Wheat genes, Watkins pangenome, EMS mutants, expression, genotypes, germplasm and papers (WheatIS)
Connect Remote server
claude mcp add --transport http askwheat https://askwheat.plantdatabases.org/mcp{
"mcpServers": {
"askwheat": {
"url": "https://askwheat.plantdatabases.org/mcp"
}
}
}{
"servers": {
"askwheat": {
"type": "http",
"url": "https://askwheat.plantdatabases.org/mcp"
}
}
}Settings > Connectors > Add custom connector
URL: https://askwheat.plantdatabases.org/mcpTools 54 found in our last check
search_dataFull-text search across all askWheat resources (genes, germplasm, genotyping datasets, files). Filters (exact values): database e.g. 'Ensembl Plants', 'Watkins Wheat Pangenome', 'CropSNPdb', 'GBIF genebank accessions'; entry_type e.g. 'Gene annotation', 'Germplasm', 'Genotyping…
find_germplasmFind wheat accessions/cultivars/lines by name or accession ID across five indexed sources: CropSNPdb (SNP-genotyped lines, incl. all Australian Grains Genebank wheat and CAIGE breeding lines), the Watkins Wheat Pangenome (sequenced landraces), OzWheat (CSIRO GWAS panel lines), F…
data_sourcesWhat askWheat currently indexes: record counts per database and data type, and data versions.
resolve_geneResolve a wheat gene symbol (e.g. Lr34, Rht-B1) or IWGSC gene ID in any RefSeq version (v1.0 TraesCS..01G, v1.1 TraesCS..02G, v2.1 TraesCS..03G, CSS2014 Traes_..) to all versions, genomic locations, curated symbol/trait (with verification status), Watkins pangenome presence and…
gene_functionIWGSC RefSeq v2.1 functional annotation (InterPro, Pfam, Gene Ontology) for a gene symbol or any-version IWGSC ID. annotation_types filters e.g. ['Gene Ontology'] or ['Pfam','InterPro'].
genes_in_regionList IWGSC genes overlapping a region. chromosome like '7D'; assembly 'v2.1' (RefSeq v2.1 coordinates) or 'v1.0' (RefSeq v1.0 coordinates, v1.1 gene IDs). Region size is capped at 20 Mb.
find_markerPosition(s) of a genetic marker (90K/80K/9K iSelect, 35K Axiom, KASP, DArT, SSR e.g. 'BS00000713', 'wmc617', 'Xgwm149'; 40K array IDs such as 'IWB61980' or 'AVRIG14047' come from CropSNPdb) on IWGSC RefSeq v2.1 (IWGSC GMAP alignments), with genes within +/- flank bp of each hit.
wheat_homologuesHomoeologues (the A/B/D copies), and orthologues in other grasses and Arabidopsis, of a bread wheat gene from Ensembl Plants Compara gene trees. gene: symbol or any IWGSC ID (converted to RefSeq v1.1). By default orthologues are listed for durum and wild emmer, T. urartu, Ae. ta…
wheat_mutantsInduced mutations and natural variants in and around a bread wheat gene. source 'ems' (default): EMS mutant lines of tetraploid Kronos and hexaploid Cadenza with exome-capture sequencing (Krasileva et al. 2017; 2,735 lines), giving the line ID to order, e.g. Cadenza1158; 'divers…
wheat_variants_in_regionEMS mutations and exome-capture variants in a bread wheat interval on IWGSC RefSeq v1.0, including intergenic ones (promoters, unannotated regions, off-target capture). region: 'chr:start-end', e.g. '3A:100000000-100500000' (max 5 Mb). source 'ems', 'diversity' or 'all' (default…
wheat_mutant_lineEvery mutation Ensembl lists for one EMS line (Cadenza or Kronos exome-capture TILLING; Krasileva et al. 2017), e.g. 'Cadenza1166' or 'Kronos2235': counts by consequence, the genes with truncating mutations, and the mutations (gene, consequence, amino-acid change, RefSeq v1.0 po…
wheat_knockout_screenWhich genes have EMS alleles in every homoeologue, i.e. can be knocked out across A, B and D by crossing Cadenza/Kronos lines. For each gene (genes: up to 300 symbols or IWGSC IDs, or region: RefSeq v1.0 interval up to 10 Mb, e.g. a QTL) the A/B/D copies come from Ensembl Compar…
watkins_gene_presencePresence/absence of one gene across the 1,038 Watkins pangenome accessions: present count, core/variable, counts by ancestral group (AG1-AG7, Modern), continent and growth habit, UniProt/GO annotation and links. gene: symbol, any IWGSC RefSeq ID, or a pangenome gene-model ID.
