askBrassica

Function of a gene through its Arabidopsis thaliana orthologue(s): Ensembl Plants Compara orthologues, then UniProtKB curated function, protein and gene names, mutant (disruption) phenotype, subcellular location and GO terms. gene: an Ensembl gene ID or name of any crop genome here, or an AGI (AT5G10140) / Arabidopsis name (FLC); in askBrassica also a B. napus pangenome gene (BnaA01g00010.1D2, BnaPanG...). one2many / many2many orthologues are all listed; the crop gene's own function is inferred, not shown.

B. napus (ZS11) RNA-seq expression in TPM from BnIR: 'stress' (leaf and root time courses, 0.25-24 h, under salt, drought, osmotic, heat, cold 4 C and freezing -4 C, with controls at the same time points), 'hormone' (leaf and root, IAA, ACC, GA, ABA, trans-zeatin, JA, brassinolide) or 'tissue' (BnTIR: 91 libraries of bud, flower, leaf, stem, root, silique and seed stages). gene: ZS11 ID (BnaA02G0156900ZS), Darmor-bzh v4.1 name, pangenome ID, or a name/AGI (FLC, AT5G10140: all B. napus copies). Filter by treatment ('salt', 'cold') or tissue ('root'). Stress/hormone rows give each time point with the control at the same tissue and time.

Genome-wide association peaks for B. napus traits from BnIR (HZAU): 135 traits from 10 GWAS studies (seed oil fatty acids and erucic acid, glucosinolates, oil content, flowering time, plant height, branching, silique and seed traits, cadmium, salt and other stress responses...). Each peak (adjacent 500-kb windows with p <= 1e-6) gives the study, lead SNP with alleles, consequence, p-value, effect (beta) and variance explained, and the genes within 25 kb of the lead SNP with their Arabidopsis best hit and Darmor-bzh v4.1 ID (= Ensembl Plants B. napus). Search by trait words ('erucic', 'flowering'), a ZS11 region (chromosome 'A08' with start/end in bp), or gene (ZS11 BnaA08G0133900ZS, Darmor v4.1 BnaA08g11040D, Arabidopsis AGI or name such as FAE1). No arguments lists the traits.

Phenotyping studies (field and glasshouse trials) with trait data for a Brassica line, live from the BrAPI nodes (currently the INRAE Brassica trials in GnpIS (rapeseed and cabbage collections), served through FAIDARE). germplasm: a cultivar or line name (matched exactly; upper/title case are tried too, e.g. 'Soissons' -> 'SOISSONS'). Returns the matching germplasm records (source, holding institute, accession) and each study's name, trial/network, season, location, number of observations, variables measured and link. Use brapi_observations for the trait values.

Trait observations for a Brassica line from the BrAPI nodes (currently the INRAE Brassica trials in GnpIS (rapeseed and cabbage collections), served through FAIDARE), summarised per study and variable: n, mean, min, max (numeric values) or the distinct values, season and location. germplasm: line name (as in brapi_germplasm_studies). trait filters variables by name or ontology ID part (e.g. 'rdt', 'CO_321:1000074', 'yield'; INRAE short names are glossed: rdt = grain yield, prot = grain protein, pmg = thousand-grain weight, ht = plant height, rj/rb = yellow/brown rust). study filters by study name part (e.g. 'Le_Moulon', '2015'). Compare values within a study.

Interactive gene view for one Brassica gene: a relationship map of its orthologues in B. rapa, B. oleracea, B. juncea, Camelina and Arabidopsis, Arabidopsis function, presence/absence across the B. napus (53 accessions) or B. oleracea (10) pangenome by crop form, BnIR stress responses (ZS11 copies), Expression Atlas contrasts and recent papers, with tabs for pangenome presence by form, a BnIR stress time-course heatmap and baseline expression. Clients that support MCP Apps show it in the chat; the result also lists the nodes, the panel data and the gene page link (page) to share. gene: gene name or Ensembl/LIS ID.

What askBrassica currently indexes: record counts per database and data type, and data versions.

