Abstract
Root morphology is known to be affected by light quality, quantity and direction. Light signal is perceived at the shoot, translocated to roots through vasculature and further modulates the root development. Photoreceptors are differentially expressed in both shoot and root cells. The light irradiation to the root affects shoot morphology as well as whole plant development. The current work aims to understand the white light intensity dependent changes in root patterning and correlate that with the global gene expression profile. Different fluence of white light (WL) regulate overall root development via modulating the expression of a specific set of genes. Phytochrome A deficient Arabidopsis thaliana ( phyA-211 ) showed shorter primary root compared to phytochrome B deficient ( phyB-9 ) and wild type (WT) seedlings at a lower light intensity. However, at higher intensity, both mutants showed shorter primary root in comparison to WT. The lateral root number was observed to be lowest in phyA-211 at intensities of 38 and 75 μmol m − 2 s − 1 . The number of adventitious roots was significantly lower in phyA-211 as compared to WT and phyB-9 under all light intensities tested. With the root phenotypic data, microarray was performed for four different intensities of WL light in WT. Here, we identified ~ 5243 differentially expressed genes (DEGs) under all light intensities. Gene ontology-based analysis indicated that different intensities of WL predominantly affect a subset of genes having catalytic activity and localized to the cytoplasm and membrane. Furthermore, when root is irradiated with different intensities of WL, several key genes involved in hormone, light signaling and clock-regulated pathways are differentially expressed. Using genome wide microarray-based approach, we have identified candidate genes in Arabidopsis root that responded to the changes in light intensities. Alteration in expression of genes such as PIF4 , COL9 , EPR1, CIP1, ARF18, ARR6, SAUR9, TOC1 etc. which are involved in light, hormone and clock pathway was validated by qRT-PCR. This indicates their potential role in light intensity mediated root development.
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Claims 8
Claim · model-written summary
At lower light intensity, phyA-211 had shorter primary roots than phyB-9 and WT.
- Taxon
- Arabidopsis thaliana
Arabidopsis thalianae0 - Material
- phyA-211e0
- Outcome
- primary roote0
- Direction
- shortere0
- Qualifier
- at a lower light intensitye0
- Comparator
- phyB-9e0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Phytochrome A deficient Arabidopsis thaliana ( phyA-211 ) showed shorter primary root compared to phytochrome B deficient ( phyB-9 ) and wild type (WT) seedlings at a lower light intensity.”
Claim · model-written summary
At higher light intensity, both photoreceptor mutants had shorter primary roots than WT.
- Taxon
- Arabidopsis thalianaArabidopsis thalianat0
- Material
- both mutantse0
- Outcome
- primary roote0
- Direction
- shortere0
- Qualifier
- at higher intensitye0
- Comparator
- WTe0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“However, at higher intensity, both mutants showed shorter primary root in comparison to WT.”
t0“Arabidopsis thaliana”
Claim · model-written summary
phyA-211 had the lowest lateral root number at 38 and 75 μmol m − 2 s − 1.
- Taxon
- Arabidopsis thalianaArabidopsis thalianat0
- Material
- phyA-211e0
- Outcome
- lateral root numbere0
- Direction
- loweste0
- Qualifier
- at intensities of 38 and 75 μmol m − 2 s − 1e0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“The lateral root number was observed to be lowest in phyA-211 at intensities of 38 and 75 μmol m − 2 s − 1 .”
t0“Arabidopsis thaliana”
Claim · model-written summary
phyA-211 had significantly fewer adventitious roots than WT and phyB-9 at all tested intensities.
- Taxon
- Arabidopsis thalianaArabidopsis thalianat0
- Material
- phyA-211e0
- Outcome
- number of adventitious rootse0
- Direction
- lowere0
- Qualifier
- under all light intensities testede0
- Comparator
- WT and phyB-9e0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“The number of adventitious roots was significantly lower in phyA-211 as compared to WT and phyB-9 under all light intensities tested.”
t0“Arabidopsis thaliana”
Claim · model-written summary
Across all light intensities, about 5243 genes were differentially expressed.
- Taxon
- Arabidopsis thalianaArabidopsis thalianat0
- Outcome
- differentially expressed genes (DEGs)e0
- Value
- ~ 5243e0
- Qualifier
- under all light intensitiese0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Here, we identified ~ 5243 differentially expressed genes (DEGs) under all light intensities.”
t0“Arabidopsis thaliana”
Claim · model-written summary
White light intensity predominantly affected genes with catalytic activity located in cytoplasm and membrane.
- Taxon
- Arabidopsis thalianaArabidopsis thalianat0
- Outcome
- a subset of genes having catalytic activity and localized to the cytoplasm and membranee0
- Qualifier
- different intensities of WLe0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Gene ontology-based analysis indicated that different intensities of WL predominantly affect a subset of genes having catalytic activity and localized to the cytoplasm and membrane.”
t0“Arabidopsis thaliana”
Claim · model-written summary
Root irradiation at different white light intensities changed expression of key hormone, light signaling and clock pathway genes.
- Taxon
- Arabidopsis thalianaArabidopsis thalianat0
- Organ / stage
- roote0
- Outcome
- several key genes involved in hormone, light signaling and clock-regulated pathways are differentially expressede0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“when root is irradiated with different intensities of WL, several key genes involved in hormone, light signaling and clock-regulated pathways are differentially expressed.”
t0“Arabidopsis thaliana”
Claim · model-written summary
qRT-PCR validated altered expression of the listed light, hormone and clock genes.
- Taxon
- Arabidopsis thalianaArabidopsis thalianat0
- Gene
- PIF4e0
- Outcome
- Alteration in expressione0
Not reportedComparatorValue
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Alteration in expression of genes such as PIF4 , COL9 , EPR1, CIP1, ARF18, ARR6, SAUR9, TOC1 etc. which are involved in light, hormone and clock pathway was validated by qRT-PCR.”
t0“Arabidopsis thaliana”