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Data Provenance

Data

Data Provenance

trace dataset origins, understand study populations and sample counts, and find phenotype data and source publications

data sources

PlantQTLdb integrates 30 population-scale RNA-seq datasets linked to 31 source publications. For each dataset, this page records the study population, sample collection, PlantQTLdb analysis reference, data accessions, sample count notes, phenotype data and original publication. Source review completed 2026-09-16.

Sample-collection descriptions are concise paraphrases of the original methods or archive metadata. Follow the linked publication for exact methods; a source is described as a phenotype download only after its file contents have been inspected.

sample and population information

study population
Plant accessions, lines, genotypes or individuals represented by the dataset, together with the number of RNA-seq samples
sample collection
Biological material, developmental stage, growth conditions, treatment, collection unit, pooling and biological replication reported by the source
analysis reference
Genome assembly and annotation used for PlantQTLdb molecular processing; the original publication may have used a different release
sample count notes
Differences among the numbers of plant accessions, collected biological samples, sequencing libraries and samples retained after quality control
phenotype data
Traits used in the study, followed after the semicolon by download availability, source location and accession-matching limits

rice datasets

S001 Oryza sativa · leaf
study population
287 accessions · 287 RNA-seq samples
sample collection
Plants were field-grown in Wuhan in 2016; at heading, three flag leaves with similar growth were pooled per accession and immediately frozen in liquid nitrogen.
analysis reference
Nipponbare IRGSP-1.0 · MSU7 annotation
RNA-seq accessions
PRJNA858547
genotype source
https://ricevarmap.ncpgr.cn/v2/
sample count notes
The study selected 287 accessions from 533 planted accessions. Three flag leaves were pooled into one RNA sample per accession.
phenotype data
Heading date / plant height / panicle number / effective panicle number / yield / grain weight / spikelet length / grain length / grain width / grain thickness; A local matrix contains these ten agronomic traits for 287 accessions from RiceVarMap, the same population resource used for the study's genomic SNP data. The RNA-seq study separately measured flag-leaf starch in the same panel; a complete accession-level starch matrix was not included in the published supplementary files
S002 Oryza sativa · leaf; panicle
study population
250 materials · 443 RNA-seq samples
sample collection
Young leaves were collected from one-month-old seedlings, while 2–3 cm young panicles from three plants per accession were pooled and flash-frozen.
analysis reference
Nipponbare IRGSP-1.0 · MSU7 annotation
RNA-seq accessions
PRJNA692672 (leaf); PRJNA682327 (panicle)
genotype source
PRJNA656318; PRJNA692836
sample count notes
The catalog combines leaf and panicle RNA-seq under one rice panel. Its 443 RNA samples are not 443 independent accessions. The two source papers must be cited for their respective tissues.
phenotype data
Ten agronomic and grain traits; No complete phenotype matrix matched to the study materials has been verified. The links below provide the pan-genome resources and original publications, not a confirmed phenotype download
S003 Oryza sativa · leaf
study population
201 accessions · 402 RNA-seq samples
sample collection
Leaves from 16-day-old seedlings were sampled under control conditions or after 24 hours of 150 mM NaCl; 2–3 plants per genotype and condition were pooled for RNA-seq.
analysis reference
Nipponbare IRGSP-1.0 · MSU7 annotation
RNA-seq accessions
PRJNA692672 (control; reused from S002); PRJNA1009219 (salt)
genotype source
PRJNA656318; PRJNA692836
sample count notes
The publication describes 202 accessions in control and salt conditions. The local catalog has 201 accessions and 402 RNA samples; its count note records the missing NH229 input and unresolved control-input QC.
phenotype data
Survival rate / dead-leaf ratio / salt-tolerance level / five additional reported salt-response measurements; No accession-level phenotype download was found in the inspected supplement. Table S1 contains summary statistics rather than a material-level matrix
S004 Oryza sativa · shoot
study population
92 accessions · 368 RNA-seq samples
sample collection
Shoots from 8-day-old seedlings were collected under control conditions or after 24 hours of salt stress at an electrical conductivity of 6 dS m−1, with two biological replicates.
analysis reference
Nipponbare IRGSP-1.0 · MSU7 annotation
RNA-seq accessions
PRJNA385135
genotype source
http://www.ricediversity.org
sample count notes
92 accessions were profiled in two conditions with two biological replicates, giving 368 libraries. The network analysis used the 184 salt-treated libraries.
phenotype data
Root biomass / shoot biomass / root sodium / shoot sodium / root potassium / shoot potassium / sodium-to-potassium ratio; Downloadable from Campbell et al. S1 File below. The phenotype panel contains 390–392 accessions and must be matched by identifier to the 92-accession RNA-seq population
S005 Oryza sativa · leaf; root; whole seedling; panicle
study population
149 accession labels · 554 RNA-seq samples
sample collection
RNA was collected from vegetative leaves, roots, approximately 15-day-old whole seedlings and 3–5 cm panicles.
analysis reference
Nipponbare IRGSP-1.0 · MSU7 annotation
RNA-seq accessions
PRJEB73710
genotype source
PRJEB73710
sample count notes
149 leaf, 146 root, 137 seedling and 122 panicle libraries total 554 RNA samples. Tissue coverage is incomplete across the 149-accession panel.
phenotype data
No material-level organismal phenotype data were used in the core analysis; The linked resources provide assemblies, variants and expression data rather than a verified phenotype matrix

