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Curation

Curation. Maps & Markers - Noel Yap Proteins - Pankaj Jaiswal Phenotypes Mutants –Junjian Ni QTLs- Literature - all. Genetic Maps & Markers. Study : population & set of markers Map : single linkage group (nuclear or plastid) Comparative map : (within or between species) Marker_ID

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Curation

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  1. Curation • Maps & Markers - Noel Yap • Proteins - Pankaj Jaiswal • Phenotypes Mutants –Junjian Ni QTLs- • Literature - all

  2. Genetic Maps & Markers • Study: population & set of markers • Map: single linkage group (nuclear or plastid) • Comparative map: (within or between species) • Marker_ID • Sequence • Markers: • morphological, isozyme, DNA (cDNA, TE’s, random genomic) • Other features: • centromeres, QTL (presented as intervals)

  3. Phenotypes • Mutant Instance of a gene = allele Detected by assaying a particular allele in a particular genetic background (germplasm) in a particular environment (location, condition, time) and comparing it to a reference (wt)

  4. Gramene’s approach to mutant curation • Provide capability of mining down from description of a phenotype to map locus to gene to allele • Provide multiple entry points for associating genotype and phenotype: phenotype (trait), genotype, environment, locus (map position), biochemical pathway, gene (sequence), protein

  5. Phenotypic Assay • Observable/measurable difference due to: • one or more mutations (alleles) • at specific loci (genes) • that interact with the rest of the genetic background (germplasm) • under a given abiotic environmental regime defined by temperature, light, moisture, nutrition, space • and biotic regime, i.e., exposed to specific microbes, insects, plants • measured in a given location, time (season, year) • and stage of development.

  6. Phenotype of mutant sd1 Association feature of mutant sd1

  7. Phenotypic comparison of sd1 and wild type Sd1, semidwarf-1 (dee-geo-woo-gen dwarf, d47) Right: normal-type (Sasanishiki, a japonica cultivar). Left: semidwarf-type (isogenic line of Sasanishiki with sd-1). Image from Monna-2002 (DNA Research 9: 11-17). Semidwarfness of an isogenic line (sd1) in the ‘Shiokari’ background. The mutant image was kindly provided by Dr. Kinoshita.

  8. Association feature for mutant sd1

  9. Map information for mutant sd1

  10. Outlink, allele and study for mutant sd1

  11. References for sd1

  12. Reference page in Gramene Search result for one reference for mutant sd1

  13. Curation tool for adding reference in Gramene

  14. Gene Product and outlink to NCBI of sd1

  15. Quantitative Trait Loci (QTL) • 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 set of markers

  16. RiceGenes QTL display TIGR BAC QTL Consensus map Homoeologous regions

  17. Limitations • Genetic position poorly comparable bt/n studies, map types (genetic/physical), species • Misleading sense of accuracy • Consensus (integrated) map difficult to update and keep consistent • Replaced with sequence-based I-Map which will continue to develop as the FPC contigs are extended

  18. Queries of interest related to QTL • What mutants have been mapped to the region containing QTL ”a"? • What ORF's are associated with the region containing QTL “a”? • What are the GO/TO terms associated with candidate ORFs in interval ”a"? • Given interval ”a" in rice, identify homeologous regions of other grasses and show the array of mutants/QTLs associated with similar phenotypes (same TO ID’s) that map to each region on the comparative maps.

  19. Queries, con’t. • Which genotypes (i.e. rice strains) are associated with an increase in trait ”b” due to a QTL locus ”a"? • Cloned gene ”c” is associated with trait "a”. Is it a member of a gene family? If so, what is the association of family members with specific biochemical pathways, phenotypes, or conditions? • Cloned gene “c” codes for protein “x”, which is part of pathway “y”. What other proteins and pathways are associated with trait “a”? Do any of the genes coding for these proteins map to the region containing QTL locus “a”?

  20. Outreach • Distributed Annotation of Mutants & QTL • Jonaliza Lanceras - drought-related QTLs - Kasetsart Univ. (Thailand) • Toshiro Kinoshita - rice mutants - Hokkaido Univ. (Japan) • Ying Wei - disease resistant genes - Plant Path, Cornell Univ. • Workshops • September - Dale Bumpers National Rice Research Center • December - Cold Spring Harbor Genome Conference

  21. Physical Maps Rice - Rod Wing & Cari Soderland Maize - Mary Polacco & Ed Coe ESTs Maize - Mary Polacco & Ed Coe Triticeae - Dave Matthews & Olin Anderson Comparative - Robin Buell & John Quackenbush - TIGR 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 Edwin Javier - INGER (IRRI) Toshiro Kinoshita - RGN Atutshi Yoshimura & Yukiko Yamazaki - OryzaBase Mary Polacco & Ed Coe - MaizeDB Jackson Lab Ed Buckler - ARS References Jon Corson-Rikert, Kathy Chiang, Tim Lynch - Mann Library David Goldberg - Agricola Collaborations

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