Root Patterning: Tuning SHORT ROOT Function Creates Diversity in Form

Transcriptional control of hydrogen peroxide homeostasis regulates ground tissue patterning in the Arabidopsis root

In multicellular organisms, including higher plants, asymmetric cell divisions (ACDs) play a crucial role in generating distinct cell types. The Arabidopsis root ground tissue initially has two layers: endodermis (inside) and cortex (outside). In the mature root, the endodermis undergoes additional ACDs to produce the endodermis itself and the middle cortex (MC), located between the endodermis and the pre-existing cortex. In the Arabidopsis root, gibberellic acid (GA) deficiency and hydrogen peroxide (H2O2) precociously induced more frequent ACDs in the endodermis for MC formation. Thus, these findings suggest that GA and H2O2 play roles in regulating the timing and extent of MC formation. However, details of the molecular interaction between GA signaling and H2O2 homeostasis remain elusive. In this study, we identified the PEROXIDASE 34 (PRX34) gene, which encodes a class III peroxidase, as a molecular link to elucidate the interconnected regulatory network involved in H2O2- and GA-mediated MC formation. Under normal conditions, prx34 showed a reduced frequency of MC formation, whereas the occurrence of MC in prx34 was restored to nearly WT levels in the presence of H2O2. Our results suggest that PRX34 plays a role in H2O2-mediated MC production. Furthermore, we provide evidence that SCARECROW-LIKE 3 (SCL3) regulates H2O2 homeostasis by controlling transcription of PRX34 during root ground tissue maturation. Taken together, our findings provide new insights into how H2O2 homeostasis is achieved by SCL3 to ensure correct radial tissue patterning in the Arabidopsis root.

Asymmetric gene expression and cell-type-specific regulatory networks in the root of bread wheat revealed by single-cell multiomics analysis

BACKGROUND

Homoeologs are defined as homologous genes resulting from allopolyploidy. Bread wheat, Triticum aestivum, is an allohexaploid species with many homoeologs. Homoeolog expression bias, referring to the relative contribution of homoeologs to the transcriptome, is critical for determining the traits that influence wheat growth and development. Asymmetric transcription of homoeologs has been so far investigated in a tissue or organ-specific manner, which could be misleading due to a mixture of cell types.

RESULTS

Here, we perform single nuclei RNA sequencing and ATAC sequencing of wheat root to study the asymmetric gene transcription, reconstruct cell differentiation trajectories and cell-type-specific gene regulatory networks. We identify 22 cell types. We then reconstruct cell differentiation trajectories that suggest different origins between epidermis/cortex and endodermis, distinguishing bread wheat from Arabidopsis. We show that the ratio of asymmetrically transcribed triads varies greatly when analyzing at the single-cell level. Hub transcription factors determining cell type identity are also identified. In particular, we demonstrate that TaSPL14 participates in vasculature development by regulating the expression of BAM1. Combining single-cell transcription and chromatin accessibility data, we construct the pseudo-time regulatory network driving root hair differentiation. We find MYB3R4, REF6, HDG1, and GATAs as key regulators in this process.

CONCLUSIONS

Our findings reveal the transcriptional landscape of root organization and asymmetric gene transcription at single-cell resolution in polyploid wheat.

Genome-Wide Investigation and Co-Expression Network Analysis of SBT Family Gene in Gossypium

Subtilases (SBTs), which belong to the serine peptidases, control plant development by regulating cell wall properties and the activity of extracellular signaling molecules, and affect all stages of the life cycle, such as seed development and germination, and responses to biotic and abiotic environments. In this study, 146 Gossypium hirsutum, 138 Gossypium barbadense, 89 Gossypium arboreum and 84 Gossypium raimondii SBTs were identified and divided into six subfamilies. Cotton SBTs are unevenly distributed on chromosomes. Synteny analysis showed that the members of SBT1 and SBT4 were expanded in cotton compared to Arabidopsis thaliana. Co-expression network analysis showed that six Gossypium arboreum SBT gene family members were in a network, among which five SBT1 genes and their Gossypium hirsutum and Arabidopsis thaliana direct homologues were down-regulated by salt treatment, indicating that the co-expression network might share conserved functions. Through co-expression network and annotation analysis, these SBTs may be involved in the biological processes of auxin transport, ABA signal transduction, cell wall repair and root tissue development. In summary, this study provides valuable information for the study of SBT genes in cotton and excavates SBT genes in response to salt stress, which provides ideas for cotton breeding for salinity resistance.

Genome-wide identification of RsGRAS gene family reveals positive role of RsSHRc gene in chilling stress response in radish (Raphanus sativus L.)

Radish (Raphanus sativus L.) is an important worldwide root vegetable crop. Little information of the GRAS gene family was available in radish. Herein, a total of 51 GRAS family members were firstly identified from radish genome, and unevenly located onto nine radish chromosomes. Expression analysis of RsGRAS genes in taproot displayed that RsSCL15a and RsSHRc were highly expressed in the radish cambium, and its expression level was increased with the taproot thickening. Comparative transcriptome analysis revealed that the expression patterns of RsGRAS genes varied upon exposure to different abiotic stresses including heavy metals, salt and heat. The expression level of six RsGRAS genes including RsSHRc was increased under chilling stress in two radish genotypes with different cold tolerance. Further analysis indicated that RsGRAS genes could respond to cold stress rapidly and the expression of RsSHRc was up-regulated at different development stages (cortex splitting and thickening stages) under long-term cold treatment. Transient expression of RsSHRc gene in radish showed that RsSHRc possessed the reliable function of eliminating reactive oxygen species (ROS), inhibiting the formation of malondialdehyde (MDA) and promoting to accumulate proline under cold stress. Together, these findings provided insights into the function of RsGRAS genes in taproot development and chilling stress response in radish.

(Don't) Look Up!: Is short-root just a short-root plant?

SHORT-ROOT (SHR) is a mobile transcription factor that plays important roles in ground tissue patterning, stem cell niche specification and maintenance, and vascular development in Arabidopsis roots. Although mRNA and protein of SHR are also found in hypocotyls, inflorescence stems, and leaves, its role in the above-ground organs has been less explored. In most developmental cases, SHR, together with its partner SCARECROW (SCR), regulates the expression of downstream target genes in controlling formative and proliferative cell divisions. Accumulating evidence on the regulatory role of SHR in shoots suggests that SHR may also play key roles in the above-ground organs. Interestingly, recent work has provided new evidence that SHR is also required for cell elongation in the hypocotyl of the etiolated seedling. This suggests that the novel roles of SHR and SHR-mediated regulatory networks can be found in shoots. Furthermore, comparative research on SHR function in roots and shoots will broaden and deepen our understanding of plant growth and development.