soybean datasets

S006 Glycine max · shoot
study population
622 accessions · 622 RNA-seq samples
sample collection
Plants were field-grown in Sanya; at V2, all tissue above the cotyledon node was pooled from 2–3 plants per cultivated accession or five plants per wild accession and collected between 9:00 and 11:00 a.m.
analysis reference
Williams 82 Gmax_275_v2.0 · Wm82.a2.v1 annotation
RNA-seq accessions
CRA009979
genotype source
variants called from RNA-seq
sample count notes
The RNA panel has 622 accessions: 70 wild, 304 landrace and 248 improved accessions. Larger genotyped and phenotyped panels in the paper are separate study populations.
phenotype data
Pod color / flowering time / maturity time / plant height / grain yield per plant / branch number / canopy coverage; Phenotype matrices are available from the author repositories linked below and in local source files. Their accession overlap with the 622-accession RNA-seq population still requires identifier matching
S007 Glycine max · seed
study population
238 accessions · 238 RNA-seq samples
sample collection
The RNA-seq subset was grown in Nanjing in 2019, and seeds were collected at 21 days after flowering for 3′ RNA-seq.
analysis reference
Williams 82 Gmax_275_v2.0 · Wm82.a2.v1 annotation
RNA-seq accessions
PRJCA016545
genotype source
PRJCA016545
sample count notes
421 accessions were phenotyped in Harbin in 2019 and 2020; the 238-accession RNA subset was grown in Nanjing in 2019 and sampled at 21 days after flowering.
phenotype data
Seed weight / seed oil content; No complete accession-level phenotype download was found in the inspected supplement. The original publication is linked below
S008 Glycine max · seed
study population
238 accessions · 238 RNA-seq samples
sample collection
Soybean accessions were grown at the Liuhe experimental station in Nanjing in 2019; seeds were collected at 14 days after flowering between 10:00 and 11:00 a.m. in August for 3′ RNA-seq.
analysis reference
Williams 82 Gmax_275_v2.0 · Wm82.a2.v1 annotation
RNA-seq accessions
PRJCA031929
genotype source
GVM000063 (BIG Data Center)
sample count notes
The 238-accession seed panel was sampled at 14 days after flowering. The study reuses the earlier 21-day data represented by S007; the two stages are not independent populations.
phenotype data
100-seed weight; No public 238-accession phenotype matrix has been verified. The original publication and its supplementary tables are linked below, but they do not provide a confirmed accession-level download

sorghum datasets

S009 Sorghum bicolor · leaf
study population
748 genotypes · 748 RNA-seq samples
sample collection
On 5 August 2021, mature leaf tissue was collected from one representative plant per plot between 9:24 and 11:51 a.m.; the fourth leaf below the flag leaf, or the uppermost fully expanded leaf, was sampled and immediately flash-frozen.
analysis reference
BTx623 v5.0 · v5.1 annotation
RNA-seq accessions
PRJEB83049
genotype source
10.6084/m9.figshare.27936195
sample count notes
The catalog lists 748 accessions and RNA samples; the paper reports 738 accessions for downstream transcriptome analysis. The phenotyping files include broader panels and different environments.
phenotype data
Flowering time / raw field observations / spatially adjusted flowering values; Downloadable from the author phenotype files linked below. Retain the experiment, environment and treatment columns and subset by genotype ID

