maps & markers - noel yap proteins - pankaj jaiswal phenotypes mutants –junjian ni qtls-...

• Maps & Markers - Noel Yap

• Proteins - Pankaj Jaiswal

• Phenotypes Mutants –Junjian NiQTLs-

• Literature - all

Curation

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)

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)

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

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.

Association feature of mutant sd1

Phenotype of mutant sd1

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).

Phenotypic comparison of sd1 and wild type

Sd1, semidwarf-1 (dee-geo-woo-gen dwarf, d47)

Semidwarfness of an isogenic line (sd1) in the ‘Shiokari’ background. The mutant image was kindly provided by Dr. Kinoshita.

Association feature for mutant sd1

Map information for mutant sd1

Outlink, allele and study for mutant sd1

References for sd1

Search result for one reference for mutant sd1

Reference page in Gramene

Curation tool for adding reference in Gramene

Gene Product and outlink to NCBI of sd1

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

RiceGenes QTL display

QTLHomoeologousregions

TIGR BACConsensus map

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

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.

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”?

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

Collaborations• 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