watkins_gene_accessionsWatkins accessions that carry (present=True) or lack (present=False) a gene, optionally filtered by country, continent, ancestral_group (AG1-AG7 or Modern) or growth_habit. Returns metadata, coordinates and Seedstor ordering links.
watkins_compare_groupsGenes whose presence frequency differs most between two sets of Watkins accessions. group_a / group_b as '<field>:<value>' with field one of group (ancestral group), country, continent, growth_habit, e.g. 'group:AG3' vs 'group:Modern', 'country:India' vs 'country:China'. min_dif…
watkins_find_genesFind Watkins pangenome genes by UniProt protein name, gene name, protein family or ID fragment (e.g. 'FAR1', 'NLR', 'Disease resistance protein RGA'). Returns gene IDs with UniProt/GO annotation.
watkins_accessionOne Watkins accession (e.g. WATDE0063, or a synonym): origin, ancestral group, coordinates, Seedstor link, number of genes present, presence/absence of the listed genes (symbols or any IWGSC IDs accepted), all its phenotype records (trial, trait, value, units) and any RIL popula…
watkins_phenotypesField/glasshouse phenotypes of Watkins accessions (heading, height, grain size/weight/quality, senescence, lodging, rust and mildew scores, morphology). With no arguments, lists the trials (JIC UK 2006-2020, Egypt 2019-2021, Limagrain seedling yellow rust 2020, Kenya/Ethiopia ru…
watkins_gene_traitCompare a trait between Watkins accessions that carry vs lack a gene, per trial: n, mean and median per group and a Mann-Whitney p-value (exploratory; no correction for population structure). gene: symbol, any IWGSC RefSeq ID or pangenome gene-model ID. trait: exact name from wa…
watkins_populationsParagon x Watkins (and a few Robigus/other x Watkins) RIL populations: Watkins parent, country, ancestral group, number of RILs, GRU seed code, genetic map type and whether it donated TK-NILs. With population (e.g. 'ParW034') or watkins_parent (e.g. 'WATDE0005') also lists the t…
watkins_population_phenotypesTrial phenotypes (line means per trial) of Paragon x Watkins RILs and TK-NILs: heading, height, yield, grain traits, biomass, N content and more from JIC, Rothamsted and Nottingham trials (2011-2022). population_type 'RIL', 'NIL' or 'check' (parents and controls, e.g. Paragon).…
watkins_trait_genesWhich variable genes differ in presence between Watkins accessions with high vs low values of a trait in one trial (e.g. late vs early heading). Accessions are split into top/bottom quartile (split: quartile, tercile, median) within each ancestral group (stratify_by_group) and e…
watkins_nil_genesGenes inside the Watkins introgression of a TK-NIL (Watkins segment in a Paragon background), with presence in the Watkins donor and frequency in modern cultivars and landraces. nil_line is a NIL line name from watkins_population_phenotypes (e.g. 'ParW141_0016-7-10-Q2D-Hd-P'). T…
watkins_gene_haplotypesHaplotypes of a gene across the Watkins landraces and modern cultivars (WatSeq, 1,051 accessions). 'snp' (default where built): accessions grouped by their SNP alleles in the gene +-2 kb (MAF >= 0.02), each haplotype with its coding changes (e.g. p.Arg134Gln), whether it is Chin…
watkins_haplotype_traitTrait values per haplotype of a gene (watkins_gene_haplotypes) in each Watkins trial: n, mean and median per haplotype and a Kruskal-Wallis test across haplotypes with >= min_n accessions. Exploratory: no correction for population structure or multiple testing, so a difference c…
watkins_lof_allelesWatkins landraces and modern cultivars carrying a predicted loss-of-function allele of a gene (WatSeq, 1,051 accessions): each stop-gained, start/stop-lost or splice-site SNP with its protein change, the number of homozygous and heterozygous carriers, and the carriers (accession…
watkins_accession_lofGenes with a predicted loss-of-function allele (stop gained, start/stop lost, splice site) in one Watkins landrace or modern cultivar (WatSeq). accession: Watkins store code or WatSeq sample name (e.g. 'Watkins 1190027', 'WATDE0027', 'Paragon'). genes optionally restricts to a g…
expression_experimentsBread wheat RNA-seq experiments held by askWheat (Expression Atlas and SRA study SRP045409 (seedling drought, heat and combined stress; quantified by askWheat)): baseline (TPM by tissue / developmental stage / treatment) and differential (stress, pathogen, genotype contrasts). q…
