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

Best practices for the execution, analysis, and data storage of plant single-cell/nucleus transcriptomics DOI Creative Commons

Carolin Grones,

Thomas Eekhout, Dongbo Shi

et al.

The Plant Cell, Journal Year: 2024, Volume and Issue: 36(4), P. 812 - 828

Published: Jan. 17, 2024

Abstract Single-cell and single-nucleus RNA-sequencing technologies capture the expression of plant genes at an unprecedented resolution. Therefore, these are gaining traction in molecular developmental biology for elucidating transcriptional changes across cell types a specific tissue or organ, upon treatments, response to biotic abiotic stresses, between genotypes. Despite rapidly accelerating use technologies, collective standardized experimental analytical procedures support acquisition high-quality data sets still missing. In this commentary, we discuss common challenges associated with single-cell transcriptomics plants propose general guidelines improve reproducibility, quality, comparability, interpretation make readily available community fast-developing field research.

Language: Английский

Citations

25
A Single-Nucleus Atlas of Seed-to-Seed Development in Arabidopsis DOI Creative Commons
Travis Lee, Tatsuya Nobori, Natanella Illouz‐Eliaz

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: March 24, 2023

SUMMARY Extensive studies of the reference plant Arabidopsis have enabled a deep understanding tissues throughout development, yet census cell types and states development is lacking. Here, we present single-nucleus transcriptome atlas seed-to-seed employing over 800,000 nuclei, encompassing diverse set across ten developmental stages, with spatial transcriptomic validation dynamic seed silique. Cross-organ analyses revealed transcriptional conservation heterogeneity within individual influenced by organ-of-origin timing, including groups transcription factors, suggesting gatekeeping factor activation. This provides resource for study type specification continuum stimulus-response genetic perturbations at single-cell resolution.

Language: Английский

Citations

33
The transcriptome landscape of developing barley seeds DOI
Martin Kovačik, Anna Nowicka, Jana Zwyrtková

et al.

The Plant Cell, Journal Year: 2024, Volume and Issue: 36(7), P. 2512 - 2530

Published: April 18, 2024

Abstract Cereal grains are an important source of food and feed. To provide comprehensive spatiotemporal information about biological processes in developing seeds cultivated barley (Hordeum vulgare L. subsp. vulgare), we performed a transcriptomic study the embryo, endosperm, seed maternal tissues collected from 4–32 days after pollination. Weighted gene co-expression network motif enrichment analyses identified specific groups genes transcription factors (TFs) potentially regulating tissue development. We defined set tissue-specific marker families TFs for functional studies pathways controlling grain Assessing selected chromatin regulators revealed that epigenetic highly dynamic likely play major role during endosperm The repressive H3K27me3 modification is globally reduced at related to development storage compounds. Altogether, this atlas uncovers complexity developmentally regulated expression grains.

Language: Английский

Citations

13
Single-cell transcriptomics reveals heterogeneity in plant responses to the environment: a focus on biotic and abiotic interactions DOI
Rubén Tenorio Berrío, Marieke Dubois

Journal of Experimental Botany, Journal Year: 2024, Volume and Issue: 75(17), P. 5188 - 5203

Published: March 11, 2024

Biotic and abiotic environmental cues are major factors influencing plant growth productivity. Interactions with biotic (e.g. symbionts pathogens) changes in temperature, water, or nutrient availability) trigger signaling downstream transcriptome adjustments plants. While bulk RNA-sequencing technologies have traditionally been used to profile these transcriptional changes, tissue homogenization may mask heterogeneity of responses resulting from the cellular complexity organs. Thus, whether different cell types respond equally fluctuations, subsets cell-type specific, long-lasting questions biology. The recent breakthrough single-cell transcriptomics research offers an unprecedented view under changing conditions. In this review, we discuss contribution understanding cell-type-specific interactions. Besides biological findings, present some technical challenges coupled studies plant-environment interactions, proposing possible solutions exciting paths for future research.

Language: Английский

Citations

11
Establishment of single-cell transcriptional states during seed germination DOI Creative Commons
Lim Chee Liew, Yue You, Lucas Auroux

et al.