Brassica RNA-seq experiments held by askBrassica (Expression Atlas and SRA study SRP159041 (B. napus leaf cold, heat and drought; quantified by askBrassica)): baseline (TPM by tissue / developmental stage / treatment) and differential (stress, pathogen, genotype contrasts). query filters descriptions/labels (e.g. 'drought', 'grain', 'Fusarium'). Gives each experiment's assay groups (baseline) or contrasts (differential).

Genes 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 groups + 1) / (max TPM in other groups + 1). Differential experiment + contrast (text matched to contrast names or IDs): significant genes, direction 'up' or 'down', ranked by |log2FC|. Use expression_experiments() for group and contrast names.

Look up a gene by Ensembl gene ID or gene name/symbol in Ensembl Plants: species, location, assembly, biotype, description and link. Names are searched in all of: brassica_napus, brassica_rapa (Chiifu), brassica_rapa_ro18 (R-o-18), brassica_rapa_z1 (Z1), brassica_oleracea, brassica_juncea, camelina_sativa, arabidopsis_thaliana (or only in species, if given). e.g. 'FLC', 'AT5G10140', 'BnaC09g12820D', 'Bra000001'.

Find Brassica genebank accessions by accession number or name: Brassica, Camelina, Sinapis and Raphanus accessions from GBIF, with the holding genebank (FAO WIEWS code) and accession number; mostly Svalbard Global Seed Vault safety duplicates. Passport data are minimal (no traits); request seed from the holding genebank. Also INRAE GnpIS Brassica collections via FAIDARE (B. napus, B. oleracea and B. rapa) with taxon, holding institute, country of origin, status, pedigree and panels.

Where and when a Brassica gene is expressed, and under which treatments it changes, from Expression Atlas and SRA study SRP159041 (B. napus leaf cold, heat and drought; quantified by askBrassica). gene: Ensembl gene ID (e.g. GSBRNA2T00000001001 for B. napus, Bra000001 for B. rapa) or a gene name find_gene resolves. Baseline: TPM (median over replicates, with range) for the top_groups highest-expressed tissues/stages per experiment. Differential: every contrast where the gene is significant (adjusted p < 0.05, |log2FC| >= 1). experiment restricts to one accession.

Plant 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 for the reverse (all genes of a pathway).

Genes overlapping a region of one Ensembl Plants genome (max 5 Mb). species is an Ensembl name, e.g. 'brassica_rapa' (chromosomes A01-A10) or 'brassica_oleracea' (C1-C9); chromosome names as in that assembly. Brassica napus is scaffold-level in Ensembl Plants (Darmor-bzh v4.1), so use B. rapa or B. oleracea for chromosome regions.

Full record for one paper: DOI (10.xxxx/..), PMID (digits) or PMCID (PMC...). Returns the abstract, open-access status and full-text links.

Orthologues of a gene from Ensembl Plants Compara (gene trees across plant genomes), e.g. the Brassica copies of an Arabidopsis gene. gene: Ensembl ID or name; target_species: Ensembl name to restrict to (e.g. 'brassica_napus'). Returns orthologue IDs, species, relationship (one2one, one2many, many2many).

Accessions in a crop pangenome with their metadata (form, genotype code, synthetic parents where known) and the number of genes each carries and lacks. dataset defaults to the first one. Datasets: 'bnapus' = B. napus pangenome (Darmor-bzh v8.1 plus 52 accessions, 94,013 genes; IDs like BnaA01g00010.1D2 for Darmor v8.1 genes and BnaPanG000163 for novel pangenome genes; chromosomes chrA01-chrA10, chrC01-chrC09); 'boleracea' = B. oleracea pangenome (TO1000 reference plus broccoli, Brussels sprouts, cabbage x2, cauliflower x2, kale, kohlrabi and B. macrocarpa; IDs Bo1g001000.1 = Ensembl Plants B. oleracea gene Bo1g001000, novel genes BOLEPAN_00000379.1; chromosomes C1-C9 of the BOL assembly). The dataset is detected from the gene ID, chromosome or accession names when not given. Accessions have a 'form': bnapus Oilseed (24), Synthetic (20, resynthesized from B. rapa x B. oleracea, with parents), Fodder (3), Vegetable (2), Swede (2), Elite (2); boleracea broccoli, cauliflower, cabbage, Brussels sprouts, kale, kohlrabi, reference line, wild relative.

