RSL Class II Transcription Factors Guide the Nuclear Localization of RHL1 to Regulate Root Hair Development

Physiology, genomics, and evolutionary aspects of desert plants

BACKGROUND

Despite the exposure to arid environmental conditions across the globe ultimately hampering the sustainability of the living organism, few plant species are equipped with several unique genotypic, biochemical, and physiological features to counter such harsh conditions. Physiologically, they have evolved with reduced leaf size, spines, waxy cuticles, thick leaves, succulent hydrenchyma, sclerophyll, chloroembryo, and photosynthesis in nonfoliar and other parts. At the biochemical level, they are evolved to perform efficient photosynthesis through Crassulacean acid metabolism (CAM) and C4 pathways with the formation of oxaloacetic acid (Hatch-Slack pathway) instead of the C3 pathway. Additionally, comparative genomics with existing data provides ample evidence of the xerophytic plants' positive selection to adapt to the arid environment. However, adding more high-throughput sequencing of xerophyte plant species is further required for a comparative genomic study toward trait discovery related to survival. Learning from the mechanism to survive in harsh conditions could pave the way to engineer crops for future sustainable agriculture.

AIM OF THE REVIEW

The distinct physiology of desert plants allows them to survive in harsh environments. However, the genomic composition also contributes significantly to this and requires great attention. This review emphasizes the physiological and genomic adaptation of desert plants. Other important parameters, such as desert biodiversity and photosynthetic strategy, are also discussed with recent progress in the field. Overall, this review discusses the different features of desert plants, which prepares them for harsh conditions intending to translate knowledge to engineer plant species for sustainable agriculture.

KEY SCIENTIFIC CONCEPTS OF REVIEW

This review comprehensively presents the physiology, molecular mechanism, and genomics of desert plants aimed towards engineering a sustainable crop.

PRX102 Participates in Root Hairs Tip Growth of Rice

Root hairs are extensions of epidermal cells on the root tips that increase the root contract surface area with the soil. For polar tip growth, newly synthesized proteins and other materials must be incorporated into the tips of root hairs. Here, we report the characterization of PRX102, a root hair preferential endoplasmic reticulum peroxidase. During root hair growth, PRX102 has a polar localization pattern within the tip regions of root hairs but it loses this polarity after growth termination. Moreover, PRX102 participates in root hair outgrowth by regulating dense cytoplasmic streaming toward the tip. This role is distinct from those of other peroxidases playing roles in the root hairs and regulating reactive oxygen species homeostasis. RNA-seq analysis using prx102 root hairs revealed that 87 genes including glutathione S-transferase were downregulated. Our results therefore suggest a new function of peroxidase as a player in the delivery of substances to the tips of growing root hairs.

Low phosphorus promotes NSP1-NSP2 heterodimerization to enhance strigolactone biosynthesis and regulate shoot and root architecture in rice

Phosphorus is an essential macronutrient for plant development and metabolism, and plants have evolved ingenious mechanisms to overcome phosphate (Pi) starvation. However, the molecular mechanisms underlying the regulation of shoot and root architecture by low phosphorus conditions and the coordinated utilization of Pi and nitrogen remain largely unclear. Here, we show that Nodulation Signaling Pathway 1 (NSP1) and NSP2 regulate rice tiller number by promoting the biosynthesis of strigolactones (SLs), a class of phytohormones with fundamental effects on plant architecture and environmental responses. We found that NSP1 and NSP2 are induced by Oryza sativa PHOSPHATE STARVATION RESPONSE2 (OsPHR2) in response to low-Pi stress and form a complex to directly bind the promoters of SL biosynthesis genes, thus markedly increasing SL biosynthesis in rice. Interestingly, the NSP1/2-SL signaling module represses the expression of CROWN ROOTLESS 1 (CRL1), a newly identified early SL-responsive gene in roots, to restrain lateral root density under Pi deficiency. We also demonstrated that GR244DO treatment under normal conditions inhibits the expression of OsNRTs and OsAMTs to suppress nitrogen absorption but enhances the expression of OsPTs to promote Pi absorption, thus facilitating the balance between nitrogen and phosphorus uptake in rice. Importantly, we found that NSP1p:NSP1 and NSP2p:NSP2 transgenic plants show improved agronomic traits and grain yield under low- and medium-phosphorus conditions. Taken together, these results revealed a novel regulatory mechanism of SL biosynthesis and signaling in response to Pi starvation, providing genetic resources for improving plant architecture and nutrient-use efficiency in low-Pi environments.

Arabidopsis ABRE-binding factors modulate salinity-induced inhibition of root hair growth by interacting with and suppressing RHD6

Soil salinity causes crop losses worldwide. Root hairs are the primary targets of salt stress, however, the signaling networks involved in the precise regulation of root hair growth and development by salinity are poorly understood. Here, we confirmed that salt stress inhibits the number and length of root hairs in Arabidopsis. We found that the master regulator of root hair development and growth, the RHD6 transcription factor, is involved in this process, as salt treatment largely compromised root hair overaccumulation in RHD6-overexpressing plants. Yeast-two-hybrid and co-immunoprecipitation analyses revealed that RHD6 physically interacts with ABF proteins, the master transcription factors in abscisic acid signaling, which is involved in tolerance to several stresses including salinity. Phenotypic analyses showed that ABF proteins, which function upstream of RHD6, positively modulate the salinity-induced inhibition of root hair development. Further analyses showed that ABF3 suppresses the transcriptional activation activity of RHD6, thereby regulating the expression of genes related to root hair development. Overexpression of ABF3 reduced the root hair-overgrowing phenotype of RHD6-overexpressing plants. Collectively, our results demonstrate an essential signaling module in which ABF proteins directly suppress the transcriptional activation activity of RHD6 to reduce the length and number of root hairs under salt stress conditions.