Nature Plants, Journal Year: 2024, Volume and Issue: 10(9), P. 1418 - 1434

Published: Sept. 10, 2024

Language: Английский

Citations

8
Development and application of transcriptomics technologies in plant science DOI Creative Commons
H.W. Wang, Yueting Xu, Zhizhong Zhang

et al.

Crop Design, Journal Year: 2024, Volume and Issue: 3(2), P. 100057 - 100057

Published: Feb. 24, 2024

Over the past decade, bulk RNA sequencing (RNA-seq) has become an indispensable tool in molecular biology, and have made novel development, with two innovative methodologies being developed, single-cell (scRNA-seq) technology spatial transcriptome (ST) technology. The scRNA-seq allows researchers to analyze gene expression individual cells, providing more detailed information relative technologies. Meanwhile, ST overcomes limitations of terms loss information, enabling scientists better understand distribution within tissues. These advancements transcriptomics technologies revolutionize field genomics been widely used disease diagnosis medicine. However, they are less utilized plant research. This review describes advantage three technologies, presents their applications sciences.

Language: Английский

Citations

6
Applications for single-cell and spatial transcriptomics in plant research DOI Creative Commons
Qing Sang, Fanjiang Kong

New Crops, Journal Year: 2024, Volume and Issue: 1, P. 100025 - 100025

Published: May 12, 2024

Cells of multicellular plants possess inherent heterogeneity. Recent progress in single-cell RNA sequencing (scRNA-seq) allows researchers to classify, characterize, and distinguish individual cells at the transcriptome level, enabling identification rare cell populations with functional importance. However, scRNA-seq obscures spatial information about cells. Spatial transcriptomics approaches have substantially improved our capacity detect distribution transcripts throughout tissues, yet it remains challenging characterize whole-transcriptome-level data for single spatially. In this review, we offer a concise overview experimental computational procedures strategies required integrate transcriptomics. We demonstrate their impact on plant fundamental biology, discuss advantages current challenges, provide an outlook future.

Language: Английский

Citations

4
An overview of single-cell high-throughput technology in plants DOI
Lucas Auroux, Lim Chee Liew, Mathew G. Lewsey

et al.

Elsevier eBooks, Journal Year: 2025, Volume and Issue: unknown, P. 1 - 34

Published: Jan. 1, 2025

Language: Английский

Citations

0
Deciphering seed development and germination in the single-cell era DOI Creative Commons
Paul Schouveiler, Lim Chee Liew, Massimiliano Corso

et al.

Seed Science Research, Journal Year: 2025, Volume and Issue: unknown, P. 1 - 10

Published: March 3, 2025

Abstract Seeds are complex structures that serve as dispersal units in angiosperms. consist of three specialized tissues with distinct roles and molecular compositions. Hence, the characterization genetic regulators act within individual seed tissues, how their activity changes during development germination, has been a primary focus research. However, our knowledge spatiotemporal modulation seeds, across different cell types, limited by resolution available techniques. In last few years, application single-cell technologies plants have enabled elucidation gene networks involved various developmental processes at cellular level. Some studies applied these to enabling further germination Here, we review current status seeds present workflow for conducting transcriptomics. Additionally, discuss integration multi-omics, aiming demonstrate potential enhancing comprehension regulations governing germination.

Language: Английский

Citations

0
Spatial transcriptome and single‐cell RNA sequencing reveal the molecular basis of cotton fiber initiation development DOI
Jun Zhang, Runsheng Chen,

Fan Dai

et al.

The Plant Journal, Journal Year: 2025, Volume and Issue: 121(6)

Published: March 1, 2025

SUMMARY Recent advances in single‐cell transcriptomics have greatly expanded our knowledge of plant development and cellular responses. However, analyzing fiber cell differentiation plants, particularly cotton, remains a complex challenge. A spatial transcriptomic map ovule from −1 DPA, 0 1 DPA cotton was successfully constructed, which helps to explain the important role sucrose synthesis lipid metabolism during early development. Additionally, RNA sequencing (scRNA‐seq) further highlighted heterogeneity identified clusters developmental marker genes. Integration scRNA‐seq data unveiled key genes SVB SVBL involved initiation, suggesting functional redundancy between them. These findings provide detailed molecular landscape development, offering valuable insights for enhancing lint yield.

Language: Английский

Citations

0