Callus is a reprogrammed cell mass involved in plant regeneration and gene transformation in crop engineering. Pluripotent callus cells develop into fertile shoots through shoot regeneration. The molecular basis of the shoot regeneration process in crop callus remains largely elusive. This study pioneers the exploration of the spatial transcriptome of tomato callus during shoot regeneration. The findings reveal the presence of highly heterogeneous cell populations within the callus, including epidermis, vascular tissue, shoot primordia, inner callus, and outgrowth shoots. By characterizing the spatially resolved molecular features of shoot primordia and surrounding cells, specific factors essential for shoot primordia formation are identified. Notably, chlorenchyma cells, enriched in photosynthesis-related processes, play a crucial role in promoting shoot primordia formation and subsequent shoot regeneration. Light is shown to promote shoot regeneration by inducing chlorenchyma cell development and coordinating sugar signaling. These findings significantly advance our understanding of the cellular and molecular aspects of shoot regeneration in tomato callus and demonstrate the immense potential of spatial transcriptomics in plant biology.

Spatial transcriptomics reveals light-induced chlorenchyma cells involved in promoting shoot regeneration in tomato callus.

Our current food production systems are unsustainable, driven in part through the application of chemically fixed nitrogen. We need alternatives to empower farmers to maximise their productivity sustainably. Therefore, we explore the potential for transferring the root nodule symbiosis from legumes to other crops. Studies over the last decades have shown that preexisting developmental and signal transduction processes were recruited during the evolution of legume nodulation. This allows us to utilise these preexisting processes to engineer nitrogen fixation in target crops. Here, we highlight our understanding of legume nodulation and future research directions that might help to overcome the barrier of achieving self-fertilising crops.

/pdf/dancing-to-a-different-tune-can-we-switch-from-chemical-to-3rp6v7ao.pdf

Dancing to a different tune, can we switch from chemical to biological nitrogen fixation for sustainable food security?

The plant community lags far behind the animal and human fields concerning the application of single-cell methodologies. This is primarily due to the challenges associated with plant tissue dissection and the limitations of the available technologies. However, recent advances in spatial transcriptomics enable the study of single-cells derived from plant tissues from a spatial perspective. This technology is already successfully used to identify cell types, reconstruct cell-fate lineages, and reveal cell-to-cell interactions. Future technological advancements will overcome the challenges in sample processing, data analysis, and the integration of multiple-omics technologies. Thanks to spatial transcriptomics, we anticipate several plant research projects to significantly advance our understanding of critical aspects of plant biology. 

Spatial transcriptomics drives a new era in plant research.

Plants are in contact with diverse pathogens and microorganisms. Intense investigation over the last 30 years has resulted in the identification of multiple immune receptors in model and crop species as well as signaling overlap in surface-localized and intracellular immune receptors. However, scientists still have a limited understanding of how plants respond to diverse pathogens with spatial and cellular resolution. Recent advancements in single-cell, single-nucleus and spatial technologies can now be applied to plant-pathogen interactions. Here, we outline the current state of these technologies and highlight outstanding biological questions that can be addressed in the future. 

Understanding plant pathogen interactions using spatial and single-cell technologies

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

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

Legumes form symbiosis with rhizobium leading to the development of nitrogen-fixing nodules. By integrating single-nucleus and spatial transcriptomics, we established a cell atlas of soybean nodules and roots. In central infected zones of nodules, we found that uninfected cells specialize into functionally distinct subgroups during nodule development, and revealed a transitional subtype of infected cells with enriched nodulation-related genes. Overall, our results provide a single-cell perspective for understanding rhizobium-legume symbiosis. 

https://www.researchsquare.com/article/rs-1772944/latest.pdf

Integrated single-nucleus and spatial transcriptomics captures transitional states in soybean nodule maturation

Legumes form symbiosis with rhizobium leading to the development of nitrogen-fixing nodules. By integrating single-nucleus and spatial transcriptomics, we established a cell atlas of soybean nodules and roots. In central infected zone of nodule, we found that uninfected cells specialize into functionally distinct sub-groups during nodule development and revealed a transitional subtype of infected cells with enriched nodulation-related genes. Overall, our results provide a single-cell perspective for understanding rhizobium-legume symbiosis.

Integrated single-nucleus and spatial transcriptomics captures transitional states in soybean nodule symbiosis establishment

DCL2-dependent regulation of sRNA biogenesis and translocation in soybean

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Integrated single-nucleus and spatial transcriptomics captures transitional states in soybean nodule maturation

Integrated single-nucleus and spatial transcriptomics captures transitional states in soybean nodule symbiosis establishment

DCL2-dependent regulation of sRNA biogenesis and translocation in soybean