

• Entry into DB different than with mutants but information intersects with mutants

phenotypic assay, gene, allele

• Entry is always via linkage to a set of markers

Level-2

• Large number of QTL references (200-300 papers in rice)• Inconsistent reporting style and format requires manual

curation by experts • Efforts to develop curation strategies using ontology etc.

encouraged. • Complicated data relationship and structure• Prioritize based on data availability• Prioritize based on trait

• Biotic and abiotic stress

Discussion points

• What linkage analysis tools should we make available to Gramene users, if any?

• How best to visualize QTLs on the comparative maps?

Updates to rice mutant database

1320 Genes characterized by phenotype• 424 Genes fully annotated (562 references):

• Phenotypic description• Associations to controlled vocabularies (TO, PO, GO)• Map position• Alleles, phenotypic study, germplasm, environment• Sequence and gene product• DBxref link to Oryzabase

• 896 Genes with only basic Info:• Gene name and symbol;• Map position• DBxref link to Oryzabase

Annotated mutant gene an example

Linking phenotypes across genetic maps

Linking phenotypes across genetic and physical maps

Outreach and Acknowledgement

• 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)

– Dr. Longxi Yu – drought-related QTLs in Maize

• Contributed Map Position Info to Gramene:

• Dr. H. W. Cai; Dr. Y. Fukuta; Dr. J. Leach;

• Dr. H. Leung; Dr. Z. Li; Dr. M. Maheswaran;

• Dr. D. Mackill; Dr. Adam Price; Dr. J. Xiao;

• Dr. M. Yano; Dr. Q. Zhang; Dr. K. Zheng, etc.