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Intervention effect 21

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Intervention effectobservedoriginal resultnegativemeasured

Claim · model-written summary

HIC knockdown markedly decreases trichome density.

Treatment
knockdown of HICe0
Gene
HICe0
Outcome
densitye0
Direction
decreasee0

Not reportedComparator

Verbatim

e0

“knockdown of HIC results in a marked decrease in density”

✓ located verbatim in the source · abstract, characters 740–796
t0

“cotton”

✓ located verbatim in the source · title, characters 25–31

Title

Natural variation at the cotton HIC locus increases trichome density and enhances resistance to aphids

Yanan Wang; Qi Zhou; Jilong Zhang; et al. The Plant Journal 2024. doi:10.1111/tpj.17050

Other claims from this paper (8)
Intervention effectobservedoriginal resultsignificant (as stated)measured

Claim · model-written summary

OsYDA1 overexpression significantly decreased stomatal density in Arabidopsis.

Taxon
ArabidopsisArabidopsise0
Treatment
Overexpressione0
Gene
OsYDA1e1
Outcome
stomatal densitye0
Direction
decreasee0

Not reportedComparator

Verbatim

e0

“Overexpression of either of these genes in Arabidopsis resulted in a significant decrease in stomatal density and water-loss rate.”

✓ located verbatim in the source · abstract, characters 555–685
e1

“OsYDA1 and OsYDA2”

✓ located verbatim in the source · abstract, characters 537–554

Title

Characterization of Rice OsYDA Gene in Regulating Stomatal Development

Zheng Guo 2011

Other claims from this paper (6)
Intervention effectobservedoriginal resultsignificant (as stated)measured

Claim · model-written summary

OsYDA2 overexpression significantly decreased stomatal density in Arabidopsis.

Taxon
ArabidopsisArabidopsise0
Treatment
Overexpressione0
Gene
OsYDA2e1
Outcome
stomatal densitye0
Direction
decreasee0

Not reportedComparator

Verbatim

e0

“Overexpression of either of these genes in Arabidopsis resulted in a significant decrease in stomatal density and water-loss rate.”

✓ located verbatim in the source · abstract, characters 555–685
e1

“OsYDA1 and OsYDA2”

✓ located verbatim in the source · abstract, characters 537–554

Title

Characterization of Rice OsYDA Gene in Regulating Stomatal Development

Zheng Guo 2011

Other claims from this paper (6)

Association 8

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Associationobservedoriginal resultnegativemeasured

Claim · model-written summary

Down-regulation of stomatal development genes correlated with lower stomatal density under boron deficiency.

Taxon
Pisum sativumLathyrus oleraceust0
Gene
MUTE and TOO MANY MOUTHSe0
Outcome
stomatal densitye0
Direction
decreasee0

Verbatim

e0

“the down-regulation of stomatal development genes in guard cells, including homologs of MUTE and TOO MANY MOUTHS, correlated with a decrease in stomatal density under B deficiency.”

✓ located verbatim in the source · abstract, characters 676–856
t0

“shoot apices of Pisum sativum grown under boron (B) deficiency”

✓ located verbatim in the source · abstract, characters 215–277

Title

Single‐cell transcriptomic analysis of pea shoot development and cell‐type‐specific responses to boron deficiency

Xi Chen; Yanqi Ru; Hirokazu Takahashi; et al. The Plant Journal 2023. doi:10.1111/tpj.16487

Other claims from this paper (7)
Associationobservedoriginal resultmeasured

Claim · model-written summary

TE abundance shows a consistent negative correlation with gene density in A. thaliana.

Taxon
Arabidopsis thalianaArabidopsis thalianae0
Treatment
gene densitye2
Outcome
TE abundancee2
Direction
decreaseinferrede2

Verbatim

e0

“the genome sequence of Arabidopsis thaliana”

✓ located verbatim in the source · abstract, characters 334–377
e2

“a consistent negative correlation between gene density and TE abundance”

✓ located verbatim in the source · abstract, characters 711–782

Title

Effects of Recombination Rate and Gene Density on Transposable Element Distributions in Arabidopsis thaliana

Stephen I. Wright; Newton Agrawal; Thomas E. Bureau Genome Research 2003. doi:10.1101/gr.1281503

Other claims from this paper (4)
Associationobservedoriginal resultmeasured

Claim · model-written summary

In Arabidopsis ecotypes, expression of epi-alleles at these loci decreases as methylation density increases, mainly within the transcribed region.

Taxon
ArabidopsisArabidopsise3
Material
Arabidopsis ecotypese3
Outcome
expression patternse3
Direction
decreaseinferrede3
Qualifier
with methylation densitye3

Verbatim

e3

“Arabidopsis ecotypes contain distinct epi-alleles of these loci with expression patterns that inversely correlate with methylation density, predominantly within the transcribed region”

✓ located verbatim in the source · abstract, characters 1223–1406

Title

Transmission of Epi-Alleles with MET1-Dependent Dense Methylation in Arabidopsis thaliana

Michael Watson; Emily Hawkes; Peter Meyer PLoS ONE 2014. doi:10.1371/journal.pone.0105338

Other claims from this paper (6)

Observation 7

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Observationobservedoriginal resultmeasured

Claim · model-written summary

Lineage-specific alleles that decrease trichome density persist in natural populations.