arabidopsis datasets

S010 Arabidopsis thaliana · whole basal leaf cluster
study population
666 accessions · 666 RNA-seq samples
sample collection
Ten whole basal leaf rosettes were pooled per accession immediately before flowering-stem elongation.
analysis reference
Col-0 TAIR10
RNA-seq accessions
GSE80744
genotype source
https://1001genomes.org/data/GMI-MPI/releases/v3.1/
sample count notes
The database count of 666 accessions describes the locally selected AtMAD expression panel, not the total size of the original global epigenome collection.
phenotype data
Flowering / growth / root architecture / germination / ionomic traits / treatment-response traits; Downloadable by study from AraPheno below. These studies do not form one complete phenotype matrix for all 666 RNA accessions

brassica datasets

S011 Brassica napus · leaf
study population
278 accessions · 278 RNA-seq samples
sample collection
Plants were grown in a chamber under 16 hours of light at 23 °C and 8 hours of darkness at 20 °C; at the five-true-leaf stage, the second-youngest leaves from four plants were combined per accession.
analysis reference
Darmor-bzh v4.1
RNA-seq accessions
PRJNA428769 (SRP128554)
genotype source
https://figshare.com/s/20afe1aa9cc682304163
sample count notes
The publication describes 277 B. napus transcriptomes, compared with 278 in the archive-based catalog. It also reuses 102 B. rapa transcriptomes from SRP072186; those records belong to a different species and dataset.
phenotype data
No material-level quantitative phenotype data were used in the core analysis; Morphotype and accession annotations are available in the author supporting data below, but they are not an accession-level quantitative phenotype matrix
S012 Brassica napus · seed
study population
309 accessions · 599 RNA-seq samples
sample collection
Developing seeds were collected at 20 and 40 days after flowering for population RNA-seq.
analysis reference
Darmor-bzh v4.1
RNA-seq accessions
CRA003544 (PRJCA002836)
genotype source
PRJCA002835
sample count notes
The catalog contains 309 accessions with 599 seed libraries: 309 at 20 days and 290 at 40 days after flowering. The GWAS population is larger than the RNA subset.
phenotype data
Seed oil content; The RGMI phenotype resource is linked below, but its accession-level download was not accessible or verified during this review
S013 Brassica napus · leaf
study population
100 accessions · 100 RNA-seq samples
sample collection
Plants were grown under a 16-hour day at 16 °C and an 8-hour night at 12 °C; leaves were harvested simultaneously after 30 days at the five- to six-leaf stage, shock-frozen and stored at −80 °C.
analysis reference
Darmor-bzh v4.1
RNA-seq accessions
PRJNA1086556
genotype source
https://osf.io/gfphb/
sample count notes
The catalog counts 100 distinct accessions and RNA samples. Additional archive experiment records should not be counted as extra independent accessions.
phenotype data
No material-level organismal phenotype data were used in the core analysis; The OSF resource linked below contains variants, expression and eQTL results rather than an agronomic phenotype matrix
S014 Brassica napus · shoot apical meristem; young leaf; silique
study population
334 accessions · 856 RNA-seq samples
sample collection
RNA-seq samples comprised shoot apical meristems, young leaves and siliques; siliques were collected 18 days after pollination, and each leaf accession was represented by two RNA-seq libraries.
analysis reference
Darmor-bzh v4.1
RNA-seq accessions
PRJNA1149544 (shoot apical meristem, 319 libraries); PRJNA1157560 (leaf, 154 accessions / 308 libraries); PRJNA1153365 (silique, 229 libraries); PRJCA013095 (GSA mirror)
genotype source
PRJNA1156901; PRJCA013095 (366 accessions); PRJCA002835 (502 accessions)
sample count notes
The catalog covers the newly deposited SAM, leaf and silique data: 334 distinct accessions and 856 RNA samples. The paper also incorporates earlier seed RNA-seq; its 2,105-genome panel is a different denominator.
phenotype data
Morphology / yield components / quality traits / chemical compounds; No complete measured-trait matrix matched to the 334-accession RNA-seq population was verified. BnaOmics and the original publication are linked below

