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Wheat genes, Watkins pangenome, EMS mutants, expression, genotypes, germplasm and papers (WheatIS)
Remote server: your requests and data go to askwheat.plantdatabases.org. Claude Code: claude mcp add --transport http askwheat https://askwheat.plantdatabases.org/mcp · Claude app: Settings → Connectors → Add custom connector.
The tools this server listed when we connected to it, in its own words.
search_data — Full-text search across all askWheat resources (genes, germplasm, genotyping datasets, files). Filters (exact values): database e.g. 'Ensembfind_germplasm — Find wheat accessions/cultivars/lines by name or accession ID across five indexed sources: CropSNPdb (SNP-genotyped lines, incl. all Australdata_sources — What askWheat currently indexes: record counts per database and data type, and data versions.resolve_gene — Resolve 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..gene_function — IWGSC RefSeq v2.1 functional annotation (InterPro, Pfam, Gene Ontology) for a gene symbol or any-version IWGSC ID. annotation_types filters genes_in_region — List IWGSC genes overlapping a region. chromosome like '7D'; assembly 'v2.1' (RefSeq v2.1 coordinates) or 'v1.0' (RefSeq v1.0 coordinates, vfind_marker — Position(s) of a genetic marker (90K/80K/9K iSelect, 35K Axiom, KASP, DArT, SSR e.g. 'BS00000713', 'wmc617', 'Xgwm149'; 40K array IDs such awheat_homologues — Homoeologues (the A/B/D copies), and orthologues in other grasses and Arabidopsis, of a bread wheat gene from Ensembl Plants Compara gene trwheat_mutants — Induced mutations and natural variants in and around a bread wheat gene. source 'ems' (default): EMS mutant lines of tetraploid Kronos and hwheat_variants_in_region — EMS mutations and exome-capture variants in a bread wheat interval on IWGSC RefSeq v1.0, including intergenic ones (promoters, unannotated rwheat_mutant_line — Every mutation Ensembl lists for one EMS line (Cadenza or Kronos exome-capture TILLING; Krasileva et al. 2017), e.g. 'Cadenza1166' or 'Kronowheat_knockout_screen — Which 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 genewatkins_gene_presence — Presence/absence of one gene across the 1,038 Watkins pangenome accessions: present count, core/variable, counts by ancestral group (AG1-AG7watkins_gene_accessions — Watkins accessions that carry (present=True) or lack (present=False) a gene, optionally filtered by country, continent, ancestral_group (AG1watkins_compare_groups — Genes whose presence frequency differs most between two sets of Watkins accessions. group_a / group_b as '<field>:<value>' with field one ofwatkins_find_genes — Find Watkins pangenome genes by UniProt protein name, gene name, protein family or ID fragment (e.g. 'FAR1', 'NLR', 'Disease resistance protwatkins_accession — One Watkins accession (e.g. WATDE0063, or a synonym): origin, ancestral group, coordinates, Seedstor link, number of genes present, presencewatkins_phenotypes — Field/glasshouse phenotypes of Watkins accessions (heading, height, grain size/weight/quality, senescence, lodging, rust and mildew scores, watkins_gene_trait — Compare 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 (exwatkins_populations — Paragon x Watkins (and a few Robigus/other x Watkins) RIL populations: Watkins parent, country, ancestral group, number of RILs, GRU seed cowatkins_population_phenotypes — Trial phenotypes (line means per trial) of Paragon x Watkins RILs and TK-NILs: heading, height, yield, grain traits, biomass, N content and watkins_trait_genes — Which variable genes differ in presence between Watkins accessions with high vs low values of a trait in one trial (e.g. late vs early headiwatkins_nil_genes — Genes inside the Watkins introgression of a TK-NIL (Watkins segment in a Paragon background), with presence in the Watkins donor and frequenwatkins_gene_haplotypes — Haplotypes of a gene across the Watkins landraces and modern cultivars (WatSeq, 1,051 accessions). 'snp' (default where built): accessions gwatkins_haplotype_trait — Trait values per haplotype of a gene (watkins_gene_haplotypes) in each Watkins trial: n, mean and median per haplotype and a Kruskal-Wallis watkins_lof_alleles — Watkins landraces and modern cultivars carrying a predicted loss-of-function allele of a gene (WatSeq, 1,051 accessions): each stop-gained, watkins_accession_lof — Genes with a predicted loss-of-function allele (stop gained, start/stop lost, splice site) in one Watkins landrace or modern cultivar (WatSeexpression_experiments — Bread wheat RNA-seq experiments held by askWheat (Expression Atlas and SRA study SRP045409 (seedling drought, heat and combined stress; quangene_expression — Where and when a wheat gene is expressed, and under which treatments it changes, from Expression Atlas and SRA study SRP045409 (seedling droexpression_genes — Genes characteristic of a tissue/stage or responsive to a treatment in one Expression Atlas experiment. Baseline experiment + group (text mawheat_homoeologue_expression — Relative expression of a wheat gene's A, B and D homoeologues per tissue/stage (Expression Atlas baseline experiments), with the homoeologuesnp_lines — Find SNP-genotyped lines in CropSNPdb by name or AGG accession (e.g. 'Cadenza', 'AGG 38862', 'CAIGE ZWB17' or a CAIGE GID '7396745'). Returnsnp_genotypes — SNP genotype calls for up to 50 lines in a region (chromosome like '2D'). Returns markers with positions and each line's call. Keep regions snp_compare_lines — Compare two lines' SNP genotypes on a chromosome (optionally a region): markers compared, identical, different, % identity and the regions wsnp_haplotype_carriers — Lines 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 gensnp_markers — SNP array markers (IDs and positions) in a region, with the total count.snp_phenotypes — Field trial trait data held in CropSNPdb for this crop (T3 trials with Crop Ontology trait IDs, Australian Grains Genebank records). With noozwheat_mtas — Marker-trait associations from the OzWheat GWAS (285 Australian and international wheat cultivars and lines; glasshouse 2016 and field trialozwheat_lines — OzWheat diversity panel lines (285 Australian and international cultivars and breeding lines): name, OzWheat ID, Australian Grains Genebank genebank_phenotypes — Field phenotypes of wheat cultivars and genebank accessions from IPK e!DAL (CC BY 4.0). Datasets: 'GABI-WHEAT' (372 European elite cultivarsNot tested by KitScout yet. When our harness runs it, pros, cons and the tasks we tried appear here, with the date and evidence.