Taxon
Arabidopsis thalianaArabidopsis thalianat0
Material
lineage-specific allelese0
Outcome
trichome densitye0
Direction
decreasee0

Verbatim

e0

“many lineage-specific alleles that either increase or decrease trichome density persist in natural populations”

✓ located verbatim in the source · abstract, characters 1046–1156
t0

“Arabidopsis thaliana”

✓ located verbatim in the source · title, characters 59–79

Title

Mapping Quantitative Trait Loci in Multiple Populations of Arabidopsis thaliana Identifies Natural Allelic Variation for Trichome Density

V Vaughan Symonds; A Veronica Godoy; Teresa Alconada; et al. Genetics 2005. doi:10.1534/genetics.104.031948

Other claims from this paper (5)
Observationobservedreview summarybasis n/a

Claim · model-written summary

Chilling, planting density, rubbing, cutting and repeated subculture generally decrease plant DNA methylation.

Taxon
plantt0
Treatment
chilling, planting density, rubbing, cutting, and successive rounds of subculturee0
Outcome
levels of DNA methylatione0
Direction
decreasee0

Verbatim

e0

“Abiotic stresses such as chilling, planting density, rubbing, cutting, and successive rounds of subculture generally decrease the levels of DNA methylation”

✓ located verbatim in the source · abstract, characters 140–295
t0

“Plant genomic DNA methylation”

✓ located verbatim in the source · title, characters 0–29

Title

Plant genomic DNA methylation in response to stresses: Potential applications and challenges in plant breeding

Hai Peng; Jing Zhang Progress in Natural Science Materials International 2009. doi:10.1016/j.pnsc.2008.10.014

Other claims from this paper (5)
Observationobservedoriginal resultno effectmeasured

Claim · model-written summary

SEC3A puncta density did not decrease after these cells stopped growing.

Taxon
ArabidopsisArabidopsist0
Outcome
density of punctae0
Direction
does not decreasee0
Qualifier
after growth terminatione0

Verbatim

t0

“Arabidopsis”

✓ located verbatim in the source · title, characters 4–15
e0

“The density of puncta does not decrease after growth termination of these cells, but decreases strongly when exocytosis is inhibited by treatment with brefeldin A.”

✓ located verbatim in the source · abstract, characters 935–1098

Title

The Arabidopsis exocyst subunit SEC3A is essential for embryo development and accumulates in transient puncta at the plasma membrane

Ying Zhang; Richard Immink; Chun‐Ming Liu; et al. New Phytologist 2013. doi:10.1111/nph.12236

Other claims from this paper (7)

Method / resource 6

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Method / resourceobservedoriginal resultpositivemeasured

Claim · model-written summary

Marker density as low as 500 did not decrease prediction accuracy.

Taxon
spring wheatTriticum aestivumt0
Outcome
prediction accuracye0
Direction
without decreasinge0
Value
500e0

Verbatim

e0

“marker density could be as low as 500 without decreasing the prediction accuracy”

✓ located verbatim in the source · abstract, characters 1018–1098
t0

“spring wheat”

✓ located verbatim in the source · title, characters 75–87

Title

Leveraging historical trials to predict Fusarium head blight resistance in spring wheat breeding programs

Charlotte Brault; Emily J. Conley; Andrew J. Green; et al. The Plant Genome 2025. doi:10.1002/tpg2.20559

Other claims from this paper (4)
Method / resourceobservedoriginal resultpositivemeasured

Claim · model-written summary

Enrichment decreased potato host genomic reads by about 1.7-fold.

Outcome
host genomic readse0
Direction
decreasee0
Value
∼1.7-folde0
Comparator
DNA extracted from the same sample without density gradient centrifugation enrichmente0

Verbatim

e0

“a ∼1.7-fold decrease in host genomic reads compared to the DNA extracted from the same sample without density gradient centrifugation enrichment.”