cotton datasets

S015 Gossypium hirsutum · anther
study population
218 accessions · 218 RNA-seq samples
sample collection
Two field replicates of 218 accessions were grown in Alear in summer 2015 under high-temperature episodes above 37 °C for more than 3 days; tetrad-stage anthers were identified microscopically from 5–8 mm buds and frozen for RNA-seq.
analysis reference
TM-1 HAU v1.1
RNA-seq accessions
PRJNA393079
genotype source
variants called from RNA-seq
sample count notes
218 accessions contribute one RNA sample each. Field replicates used for pollen phenotyping are not additional RNA libraries.
phenotype data
Pollen viability / pollen-viability BLUP / tetrad-stage bud length; Accession-level values are present in Supplementary Table 3 of the original publication linked below. A separate direct public file URL has not been recorded
S016 Gossypium hirsutum · ovule
study population
382 accessions · 382 RNA-seq samples
sample collection
Ovules were collected 5 days post anthesis from the cultivated cotton panel for RNA-seq.
analysis reference
TM-1 HAU v1.1
RNA-seq accessions
PRJNA776409
genotype source
CRA009671
sample count notes
The archive-based catalog contains 382 RNA samples; the CottonGVD resource names a 383-accession panel. Resolve the accession list before joining phenotype data.
phenotype data
Yield components / fiber length / fiber strength / micronaire / fiber elongation / maturity traits; A local source matrix is verified and exactly matches 178 of 382 RNA accessions. No public accession-matched export for the complete set of 382 RNA accessions has been confirmed; CottonGVD and CottonGen are linked below
S017 Gossypium arboreum · whole seedling
study population
214 accessions · 214 RNA-seq samples
sample collection
Plants were grown in a controlled greenhouse in Anyang under a 16-hour light/8-hour dark cycle; five whole seedlings at the two-leaf stage were pooled per accession and immediately frozen in liquid nitrogen.
analysis reference
CRI-A2 v1.0
RNA-seq accessions
PRJNA704732
genotype source
PRJNA349094
sample count notes
The original study sampled 214 Gossypium arboreum accessions at the two-leaf stage, pooling five whole seedlings into one RNA sample per accession. PlantQTLdb analysis scripts use the G. arboreum CRI-A2 v1.0 reference and its matching annotation.
phenotype data
Germination rate / fresh weight / seedling length / water content / electrical conductivity under control and salt treatment; No complete 214-accession phenotype matrix was found in the inspected supplements. The earlier diversity-panel source is linked below
S018 Gossypium hirsutum · ovule; fiber
study population
376 accessions · 2215 RNA-seq samples
sample collection
Three field replicates were grown in Huanggang in 2019; ovules at anthesis and fibers at 4, 8, 12, 16 and 20 days post anthesis were collected from at least ten bolls on different plants across two rows and stored in liquid nitrogen.
analysis reference
TM-1 HAU v1.1
RNA-seq accessions
PRJNA891378
genotype source
PRJNA917453
sample count notes
376 accessions were studied over six fiber-development stages, with 2,215 RNA libraries rather than the theoretical 2,256 complete combinations.
phenotype data
Fiber length / fiber strength / fiber elongation / fiber uniformity; No complete measured-trait matrix download was verified in the inspected supplement. Predicted improvement values are not treated as measured phenotypes
S019 Gossypium hirsutum · ovule
study population
279 accessions · 555 RNA-seq samples
sample collection
For each accession, 16–18 plants were grown and 1-day-post-anthesis ovules were bulked for total RNA extraction in two biological replicates.
analysis reference
TM-1 HAU v1.1
RNA-seq accessions
PRJNA730082
genotype source
PRJNA375965
sample count notes
279 accessions contribute 555 cataloged ovule RNA samples. The unequal library count must not be replaced by 279 × 2 without checking missing samples.
phenotype data
Seed index / boll weight / boll number / lint percentage / fiber elongation / micronaire / fiber length / fiber strength; No phenotype download matched to all 279 RNA accessions has been verified. The earlier phenotype-generating study is linked below

maize datasets

S020 Zea mays · root
study population
340 genotypes · 572 RNA-seq samples
sample collection
Each sample comprised roots from two seedlings of the same genotype grown for 14 days in hydroponics; roots were harvested between ZT5 and ZT8 under green-filtered light and flash-frozen, with independently grown repeats for 219 genotypes.
analysis reference
B73 RefGen_v4
RNA-seq accessions
PRJNA793045
genotype source
variants called from RNA-seq; https://doi.org/10.6084/m9.figshare.19126139
sample count notes
The catalog distinguishes 340 accessions from 572 root RNA samples. Repeated accessions in the expression dataset do not create additional phenotype identities.
phenotype data
Flowering / plant architecture / ear architecture / kernel weight / other agronomic traits; A local Phenotype.tsv matrix is verified, and the paper with supplementary data is linked below. Full accession overlap between the phenotype matrix and the 340-accession RNA-seq population remains to be checked
S021 Zea mays · leaf
study population
699 genotypes · 750 RNA-seq samples
sample collection
On 8 July 2020, five disks from the fourth-highest visible and emerged leaf were collected from one plant per sample in the Nebraska field; all sampling was completed within about two hours before noon and tissue was immediately flash-frozen.
analysis reference
B73 RefGen_v4
RNA-seq accessions
PRJEB67964
genotype source
https://datadryad.org/dataset/doi:10.5061/dryad.bnzs7h4f1
sample count notes
The catalog contains 699 accessions and 750 RNA samples; the final expression analysis uses 693 genotypes after outlier filtering.
phenotype data
Days to anthesis in Nebraska / days to silking in Nebraska / days to anthesis in Michigan / days to silking in Michigan; Downloadable as pheno_693.txt in InputFiles.zip from the Figshare input files linked below. The matrix contains 693 genotypes
S022 Zea mays · third leaf
study population
102 genotypes · 208 RNA-seq samples
sample collection
Plants were grown for 14 days under a 30 °C/20 °C, 12-hour/12-hour day/night cycle; third leaves from 2–3 plants per genotype were pooled after 4 hours at 40 °C or under parallel 30 °C control conditions, with three B73 checks per condition.
analysis reference
B73 RefGen_v4
RNA-seq accessions
PRJNA831425
genotype source
PRJNA661271
sample count notes
A larger selected panel was reduced to the final analysis population of 102 genotypes. The 208 cataloged libraries include experimental replication and controls; not all libraries represent a distinct accession.
phenotype data
NPQ under control and heat / YII under control and heat / YNO under control and heat; Accession-level BLUPs are present in Supplementary Table S1 of the original publication linked below. They cover 100 of the 102 catalog genotypes
S023 Zea mays · kernel
study population
318 accessions · 318 RNA-seq samples
sample collection
Maize lines were grown in Hainan in 2014 in three incompletely randomized field blocks; at 5 days after pollination, 10–20 kernels from 3–4 self-pollinated ears per block were collected, then the three block samples were pooled for RNA extraction.
analysis reference
B73 RefGen_v4
RNA-seq accessions
PRJNA413629
genotype source
variants called from RNA-seq
sample count notes
The catalog lists 318 early-kernel RNA samples, whereas the paper reports 282 high-quality 5-day-after-pollination samples. The reused 15-day sample set is separate.
phenotype data
Kernel length / kernel thickness / 100-grain weight; MODEM and ZEAMAP sources are linked below, but the target matrix and its match to the 5-day-after-pollination RNA subset have not been verified
S024 Zea mays · leaf
study population
224 genotypes · 685 RNA-seq samples
sample collection
Two-week-old plants were assigned to well-watered, 9-day drought or 13-day drought conditions; a 5 cm section from the middle of the second leaf was pooled from three plants per genotype and frozen, with 58 samples independently repeated across treatments.
analysis reference
B73 RefGen_v4
RNA-seq accessions
PRJNA637522
genotype source
variants called from RNA-seq; GVM000048
sample count notes
224 accessions were grown under WW, WS1 and WS2 conditions. The paper reports 627 retained transcriptomes: 209 WW, 208 WS1 and 210 WS2. The local catalog retains its broader count of 685 RNA samples.
phenotype data
Seedling survival under drought / relative leaf water content; No accession-level survival matrix was found in the inspected supplement. The linked study repository contains analysis materials rather than a confirmed phenotype download
S025 Zea mays · leaf tip; leaf base
study population
108 F1 families · 624 RNA-seq samples
sample collection
At V4, approximately 20 mg was taken from the tip and base of a fully expanded leaf on one healthy interior plant per row; both sites were sampled four hours after sunrise within 90 minutes, using two highland field blocks and one lowland block.
analysis reference
B73 RefGen_v4
RNA-seq accessions
PRJNA796614
genotype source
PRJNA799784
sample count notes
108 landraces were crossed to the common B73 tester, producing F1 families. The 624 RNA samples represent the experimental sampling design, not 624 independent parental lines.
phenotype data
No material-level agronomic phenotype data were used in the core analysis; Geographic origin and elevation were used for population grouping. The author repository linked below provides analysis code rather than a verified phenotype matrix
S026 Zea mays · root; shoot; leaf 3 base; leaf 3 tip; kernel; mature leaf
study population
301 accession labels · 1923 RNA-seq samples
sample collection
Seven tissues or time points were profiled: germinating roots and shoots, 2 cm sections from the base and tip of leaf 3, mature mid-leaf collected at midday or midnight, and kernels at 350 growing degree days after pollination; non-kernel tissues were pooled from three plants per genotype.
analysis reference
B73 RefGen_v4
RNA-seq accessions
PRJNA383416
genotype source
HapMap3.2.1; GBS-imputed genotypes
sample count notes
The catalog has 301 accessions and 1,923 RNA samples across seven tissues. These catalog counts should not be substituted for the number retained by every rare-allele or fitness analysis.
phenotype data
Seed-weight fitness; The publisher supplement contains sample identities but not fitness values. The Panzea phenotype portal is linked below, but a matching accession-level matrix has not been verified

tomato datasets

S027 Solanum lycopersicum · fruit pericarp
study population
399 accessions · 399 RNA-seq samples
sample collection
Pericarp from at least five orange-stage fruits, approximately 75% ripe, was pooled for each RNA sample.
analysis reference
Heinz 1706 SL5.0 · ITAG5.0 annotation
RNA-seq accessions
PRJNA396272
genotype source
SRP045767; PRJNA353161; PRJEB5235
sample count notes
The source study distinguishes 610 resequenced accessions, 442 metabolomics accessions and 399 transcriptomics accessions. Table M1 contains 884 replicate rows for the 442 metabolomics accessions; match the phenotype and RNA-seq accessions by identifier.
phenotype data
Raw fruit metabolite abundances; Downloadable as Table M1 from Mendeley Data below. The file contains 884 rows, 442 accessions and 980 metabolite signals; overlap with the 399 RNA accessions remains to be checked

wheat datasets

S028 Triticum aestivum · whole seedling
study population
204 accessions · 204 RNA-seq samples
sample collection
Each of 204 lines was grown in three biological replicates; equal amounts of ground tissue from 2-week-old whole seedlings were combined before RNA extraction.
analysis reference
Chinese Spring IWGSC RefSeq v1.0 · v1.1 annotation
RNA-seq accessions
PRJNA670223
genotype source
variants called from RNA-seq
sample count notes
204 accessions were selected for RNA sequencing; the Results section describes 198 accessions in the expression analysis. The 400-line diversity panel and approximately 800-line exome phenotype panel are distinct.
phenotype data
Heading date / plant height / awnedness / spike traits / grain traits / field productivity / stem-rust response; Wheat T3 and the earlier exome-panel source are linked below, but no observation matrix matched to all 204 RNA accessions has been verified
S029 Triticum aestivum · root
study population
406 accessions · 406 RNA-seq samples
sample collection
Roots were collected 14 days after germination in distilled water; six biological replicates were pooled per accession for RNA-seq.
analysis reference
Chinese Spring IWGSC RefSeq v1.0 · v1.1 annotation
RNA-seq accessions
PRJNA838764
genotype source
https://resource.iwheat.net/PWGBD/
sample count notes
406 accessions were profiled. The phenotype identifiers differ from the sequenced identifiers; the supplied correspondence table is required for matching.
phenotype data
Root length / root surface area / root volume / root diameter / root fresh weight / multi-environment developmental traits / architecture traits / yield traits; Source downloads are available through WGPD below, and the valid matrices are available locally. Empty E1–E4 architecture files were excluded
S030 Triticum aestivum · leaf
study population
328 accessions · 328 RNA-seq samples
sample collection
Wheat lines were grown in trays under a 14-hour light/10-hour dark cycle at 22 °C/18 °C; leaves were collected at two weeks and tissue from three biological replicates was combined for RNA extraction.
analysis reference
Chinese Spring IWGSC RefSeq v1.0 · v1.1 annotation
RNA-seq accessions
CRA022107
genotype source
GVM000315 (BIG Data Center)
sample count notes
328 accessions were sequenced. Accession 1699B was excluded for suspected contamination, leaving 327 high-quality RNA-seq samples for the published downstream analysis. The database count of 328 describes the collected and deposited sample set.
phenotype data
Thirty-four agronomic traits / resistance to eight powdery-mildew isolates; Only partial validation observations are downloadable in the Source Data below. A complete 327-accession by 42-trait matrix was not found; the linked Figshare deposit contains expression and eQTL data rather than that phenotype matrix

quality and reference coordinates

Each result should retain its species, dataset, tissue or condition, reference assembly, marker or gene identifier, method and source publication. The same accession can legitimately occur in several tissue or treatment datasets; those records are not independent biological populations.

Reference-coordinate harmonization is applied where a reliable mapping is available. Unresolved assemblies, pangenome contigs and non-reference marker labels must retain their source context and should not be assigned an invented position in a reference-genome plot. A shared chromosome label alone does not establish assembly compatibility.

This document records source evidence and availability. It does not certify that every downloaded phenotype has been harmonized or imported into PlantQTLdb, and it does not replace the sample exclusions and quality rules of an individual analysis.

cite PlantQTLdb and source evidence

Cite PlantQTLdb with the website URL and your access date. Use a formal database citation when one is provided by the site. For a result based on a particular dataset, also cite its original publication and the relevant analysis method.

If phenotype observations were reused from an earlier paper or data repository, cite that source explicitly. Record the repository version or DOI, the downloaded filename, the trait and environment, and the accession subset used in your analysis.

original data publications

  1. S001 Chang Liu, Xiya Zhu, Jin Zhang et al. (2022). eQTLs play critical roles in regulating gene expression and identifying key regulators in rice. Plant Biotechnology Journal. PMID 36087348
  2. S002 Lianguang Shang, Xiaoxia Li, Huiying He et al. (2022). A super pan-genomic landscape of rice. Cell Research. PMID 35821092
  3. S002 Hong Zhang, Wu Chen, De Zhu et al. (2024). Population-level exploration of alternative splicing and its unique role in controlling agronomic traits of rice. The Plant Cell. PMID 38916914
  4. S003 Hua Wei, Xianmeng Wang, Zhipeng Zhang et al. (2024). Uncovering key salt-tolerant regulators through a combined eQTL and GWAS analysis using the super pan-genome in rice. National Science Review. PMID 38650829
  5. S004 Qian Du, Malachy Campbell, Huihui Yu et al. (2019). Network-based feature selection reveals substructures of gene modules responding to salt stress in rice. Plant Direct. PMID 31417977
  6. S005 Dongling Guo, Yan Li, Hengyun Lu et al. (2025). A pangenome reference of wild and cultivated rice. Nature. PMID 40240605
  7. S006 Delin Li, Qi Wang, Yu Tian et al. (2024). TWAS facilitates gene-scale trait genetic dissection through gene expression, structural variations, and alternative splicing in soybean. Plant Communications. PMID 38918950
  8. S007 Xiaobo Yuan, Xinyu Jiang, Mengzhu Zhang et al. (2024). Integrative omics analysis elucidates the genetic basis underlying seed weight and oil content in soybean. The Plant Cell. PMID 38412459
  9. S008 Xiang Wang, Xinyu Jiang, Xiaobo Yuan et al. (2025). Transcriptome-Wide Association Uncovers LncRNAs Controlling Seed Weight in Soybean. Advanced Science. PMID 40789081
  10. S009 Harshita Mangal, Kyle Linders, Jonathan Turkus et al. (2025). Genes and pathways determining flowering time variation in temperate-adapted sorghum. The Plant Journal. PMID 40456184
  11. S010 Taiji Kawakatsu, Shao-Shan Carol Huang, Florian Jupe et al. (2016). Epigenomic Diversity in a Global Collection of Arabidopsis thaliana Accessions. Cell. PMID 27419873
  12. S011 Hong An, Xinshuai Qi, Michelle L. Gaynor et al. (2019). Transcriptome and organellar sequencing highlights the complex origin and diversification of allotetraploid Brassica napus. Nature Communications. PMID 31253789
  13. S012 Shan Tang, Hu Zhao, Shaoping Lu et al. (2021). Genome- and transcriptome-wide association studies provide insights into the genetic basis of natural variation of seed oil content in Brassica napus. Molecular Plant. PMID 33309900
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