From Variant to Trait

Explore gene-centered, traceable multi-omics evidence linking genetic variation to complex traits across species

Database Statistics

9
plant groups
10
indexed molecular QTL dataset groups
189,960,645
molecular QTL associations
1,895,164
GWAS associations

PlantQTLdb Framework

PlantQTLdb framework showing cross-species data resources, molecular evidence, agent-assisted evidence integration, and gene- and trait-based web applications
1. Data ResourcesCross-species population transcriptomes, genetic variation, GWAS associations and scientific literature.
2. Molecular EvidenceMolecular phenotypes, eQTLs, sQTLs and apaQTLs, together with TWAS, SMR, colocalization and EWAS evidence.
3. Evidence IntegrationA biological knowledge graph and structured multi-omics data support iterative agent research, tool execution, evidence-graph construction and LLM-assisted evidence synthesis.
4. PlantQTLdb PlatformGene and trait search, multi-omics and literature visualization, trait–gene evidence, candidate-gene prioritization and interactive, source-linked answers from PlantQTLdb Assistant.

Literature Knowledge Graph

Rice Oryza sativa
32219papers analyzed
386879relations
Maize Zea mays
11301papers analyzed
137565relations
Wheat Triticum aestivum
14950papers analyzed
195581relations
Sorghum Sorghum bicolor
3147papers analyzed
41161relations
Soybean Glycine max
15816papers analyzed
120671relations
Tomato Solanum lycopersicum
17874papers analyzed
121680relations
Arabidopsis thaliana Arabidopsis thaliana
27093papers analyzed
542310relations
Brassica napus Brassica napus
4991papers analyzed
72664relations
Cotton hirsutum / arboreum Gossypium hirsutum / arboreum
7331papers analyzed
100904relations