gene_expressionWhere and when a wheat gene is expressed, and under which treatments it changes, from Expression Atlas and SRA study SRP045409 (seedling drought, heat and combined stress; quantified by askWheat). gene: symbol or any IWGSC RefSeq ID (converted to v1.1, as used by Atlas). Baselin…
expression_genesGenes characteristic of a tissue/stage or responsive to a treatment in one Expression Atlas experiment. Baseline experiment + group (text matched to group labels, e.g. 'root', 'grain'): genes with TPM >= min_tpm in a matching group ranked by specificity = (max TPM in matching gr…
wheat_homoeologue_expressionRelative expression of a wheat gene's A, B and D homoeologues per tissue/stage (Expression Atlas baseline experiments), with the homoeologue expression balance category of each tissue: balanced, A/B/D dominant or A/B/D suppressed, by distance to the ideal proportions (Ramirez-Go…
snp_linesFind SNP-genotyped lines in CropSNPdb by name or AGG accession (e.g. 'Cadenza', 'AGG 38862', 'CAIGE ZWB17' or a CAIGE GID '7396745'). Returns line name, accession(s), country, pedigree, status, breeding organisation and donor. dataset: 'wheat40k' (default) or 'wheat90k'.
snp_genotypesSNP genotype calls for up to 50 lines in a region (chromosome like '2D'). Returns markers with positions and each line's call. Keep regions small (a few Mb) for many lines.
snp_compare_linesCompare two lines' SNP genotypes on a chromosome (optionally a region): markers compared, identical, different, % identity and the regions where they differ (useful for pedigree/introgression questions).
snp_haplotype_carriersLines that share a reference line's SNP haplotype in a region (max 5 Mb), e.g. which genebank lines carry the Cadenza haplotype around a gene. Only markers polymorphic in the panel (minor allele frequency >= min_maf) are used, and a match needs calls at >= min_called of them wit…
snp_markersSNP array markers (IDs and positions) in a region, with the total count.
snp_phenotypesField trial trait data held in CropSNPdb for this crop (T3 trials with Crop Ontology trait IDs, Australian Grains Genebank records). With no arguments, lists the available traits. Filter by line and/or trait: trait matches the exact name or any part of it (e.g. 'Height', 'grain…
ozwheat_mtasMarker-trait associations from the OzWheat GWAS (285 Australian and international wheat cultivars and lines; glasshouse 2016 and field trials at Canberra 2018-19, Wagga 2018, Narrabri 2019). Traits: days to anthesis, days to heading, degree-days to heading ('flowering'/'heading'…
ozwheat_linesOzWheat diversity panel lines (285 Australian and international cultivars and breeding lines): name, OzWheat ID, Australian Grains Genebank (AGG) accession, pedigree and phenotype BLUEs (days to anthesis/heading, degree-days to heading, height per trial). query matches name, OzW…
genebank_phenotypesField phenotypes of wheat cultivars and genebank accessions from IPK e!DAL (CC BY 4.0). Datasets: 'GABI-WHEAT' (372 European elite cultivars 1975-2007; 16 traits incl. grain yield, heading, height, TKW, protein, sedimentation, falling number, FHB, Septoria, tan spot; BLUEs per t…
brapi_germplasm_studiesPhenotyping studies (field and glasshouse trials) with trait data for a wheat line, live from the BrAPI nodes (currently the INRAE wheat trial network and Whealbi trials in GnpIS, served through FAIDARE). germplasm: a cultivar or line name (matched exactly; upper/title case are…
brapi_observationsTrait observations for a wheat line from the BrAPI nodes (currently the INRAE wheat trial network and Whealbi trials in GnpIS, served through FAIDARE), summarised per study and variable: n, mean, min, max (numeric values) or the distinct values, season and location. germplasm: l…
wheat_gene_catalogueCatalogue of Gene Symbols for Wheat (McIntosh et al., GrainGenes; 2024 edition): the official register of designated wheat genes and alleles. query: a gene or allele symbol ('Lr34', 'Rht-B1b'), locus ('Rht-B1' lists all its alleles), old synonym ('Rht1', 'Ppd1', 'NAM-B1'), trait…
search_literatureSearch publications and preprints in Europe PMC (PubMed, PMC, bioRxiv and others). query: free text or Europe PMC syntax (e.g. 'grain size QTL 6A', 'TITLE:"pan-genome"'). gene: optional gene symbol or IWGSC ID; its curated synonyms and RefSeq IDs are OR-ed into the query (e.g. g…
get_paperFull record for one paper: DOI (10.xxxx/..), PMID (digits) or PMCID (PMC...). Returns the abstract, open-access status and full-text links.
