Abstract
Understanding how nutrient stress impacts plant growth is fundamentally important to the development of approaches to improve crop production under nutrient limitation. Here we applied single-cell RNA sequencing to shoot apices of Pisum sativum grown under boron (B) deficiency. We identified up to 15 cell clusters based on the clustering of gene expression profiles and verified cell identity with cell-type-specific marker gene expression. Different cell types responded differently to B deficiency. Specifically, the expression of photosynthetic genes in mesophyll cells (MCs) was down-regulated by B deficiency, consistent with impaired photosynthetic rate. Furthermore, 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. We also constructed the developmental trajectory of the shoot apical meristem (SAM) cells and a transcription factor interaction network. The developmental progression of SAM to MC was characterized by up-regulation of genes encoding histones and chromatin assembly and remodeling proteins including homologs of FASCIATA1 (FAS1) and SWITCH DEFECTIVE/SUCROSE NON-FERMENTABLE (SWI/SNF) complex. However, B deficiency suppressed their expression, which helps to explain impaired SAM development under B deficiency. These results represent a major advance over bulk-tissue RNA-seq analysis in which cell-type-specific responses are lost and hence important physiological responses to B deficiency are missed. The reported findings reveal strategies by which plants adapt to B deficiency thus offering breeders a set of specific targets for genetic improvement. The reported approach and resources have potential applications well beyond P. sativum species and could be applied to various legumes to improve their adaptability to multiple nutrient or abiotic stresses.
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Claims 8
Claim · model-written summary
Single-cell analysis identified up to 15 shoot apex cell clusters and verified their identity with marker genes.
- Taxon
- Pisum sativum
Lathyrus oleraceust0 - Outcome
- cell clusterse0
- Value
- up to 15e0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“We identified up to 15 cell clusters based on the clustering of gene expression profiles and verified cell identity with cell-type-specific marker gene expression.”
t0“shoot apices of Pisum sativum grown under boron (B) deficiency”
Claim · model-written summary
Cell types responded differently to boron deficiency.
- Taxon
- Pisum sativumLathyrus oleraceust0
- Outcome
- responded differently to B deficiencye0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Different cell types responded differently to B deficiency.”
t0“shoot apices of Pisum sativum grown under boron (B) deficiency”
Claim · model-written summary
Boron deficiency down-regulated photosynthetic gene expression in mesophyll cells.
- Taxon
- Pisum sativumLathyrus oleraceust0
- Organ / stage
- mesophyll cellse0
- Treatment
- B deficiencye0
- Outcome
- expression of photosynthetic genese0
- Direction
- down-regulatede0
Not reportedComparator
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“the expression of photosynthetic genes in mesophyll cells (MCs) was down-regulated by B deficiency”
t0“shoot apices of Pisum sativum grown under boron (B) deficiency”
Claim · model-written summary
Boron deficiency reduced stomatal development gene expression in guard cells.
- Taxon
- Pisum sativumLathyrus oleraceust0
- Treatment
- B deficiencye1
- Gene
- MUTE and TOO MANY MOUTHSe0
- Outcome
- stomatal development genese0
- Direction
- down-regulatione0
Not reportedComparator
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“the down-regulation of stomatal development genes in guard cells, including homologs of MUTE and TOO MANY MOUTHS”
e1“Different cell types responded differently to B deficiency.”
t0“shoot apices of Pisum sativum grown under boron (B) deficiency”
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
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
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.”
t0“shoot apices of Pisum sativum grown under boron (B) deficiency”
Claim · model-written summary
The study constructed a shoot apical meristem developmental trajectory and transcription factor interaction network.
- Taxon
- Pisum sativumLathyrus oleraceust0
- Outcome
- developmental trajectory of the shoot apical meristem (SAM) cells and a transcription factor interaction networke0
Not reportedComparatorValue
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“We also constructed the developmental trajectory of the shoot apical meristem (SAM) cells and a transcription factor interaction network.”
t0“shoot apices of Pisum sativum grown under boron (B) deficiency”
Claim · model-written summary
SAM to mesophyll progression involved up-regulation of histone and chromatin assembly and remodeling genes.
- Taxon
- Pisum sativumLathyrus oleraceust0
- Gene
- FASCIATA1 (FAS1) and SWITCH DEFECTIVE/SUCROSE NON-FERMENTABLE (SWI/SNF) complexe0
- Outcome
- genes encoding histones and chromatin assembly and remodeling proteinse0
- Direction
- up-regulatione0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“The developmental progression of SAM to MC was characterized by up-regulation of genes encoding histones and chromatin assembly and remodeling proteins including homologs of FASCIATA1 (FAS1) and SWITCH DEFECTIVE/SUCROSE NON-FERMENTABLE (SWI/SNF) complex.”
t0“shoot apices of Pisum sativum grown under boron (B) deficiency”
Claim · model-written summary
Boron deficiency suppressed expression of these chromatin related genes.
- Taxon
- Pisum sativumLathyrus oleraceust0
- Treatment
- B deficiencye0
- Outcome
- their expressione0
- Direction
- suppressede0
Not reportedComparator
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“However, B deficiency suppressed their expression, which helps to explain impaired SAM development under B deficiency.”
t0“shoot apices of Pisum sativum grown under boron (B) deficiency”