Genes whose presence frequency differs most between two groups of pangenome accessions (accession names from pangenome_accessions, 'form:<form>' selectors such as 'form:Synthetic' or 'form:cauliflower', or ['all']). min_diff is the minimum absolute frequency difference (0-1); positive diff = more frequent in group_a. Datasets: 'bnapus' = B. napus pangenome (Darmor-bzh v8.1 plus 52 accessions, 94,013 genes; IDs like BnaA01g00010.1D2 for Darmor v8.1 genes and BnaPanG000163 for novel pangenome genes; chromosomes chrA01-chrA10, chrC01-chrC09); 'boleracea' = B. oleracea pangenome (TO1000 reference plus broccoli, Brussels sprouts, cabbage x2, cauliflower x2, kale, kohlrabi and B. macrocarpa; IDs Bo1g001000.1 = Ensembl Plants B. oleracea gene Bo1g001000, novel genes BOLEPAN_00000379.1; chromosomes C1-C9 of the BOL assembly). The dataset is detected from the gene ID, chromosome or accession names when not given. Accessions have a 'form': bnapus Oilseed (24), Synthetic (20, resynthesized from B. rapa x B. oleracea, with parents), Fodder (3), Vegetable (2), Swede (2), Elite (2); boleracea broccoli, cauliflower, cabbage, Brussels sprouts, kale, kohlrabi, reference line, wild relative.

Presence/absence of a gene across the accessions of a crop pangenome: how many accessions carry it, core or variable, which accessions lack it (and which carry it, if fewer), location, description and genome browser link. gene: a pangenome gene ID, a B. napus Ensembl (Darmor-bzh v4.1: GSBRNA2T..., BnaA01g00010D) or BnIR ZS11 gene ID (mapped to the pangenome gene), or words from the protein description (e.g. 'flowering locus C') to list matching genes. B. napus genes come with their Ensembl v4.1 and ZS11 counterparts. Datasets: 'bnapus' = B. napus pangenome (Darmor-bzh v8.1 plus 52 accessions, 94,013 genes; IDs like BnaA01g00010.1D2 for Darmor v8.1 genes and BnaPanG000163 for novel pangenome genes; chromosomes chrA01-chrA10, chrC01-chrC09); 'boleracea' = B. oleracea pangenome (TO1000 reference plus broccoli, Brussels sprouts, cabbage x2, cauliflower x2, kale, kohlrabi and B. macrocarpa; IDs Bo1g001000.1 = Ensembl Plants B. oleracea gene Bo1g001000, novel genes BOLEPAN_00000379.1; chromosomes C1-C9 of the BOL assembly). The dataset is detected from the gene ID, chromosome or accession names when not given. Accessions have a 'form': bnapus Oilseed (24), Synthetic (20, resynthesized from B. rapa x B. oleracea, with parents), Fodder (3), Vegetable (2), Swede (2), Elite (2); boleracea broccoli, cauliflower, cabbage, Brussels sprouts, kale, kohlrabi, reference line, wild relative.

Pangenome genes in a region (max 5 Mb) with how many accessions carry each, e.g. to see which genes in a QTL interval show presence/absence variation. chromosome like 'A01' or 'chrA01'. Datasets: 'bnapus' = B. napus pangenome (Darmor-bzh v8.1 plus 52 accessions, 94,013 genes; IDs like BnaA01g00010.1D2 for Darmor v8.1 genes and BnaPanG000163 for novel pangenome genes; chromosomes chrA01-chrA10, chrC01-chrC09); 'boleracea' = B. oleracea pangenome (TO1000 reference plus broccoli, Brussels sprouts, cabbage x2, cauliflower x2, kale, kohlrabi and B. macrocarpa; IDs Bo1g001000.1 = Ensembl Plants B. oleracea gene Bo1g001000, novel genes BOLEPAN_00000379.1; chromosomes C1-C9 of the BOL assembly). The dataset is detected from the gene ID, chromosome or accession names when not given. Accessions have a 'form': bnapus Oilseed (24), Synthetic (20, resynthesized from B. rapa x B. oleracea, with parents), Fodder (3), Vegetable (2), Swede (2), Elite (2); boleracea broccoli, cauliflower, cabbage, Brussels sprouts, kale, kohlrabi, reference line, wild relative.