gene_pathwaysPlant Reactome metabolic and signalling pathways of a gene (Gramene), with the top-level category and a link to the pathway diagram. gene: an Ensembl Plants gene ID or a gene name/symbol. Pathways are projected from rice by orthology, so say they are inferred. Use pathway_genes…
pathway_genesGenes in a Plant Reactome pathway: pathway is a name or words from it ('jasmonic acid biosynthesis', 'gibberellin', 'flavonoid') or a stable ID (R-TAE-1119332). species: a species name as Plant Reactome writes it ('Triticum aestivum', 'Brassica napus', 'Glycine max'); default al…
trait_hitsTrait-associated positions across the genome for a chromosome overview: GWAS marker-trait associations and peaks, named trait genes and mapped trait loci held by this site, with chromosome sizes, each with a genome browser link where the assembly is loaded. trait: words to match…
genes_with_annotationFind genes by function: GO term, InterPro or Pfam domain (accession or words, e.g. 'NB-ARC', 'IPR002182', 'GO:0009414', 'disease resistance', 'MADS-box') or Plant Reactome pathway ('gibberellin biosynthesis', R-TAE-...; kind='pathway'). kind: GO, InterPro, Pfam or pathway (defau…
gene_neighbourhoodGene neighbourhood (microsynteny): the gene and its flanking genes, with their orthologues in related genomes (wheat homoeologues, Ae. tauschii, durum, barley, Brachypodium, rice) from Ensembl Compara. For each target genome, the collinear block holding most orthologues of the n…
gene_papersPapers mentioning a gene: Europe PMC search for its gene IDs (all versions, in open-access full text) and its name/symbols (in title or abstract, with wheat/Triticum/Aegilops). Each paper says whether it matched an ID or a name. Name matches can be another gene with the same sym…
annotate_genesAnnotate a list of genes (up to 500 IDs or names) in one call: resolved ID, species, location, name, top InterPro/Pfam domains, GO terms, Plant Reactome pathways and orthologues in the main related genomes (['aegilops_tauschii', 'triticum_turgidum', 'hordeum_vulgare', 'brachypod…
blast_sequenceBLAST a DNA or protein sequence (raw or FASTA; up to 20 kb DNA or 5,000 aa) against this site's databases: Chinese Spring RefSeq v1.0 genome, RefSeq v1.1 CDS and proteins. The program is chosen from the query and database types (blastn, or blastn-short under 50 nt; blastx; blast…
wheat_gene_viewInteractive gene view for one bread wheat gene: a relationship map of its A/B/D homoeologues, orthologues (durum, Ae. tauschii, barley, rice, maize, Arabidopsis and others), EMS knockout lines per copy, Watkins haplotypes, expression responses and recent papers, with tabs for mu…
Details
| Endpoint | https://askwheat.plantdatabases.org/mcp (Streamable HTTP) |
| First published | 14 Nov 2026 |
| Last updated | 14 Nov 2026 |
| Registry name | org.plantdatabases/askwheat |
More search and web servers See all
Listing data from the official MCP registry. Status and tools from NestDaddy's daily check. Browse all MCP servers.