Harnessing Single-Cell and Spatial Transcriptomics for Crop Improvement DOI Creative Commons
Yuzhao Hu,

Linkan Dash,

Gregory D. May

et al.

Plants, Journal Year: 2024, Volume and Issue: 13(24), P. 3476 - 3476

Published: Dec. 11, 2024

Single-cell and spatial transcriptomics technologies have significantly advanced our understanding of the molecular mechanisms underlying crop biology. This review presents an update on application these in improvement. The heterogeneity different cell populations within a tissue plays crucial role coordinated response organism to its environment. enables dissection this heterogeneity, offering insights into cell-specific transcriptomic responses plants various environmental stimuli. Spatial complement single-cell approaches by preserving context gene expression profiles, allowing for situ localization transcripts. Together, facilitate discovery novel genes regulatory networks that can be targeted genetic manipulation breeding strategies aimed at enhancing yield, quality, resilience. highlights significant findings from recent studies, discusses expanding roles technologies, explores future opportunities their

Language: Английский

Plant secondary metabolites against biotic stresses for sustainable crop protection DOI
Tanzim Jahan, Md. Nurul Huda, Kaixuan Zhang

et al.

Biotechnology Advances, Journal Year: 2025, Volume and Issue: unknown, P. 108520 - 108520

Published: Jan. 1, 2025

Language: Английский

Citations

2
Dual and spatially resolved drought responses in the Arabidopsis leaf mesophyll revealed by single‐cell transcriptomics DOI Creative Commons
Rubén Tenorio Berrío, Eline Verhelst, Thomas Eekhout

et al.

New Phytologist, Journal Year: 2025, Volume and Issue: unknown

Published: March 3, 2025

Summary Drought stress imposes severe challenges on agriculture by impacting crop performance. Understanding drought responses in plants at a cellular level is crucial first step toward engineering improved resilience. However, the molecular to are complex as they depend multiple factors, including severity of drought, profiled organ, its developmental stage or even cell types therein. Thus, deciphering transcriptional especially challenging. In this study, we investigated tissue‐specific mild (MD) young Arabidopsis thaliana (Arabidopsis) leaves using single‐cell RNA sequencing (scRNA‐seq). To preserve integrity during isolation, inhibited synthesis transcription inhibitor actinomycin D, and demonstrated benefits transcriptome fixation for studying level. We present curated validated atlas, comprising 50 797 high‐quality cells from almost all known leaf. All type annotations were with new library reporter lines. The data available broad community an intuitive tool browsable atlas ( http://www.single‐cell.be/plant/leaf‐drought ). show that mesophyll contains two spatially separated populations distinct drought: one enriched canonical abscisic acid‐related drought‐responsive genes, another genes involved iron starvation responses. Our study thus reveals dual adaptive mechanism leaf response MD provides valuable resource future research

Language: Английский

Citations

0
Recent progress in single-cell transcriptomic studies in plants DOI Creative Commons
Yuhan Cho, Ulhas Sopanrao Kadam,

Bogun Park

et al.

Plant Biotechnology Reports, Journal Year: 2025, Volume and Issue: unknown

Published: April 3, 2025

Language: Английский

Citations

0
Single-cell proteomics of Arabidopsis leaf mesophyll identifies drought stress-related proteins DOI
James Fulcher, Pranav Dawar,

Vimal Kumar Balasubramanian

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: July 3, 2024

Abstract The application of single-cell omics tools to biological systems can provide unique insights into diverse cellular populations and their heterogeneous responses internal external perturbations. Thus far, most studies in plant have been limited RNA-sequencing approaches, which only indirect readouts functions. Here, we present a proteomics workflow for cells that integrates tape-sandwich protoplasting, piezoelectric cell sorting, nanoPOTS sample preparation, FAIMS-based MS data acquisition method label-free analysis Arabidopsis leaf mesophyll cells. From single protoplast, over 3,000 proteins were quantified with high precision. is demonstrated identify stress associated changes protein abundance by analyzing >80 protoplasts from well-watered water-deficit stressed plants. Additionally, describe new approach constructing covarying networks at the level demonstrate how covariation reveal previously unrecognized functions while also capturing stress-induced protein-protein dynamics. Highlights This study describes first scProteomics abiotic proteome regulation ∼2800 on average precision using label free leaves revealed known novel involved drought response Single-protoplast water deficit-induced independent

Language: Английский

Citations

3
Surviving a Double-Edged Sword: Response of Horticultural Crops to Multiple Abiotic Stressors DOI Open Access
Wenjing Yan, Rahat Sharif, Hamza Sohail

et al.