✓ located verbatim in the source · abstract, characters 563–708
e1

“potato infected with a ‘ Candidatus Phytoplasma australasia’-related strain”

✓ located verbatim in the source · abstract, characters 429–504

Title

Iodixanol density gradients as an effective phytoplasma enrichment approach to improve genome sequencing

Bianca Rodrigues Jardim; Lucy T. T. Tran-Nguyen; Cherie Gambley; et al. Frontiers in Microbiology 2022. doi:10.3389/fmicb.2022.937648

Other claims from this paper (9)
Method / resourceobservedoriginal resultmeasured

Claim · model-written summary

Scaffold ordering with two high-density genetic maps increased faba bean chromosome length to 14.28 Mbp

Taxon
faba beanVicia fabat0
Outcome
lengthe1
Direction
increasede1
Value
14.28 Mbpe1

Verbatim

t0

“faba bean”

✓ located verbatim in the source · title, characters 13–22
e1

“Two high-density genetic maps were used to conduct the scaffold ordering and orientation of faba bean, culminating in an increased length (i.e., 14.28 Mbp) of chromosomes and a decrease in the number of scaffolds by 45”

✓ located verbatim in the source · abstract, characters 223–441

Title

High-quality faba bean reference transcripts generated using PacBio and Illumina RNA-seq data

Na Zhao; Enqiang Zhou; Yamei Miao; et al. Scientific Data 2024. doi:10.1038/s41597-024-03204-4

Other claims from this paper (9)

Mechanism 3

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Mechanismhypothesisoriginal resultbasis n/a

Claim · model-written summary

The MtCAS31 and AtICE1 interaction is hypothesized to cause the decrease in stomatal density that enhances drought resistance in transgenic Arabidopsis.

Taxon
ArabidopsisArabidopsise6
Gene
AtICE1e6
Outcome
decrease in stomatal densitye6
Qualifier
the interaction of MtCAS31 and AtICE1e6

Verbatim

e6

“We hypothesize that the interaction of MtCAS31 and AtICE1 caused the decrease in stomatal density to enhance the drought resistance of transgenic Arabidopsis”

✓ located verbatim in the source · abstract, characters 1421–1578

Title

Overexpression of MtCAS31 enhances drought tolerance in transgenic Arabidopsis by reducing stomatal density

Can Xie; Rongxue Zhang; Yueting Qu; et al. New Phytologist 2012. doi:10.1111/j.1469-8137.2012.04136.x

Other claims from this paper (4)
Mechanismauthor interpretationoriginal resultmeasured

Claim · model-written summary

The authors linked the density induced ratio decrease to downregulation of three carbon metabolism enzymes.

Outcome
downregulation of C 4 carbon metabolism enzymese0
Qualifier
C 4 carbon metabolism enzymese0

Not reportedTaxon

Verbatim

e0

“which resulted in downregulation of C 4 carbon metabolism enzymes (phosphoenolpyruvate carboxykinase, phosphoenolpyruvate carboxylase, and pyruvate orthophosphate dikinase).”

✓ located verbatim in the source · abstract, characters 1189–1362

Title

Corn Response to Competition: Growth Alteration vs. Yield Limiting Factors

S. A. Clay; D. E. Clay; D. P. Horvath; et al. Agronomy Journal 2009. doi:10.2134/agronj2008.0213x

Other claims from this paper (12)
Mechanismobservedoriginal resultmeasured

Claim · model-written summary

ZmELF3.1 interacts with RA2 and ZmELF4.2 to form tri-protein complexes that enhance RA2 binding to the TSH4 promoter and decrease tassel branch number in maize.

Taxon
maizeZea mayse0
Gene
ZmELF3.1e3
Outcome
decreased TBNe3
Qualifier
tri-protein complexese3

Verbatim

e0

“Tassel branch number (TBN) is a key agronomic trait for adapting to high-density planting and grain yield in maize”

✓ located verbatim in the source · abstract, characters 0–114
e3

“ZmELF3.1 directly interacts with both RA2 and ZmELF4.2 to form tri-protein complexes that further enhance the binding of RA2 to the promoter of TSH4, leading to suppressed TSH4 expression and consequently decreased TBN”

✓ located verbatim in the source · abstract, characters 813–1031

Title

ZmELF3.1 integrates the RA2‐TSH4 module to repress maize tassel branching

Yurong Xie; Yongping Zhao; Lihong Chen; et al. New Phytologist 2023. doi:10.1111/nph.19329

Other claims from this paper (3)

Recommendation 1

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Recommendationauthor interpretationoriginal resultpositivebasis n/a

Claim · model-written summary

The authors recommend introgressing both QTL into potato cultivars to reduce nematode density and resistance breakdown.

Interactor
G. pallidaGlobodera pallidae0pathogen
Gene
GpaV(s)sple0
Outcome
introgress together GpaV(s)spl and GpaXI(s)spl into potato cultivarse0

Verbatim

e0

“introgress together GpaV(s)spl and GpaXI(s)spl into potato cultivars, in order to reduce the density of this quarantine pest in soil and to decrease the risk of selecting overcoming G. pallida subpopulations”

✓ located verbatim in the source · abstract, characters 1122–1329

Title

Resistance Quantitative Trait Loci Originating from Solanum sparsipilum Act Independently on the Sex Ratio of Globodera pallida and Together for Developing a Necrotic Reaction

Bernard Caromel; Didier Mugniéry; Marie-Claire Kerlan; et al. Molecular Plant-Microbe Interactions 2005. doi:10.1094/mpmi-18-1186

Other claims from this paper (8)

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