Genes 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 all species loaded for this site. Matching pathways are listed with their genes per species. Membership is projected from rice by orthology.

Resistance gene analogues (RGAs) in the B. napus pangenome (1,749 genes: NBS-LRR classes TNL, CNL, RNL, NL, TN, CN, RN, NBS, TX; receptor-like kinases RLK; receptor-like proteins RLP), with presence/absence across the 53 pangenome accessions, description and location (Darmor-bzh v8.1 with pangenome contigs). Filter by chromosome ('A10'; with start/end in bp for a region), a pangenome gene ID, rga_class ('NLR' for all NBS-LRR classes, or 'TNL', 'RLK', 'RLP'...) and variable_only (genes absent from some accessions).

Curated resistance loci of Brassica crops: blackleg (Leptosphaeria maculans: Rlm1-Rlm14, LepR1-3, RlmS), clubroot (Plasmodiophora brassicae: CRa, CRb, Crr1-5, Rcr1-10, PbBa...), and in Brassica vegetables downy mildew (BraDM, Pp523, BoDMR2...), Fusarium yellows (FocBo1, Foc-Br1), black rot (Xca1bo, XccBo, BRQTL...), turnip mosaic virus (retr01, retr02, ConTR01, TuRB01b, TuRB07...), Sclerotinia, soft rot and white rust QTL: source species and genotype, chromosome, pathotypes (clubroot), whether cloned, gene class and the Darmor-bzh v4.1 gene for cloned blackleg genes (Rlm2/LepR3 BnaA10g20720D; Rlm4/Rlm7/Rlm9 BnaA07g20220D), with references. query: a locus name or part ('Rlm', 'Crr', 'LepR3', 'TuRB'); disease: 'blackleg', 'clubroot', 'downy mildew', 'fusarium', 'black rot', 'TuMV', 'sclerotinia', 'soft rot', 'white rust'; chromosome: 'A07', 'C03', 'B04'.

Full-text search across all askBrassica resources (genes, germplasm, genotyping datasets, files). Filters (exact values): database e.g. 'Ensembl Plants', 'Brassica Genome (brassicagenome.net)', 'GBIF genebank accessions'; entry_type e.g. 'Gene annotation', 'Germplasm', 'Genotyping Experiment', 'File'; species e.g. 'Brassica napus'. Returns total count, facet counts and the top hits with source URLs.

Search 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 name or Ensembl ID; its curated synonyms and RefSeq IDs are OR-ed into the query (e.g. gene='FLC' or gene='BnaC09g12820D'). Words are matched in title and abstract; full_text=True also searches open-access full text. crop_only requires Brassica/canola/rapeseed/Camelina in title or abstract. sort: 'relevance', 'date' (newest first) or 'cited'. Returns hit count and papers with DOI/PMID, year, journal, open-access flag, citations and a short abstract.

Compare 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 genotype calls for up to 50 lines in a region (chromosome like 'A01'). Returns markers with positions and each line's call. Keep regions small (a few Mb) for many lines.

Lines that share a reference line's SNP haplotype in a region (max 5 Mb), e.g. which genebank lines carry the Westar 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 with at most max_mismatch differences. Always report informative_markers and fraction_matching; if 'note' says the haplotype is common, say it is not diagnostic.

Find SNP-genotyped lines in CropSNPdb by name or AGG accession (e.g. 'Westar', 'Darmor'). Returns line name, accession(s), country, pedigree, status, breeding organisation and donor. dataset: 'Brassica napus Darmor v81' (default, 459 lines), 'Brassica napus Darmor v41', 'Brassica rapa v3', 'Brassica oleracea v2.1', 'Brassica juncea v1.5' (all Brassica 60K array); 'bnapus_pangenome' (53 B. napus pangenome accessions, 1.36 M WGS SNPs, Darmor v8.1 chromosomes A01-C09; keep regions small for genotypes).

SNP array markers (IDs and positions) in a region, with the total count.

Field 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 yield'). Most phenotyped lines are in the Brassica napus Darmor v81 dataset.

Trait-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 (e.g. 'height', 'oil', 'alkaloid'); chromosome filters one chromosome. Map marker tracks are left out unless a chromosome is given.