International Journal of Molecular Sciences, Journal Year: 2024, Volume and Issue: 25(10), P. 5199 - 5199

Published: May 10, 2024

Climate change-induced weather events, such as extreme temperatures, prolonged drought spells, or flooding, pose an enormous risk to crop productivity. Studies on the implications of multiple stresses may vary from those a single stress. Usually, these coincide, amplifying extent collateral damage and contributing significant financial losses. The breadth investigations focusing response horticultural crops abiotic stress is immense. However, tolerance mechanisms remain poorly understood. In this review, we described most prevalent types that occur simultaneously discussed them in in-depth detail regarding physiological molecular responses crops. particular, transcriptional, posttranscriptional, metabolic stresses. Strategies breed multi-stress-resilient lines have been presented. Our manuscript presents interesting amount proposed knowledge could be valuable generating resilient genotypes for stressors.

Language: Английский

Citations

2
Breaking barriers: improving time and space resolution of arbuscular mycorrhizal symbiosis with single-cell sequencing approaches DOI Creative Commons

Sofía Cristina Somoza,

Paola Bonfante, Marco Antonio Giovannetti

et al.

Biology Direct, Journal Year: 2024, Volume and Issue: 19(1)

Published: Aug. 17, 2024

The cell and molecular bases of arbuscular mycorrhizal (AM) symbiosis, a crucial plant-fungal interaction for nutrient acquisition, have been extensively investigated by coupling traditional RNA sequencing techniques roots sampled in bulk, with methods to capture subsets cells such as laser microdissection. These approaches revealed central regulators this complex relationship, yet the requisite level detail effectively untangle intricacies temporal spatial development remains elusive.The recent adoption single-cell (scRNA-seq) plant research is revolutionizing our ability dissect intricate transcriptional profiles plant-microbe interactions, offering unparalleled insights into diversity dynamics individual during symbiosis. isolation particularly challenging due presence walls, leading researchers widely adopt nuclei methods. Despite increased resolution that analyses offer, it also comes at cost perspective, hence, necessary integration these transcriptomics obtain comprehensive overview.To date, few studies on interactions published, most which provide high-resolution atlases will become fully deciphering symbiotic addressing future questions. In AM symbiosis research, key processes mutual recognition partners arbuscule within cortical cells, or senescence degeneration, remain poorly understood, advancements are expected shed light contribute deeper understanding interaction.

Language: Английский

Citations

1
Methods in plant science DOI
Martin Janda

Journal of Experimental Botany, Journal Year: 2024, Volume and Issue: 75(17), P. 5163 - 5168

Published: Sept. 11, 2024

Language: Английский

Citations

1
Plant regeneration: REF1 calls the fouls DOI
Kenneth D. Birnbaum

Current Biology, Journal Year: 2024, Volume and Issue: 34(16), P. R788 - R790

Published: Aug. 1, 2024

Language: Английский

Citations

0
Dual and spatially resolved drought responses in the Arabidopsis leaf mesophyll revealed by single-cell transcriptomics DOI Creative Commons
Rubén Tenorio Berrío, Eline Verhelst, Thomas Eekhout

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Aug. 30, 2024

ABSTRACT Drought stress imposes severe challenges on agriculture by impacting crop performance. Understanding drought responses in plants at a cellular level is crucial first step towards engineering improved resilience. However, the molecular to are complex as they depend multiple factors including severity of drought, profiled organ, its developmental stage or even cell types therein. Thus, deciphering transcriptional specially challenging. Here, we investigated tissue-specific mild young Arabidopsis thaliana (Arabidopsis) leaves using single-cell RNA sequencing (scRNA-seq). To preserve integrity during isolation, inhibited synthesis transcription inhibitor actinomycin D, demonstrating benefits transcriptome fixation for studying level. We present curated and validated atlas comprising 50,797 high-quality cells from almost all known leaf. show that mesophyll contains two spatially separated populations with distinct drought: one enriched canonical abscisic acid-related drought-responsive genes, another depicting iron starvation responses. Our study thus reveals dual adaptive mechanism leaf response provides valuable resource future research

Language: Английский

Citations

0
Gene regulatory networks in abiotic stress responses via single-cell sequencing and spatial technologies: Advances and opportunities DOI
Mukesh Jain

Current Opinion in Plant Biology, Journal Year: 2024, Volume and Issue: 82, P. 102662 - 102662

Published: Nov. 13, 2024

Language: Английский

Citations

0