Molecular QTL Datasets

Dataset ID Species Population size RNA-seq samples Tissue or organ Developmental stage Condition or treatment RNA-seq WGS / VCF PlantQTLdb analysis reference Original data publications
S001 Oryza sativa 287 287 leaf heading stage no experimental treatment PRJNA858547 https://ricevarmap.ncpgr.cn/v2/ Nipponbare IRGSP-1.0 · MSU7 annotation PMID 36087348
S002 Oryza sativa 250 443 leaf; panicle one-month-old seedling (leaf); young panicle no experimental treatment PRJNA692672 (leaf); PRJNA682327 (panicle) PRJNA656318; PRJNA692836 Nipponbare IRGSP-1.0 · MSU7 annotation PMID 35821092 PMID 38916914
S003 Oryza sativa 201 402 leaf 16 days after sowing control; 150 mM NaCl for 24 h PRJNA692672 (control; reused from S002); PRJNA1009219 (salt) PRJNA656318; PRJNA692836 Nipponbare IRGSP-1.0 · MSU7 annotation PMID 38650829
S004 Oryza sativa 92 368 shoot 8 days after sowing control; salt stress at an electrical conductivity of 6 decisiemens per meter for 24 h PRJNA385135 http://www.ricediversity.org Nipponbare IRGSP-1.0 · MSU7 annotation PMID 31417977
S005 Oryza sativa 149 554 leaf; root; whole seedling; panicle vegetative stage (leaf); not reported (root); approximately 15 days old (whole seedling); 3–5 cm (panicle) no experimental treatment PRJEB73710 PRJEB73710 Nipponbare IRGSP-1.0 · MSU7 annotation PMID 40240605
S006 Glycine max 622 622 shoot second vegetative leaf stage (V2) no experimental treatment CRA009979 variants called from RNA-seq Williams 82 Gmax_275_v2.0 · Wm82.a2.v1 annotation PMID 38918950
S007 Glycine max 238 238 seed 21 days after flowering no experimental treatment PRJCA016545 PRJCA016545 Williams 82 Gmax_275_v2.0 · Wm82.a2.v1 annotation PMID 38412459
S008 Glycine max 238 238 seed 14 days after flowering no experimental treatment PRJCA031929 GVM000063 (BIG Data Center) Williams 82 Gmax_275_v2.0 · Wm82.a2.v1 annotation PMID 40789081
S009 Sorghum bicolor 748 748 leaf mature leaf no experimental treatment PRJEB83049 10.6084/m9.figshare.27936195 BTx623 v5.0 · v5.1 annotation PMID 40456184
S010 Arabidopsis thaliana 666 666 whole basal leaf cluster immediately before flowering-stem elongation no experimental treatment GSE80744 https://1001genomes.org/data/GMI-MPI/releases/v3.1/ Col-0 TAIR10 PMID 27419873
S011 Brassica napus 278 278 leaf five-true-leaf stage no experimental treatment PRJNA428769 (SRP128554) https://figshare.com/s/20afe1aa9cc682304163 Darmor-bzh v4.1 PMID 31253789
S012 Brassica napus 309 599 seed 20 and 40 days after flowering no experimental treatment CRA003544 (PRJCA002836) PRJCA002835 Darmor-bzh v4.1 PMID 33309900
S013 Brassica napus 100 100 leaf 30 days old (5–6-leaf stage) no experimental treatment PRJNA1086556 https://osf.io/gfphb/ Darmor-bzh v4.1 PMID 40178590
S014 Brassica napus 334 856 shoot apical meristem; young leaf; silique not reported (shoot apical meristem and young leaf); 18 days after pollination (silique) no experimental treatment PRJNA1149544 (shoot apical meristem, 319 libraries); PRJNA1157560 (leaf, 154 accessions / 308 libraries); PRJNA1153365 (silique, 229 libraries); PRJCA013095 (GSA mirror) PRJNA1156901; PRJCA013095 (366 accessions); PRJCA002835 (502 accessions) Darmor-bzh v4.1 PMID 39501128
S015 Gossypium hirsutum 218 218 anther tetrad stage field high-temperature stress (>37 °C for >3 days) PRJNA393079 variants called from RNA-seq TM-1 HAU v1.1 PMID 33665819
S016 Gossypium hirsutum 382 382 ovule 5 days post anthesis no experimental treatment PRJNA776409 CRA009671 TM-1 HAU v1.1 PMID 34992626
S017 Gossypium arboreum 214 214 whole seedling two-leaf stage no experimental treatment PRJNA704732 PRJNA349094 CRI-A2 v1.0 PMID 35886912
S018 Gossypium hirsutum 376 2215 ovule; fiber 0 days post anthesis (ovule); 4, 8, 12, 16 and 20 days post anthesis (fiber) no experimental treatment PRJNA891378 PRJNA917453 TM-1 HAU v1.1 PMID 37845354
S019 Gossypium hirsutum 279 555 ovule 1 day post anthesis no experimental treatment PRJNA730082 PRJNA375965 TM-1 HAU v1.1 PMID 37480119
S020 Zea mays 340 572 root 14 days in hydroponic culture no experimental treatment PRJNA793045 variants called from RNA-seq; https://doi.org/10.6084/m9.figshare.19126139 B73 RefGen_v4 PMID 36964601
S021 Zea mays 699 750 leaf mature leaf no experimental treatment PRJEB67964 https://datadryad.org/dataset/doi:10.5061/dryad.bnzs7h4f1 B73 RefGen_v4 PMID 38812347
S022 Zea mays 102 208 third leaf 14 days after sowing control (30 °C); heat stress (40 °C for 4 h) PRJNA831425 PRJNA661271 B73 RefGen_v4 PMID 36345007
S023 Zea mays 318 318 kernel 5 days after pollination no experimental treatment PRJNA413629 variants called from RNA-seq B73 RefGen_v4 PMID 30548709
S024 Zea mays 224 685 leaf second-to-third vegetative leaf stage (V2–V3) well-watered; moderate drought (approximately 70% relative leaf water content); severe drought (approximately 58% relative leaf water content) PRJNA637522 variants called from RNA-seq; GVM000048 B73 RefGen_v4 PMID 32631406
S025 Zea mays 108 624 leaf tip; leaf base fourth vegetative leaf stage (V4) lowland and highland field environments PRJNA796614 PRJNA799784 B73 RefGen_v4 PMID 36327321
S026 Zea mays 301 1923 root; shoot; leaf 3 base; leaf 3 tip; kernel; mature leaf germinating seedling (root and shoot); leaf 3; 350 growing degree days after pollination (kernel); mature leaf midday and midnight (mature leaf); no experimental treatment (other tissues) PRJNA383416 HapMap3.2.1; GBS-imputed genotypes B73 RefGen_v4 PMID 29539638
S027 Solanum lycopersicum 399 399 fruit pericarp orange stage no experimental treatment PRJNA396272 SRP045767; PRJNA353161; PRJEB5235 Heinz 1706 SL5.0 · ITAG5.0 annotation PMID 29328914
S028 Triticum aestivum 204 204 whole seedling 2-week-old seedling no experimental treatment PRJNA670223 variants called from RNA-seq Chinese Spring IWGSC RefSeq v1.0 · v1.1 annotation PMID 35149708
S029 Triticum aestivum 406 406 root 14 days after germination distilled-water germination; no experimental treatment PRJNA838764 https://resource.iwheat.net/PWGBD/ Chinese Spring IWGSC RefSeq v1.0 · v1.1 annotation PMID 41205820
S030 Triticum aestivum 328 328 leaf 2-week-old seedling no experimental treatment CRA022107 GVM000315 (BIG Data Center) Chinese Spring IWGSC RefSeq v1.0 · v1.1 annotation PMID 41398157

website data updated: