Spatiotemporal transcriptomic atlas of rhizome formation in Oryza longistaminata

Spatio-Temporal Regulation of Gibberellin Biosynthesis Contributes to Optimal Rhizome Bud Development

The perennial life cycle involves the reiterative development of sexual and asexual organs. Asexual structures such as rhizomes are found in various plant species, fostering extensive growth and competitive advantages. In the African wild rice Oryza longistaminata, we investigated the formation of rhizomes from axillary buds, which notably bend diagonally downward of the main stem, as the factors determining whether axillary buds become rhizomes or tillers are unclear. Our study revealed that rhizome buds initiate between the third and fifth nodes of seedlings beyond the 6-leaf stage, while the buds above the sixth node develop into tillers. We propose that precise regulation of gibberellin (GA) biosynthesis plays a pivotal role in optimal rhizome bud development, as demonstrated by a comparative transcriptome analysis between tiller buds and rhizome buds and quantification of phytohormones. Furthermore, GA4 treatment upregulated the expression of genes associated with flowering repression and cell wall modification. These findings highlight the integration of GA biosynthesis and flowering repression genes as crucial in asexual organ development, shedding new light on the molecular mechanisms governing rhizome bud development in O. longistaminata and deepening our understanding of asexual reproduction regulation in perennial plants.

Spatial omics for accelerating plant research and crop improvement

Plant cells communicate information to regulate developmental processes and respond to environmental stresses. This communication spans various 'omics' layers within a cell and operates through intricate regulatory networks. The emergence of spatial omics presents a promising approach to thoroughly analyze cells, allowing the combined analysis of diverse modalities either in parallel or on the same tissue section. Here, we provide an overview of recent advancements in spatial omics and delineate scientific discoveries in plant research enabled by these technologies. We delve into experimental and computational challenges and outline strategies to navigate these challenges for advancing breeding efforts. With ongoing insightful discoveries and improved accessibility, spatial omics stands on the brink of playing a crucial role in designing future crops.

A single-cell and spatial wheat root atlas with cross-species annotations delineates conserved tissue-specific marker genes and regulators

Despite the broad use of single-cell/nucleus RNA sequencing in plant research, accurate cluster annotation in less-studied plant species remains a major challenge due to the lack of validated marker genes. Here, we generated a single-cell RNA sequencing atlas of soil-grown wheat roots and annotated cluster identities by transferring annotations from publicly available datasets in wheat, rice, maize, and Arabidopsis. The predictions from our orthology-based annotation approach were next validated using untargeted spatial transcriptomics. These results allowed us to predict evolutionarily conserved tissue-specific markers and generate cell type-specific gene regulatory networks for root tissues of wheat and the other species used in our analysis. In summary, we generated a single-cell and spatial transcriptomics resource for wheat root apical meristems, including numerous known and uncharacterized cell type-specific marker genes and developmental regulators. These data and analyses will facilitate future cell type annotation in non-model plant species.

The molecular coordination of tuberization: Current status and future directions

The integration of bulk transcriptomic, proteomic, and genomic data generated from numerous systems biology studies of tuberizing plants has resulted in a better understanding of the molecular and morphological aspects of tuberization. The identified conserved integrated hormonal, transcriptional, and metabolic pathways of tuberization in crops from various plant lineages support the hypothesis of a fundamental tuberization process. However, further studies are required to specify the additional processes defined by the genomics and phylogeny of the particular plant lineages, which control the morphological diversity of tubers. This review summarizes the latest molecular and morphological discoveries on the tuberization process in stem tubers and tuberous roots and discusses future trajectories of the field.