OsUGE1 is directly targeted by OsGRF6 to regulate root hair length in rice

KEY MESSAGE

Root hairs are required for water and nutrient acquisition in plants. Here, we report a novel mechanism that OsUGE1 is negatively controlled by OsGRF6 to regulate root hair elongation in rice. Root hairs are tubular outgrowths generated by the root epidermal cells. They effectively enlarge the soil-root contact area and play essential roles for nutrient and water absorption. Here, in this study, we demonstrated that the Oryza sativa UDP-glucose 4-epimerase 1-like (OsUGE1) negatively regulated root hair elongation and was directly targeted by Oryza sativa growth regulating factor 6 (OsGRF6). Knockout mutants of OsUGE1 using CRISPR-Cas9 technology showed longer root hairs than those of wild type. In contrast, overexpression lines of OsUGE1 displayed shorter root hair compared with those of wild type. GUS staining showed that it could specifically express in root hair. Subcellular localization analysis indicates that OsUGE1 is located in endoplasmic reticulum, nucleus and plasma membrane. More importantly, ChIP-qPCR, Yeast-one-hybrid and BiFC experiments revealed that OsGRF6 could bind to the promoter of OsUGE1. Furthermore, knockout mutants of OsGRF6 showed shorter root hair than those of wild type, and OsGRF6 dominantly expressed in root. In addition, the expression level of OsUGE1 is significantly downregulated in Osgrf6 mutant. Taken together, our study reveals a novel pathway that OsUGE1 is negatively controlled by OsGRF6 to regulate root hair elongation in rice.

A fungus (Trametes pubescens) resists cadmium toxicity by rewiring nitrogen metabolism and enhancing energy metabolism

As a primary goal, cadmium (Cd) is a heavy metal pollutant that is readily adsorbed and retained in rice, and it becomes a serious threat to food safety and human health. Fungi have attracted interest for their ability to remove heavy metals from the environment, although the underlying mechanisms of how fungi defend against Cd toxicity are still unclear. In this study, a Cd-resistant fungus Trametes pubescens (T. pubescens) was investigated. Pot experiments of rice seedlings colonized with T. pubescens showed that their coculture could significantly enhance rice seedling growth and reduce Cd accumulation in rice tissues. Furthermore, integrated transcriptomic and metabolomic analyses were used to explore how T. pubescens would reprogram its metabolic network against reactive oxygen species (ROS) caused by Cd toxicity. Based on multi-omic data mining results, we postulated that under Cd stress, T. pubescens was able to upregulate both the mitogen-activated protein kinase (MAPK) and phosphatidylinositol signaling pathways, which enhanced the nitrogen flow from amino acids metabolism through glutaminolysis to α-ketoglutarate (α-KG), one of the entering points of tricarboxylic acid (TCA) cycle within mitochondria; it thus increased the production of energy equivalents, adenosine triphosphate (ATP) and reduced nicotinamide adenine dinucleotide phosphate (NADPH) for T. pubescens to resist oxidative damage. This study can enable a better understanding of the metabolic rewiring of T. pubescens under Cd stress, and it can also provide a promising potential to prevent the rice paddy fields from Cd toxicity and enhance food safety.

Nanoscale Iron trioxide catalyzes the synthesis of auxins analogs in artificial humic acids to enhance rice growth

Humic acids (HAs), kinds of valuable active carbon, are critical for improving soil fertility. However, the majority of soils are poor in HAs, arousing the development of artificial HAs. In this study, two iron-based catalysts (nanoscale iron trioxide (nFe₂O₃) and FeCl₃) were used to catalyze the hydrothermal humification of waste corn straw. With the help of ultra-performance liquid chromatography-mass spectrometry, we proposed the specific humification process with the action of catalysis for the first time, which is of great significance for the design, synthesis and application of artificial HAs in the future. Moreover, the growth-promoting effect and mechanisms of the artificial HAs were determined by rice planting in a greenhouse. Results showed that compared to no catalyst treatment, the FeCl₃ and nFe₂O₃ catalysts increased the decomposition rate of macromolecular biomass by 39 and 14 %, respectively, increasing the yield of artificial HAs. During the humification process, nFe₂O₃ catalysts benefit the formation of many aromatic structure monomers including furfural and hydroxycaproic acids. These monomers were condensed into growth hormone analogs such as vanillin and methionine sulfoxide and were further built in the artificial HAs. Therefore, the artificial HAs from nFe₂O₃ catalytic treatment promoted the rice growth the best, showing that the resultant germination rate, root activity, and photosynthetic rate of rice increased by 50, 167, and 72 %, respectively; moreover, the uptake and accumulation of water and nutrient by roots as well as the contents of soluble protein and sugar of rice are also significantly increased. This could be ascribed to the upregulated expression of functional genes including OsRHL1, OsZPT5-07, OsSHR2 and OsDCL. Considering both the economic and environmental benefits, we suggested that the artificial HAs, especially that produced with the action of nFe₂O₃ catalysis, are promising in alleviating environmental stress from waste biomass and sustainably improving agricultural production.

The absorption of water from humid air by grass embryos during germination

Grass embryos possess structures that do not occur in any other flowering plants. Due to the specific embryo structure and position, grass embryo surfaces may be exposed to surrounding air under partial caryopsis-soil contact conditions, but whether caryopses of the grass family (Poaceae) can sense soil air humidity to initiate successful germination under partial caryopsis-soil contact conditions remain unknown. Here, we found that grass embryos have the unique ability to absorb water from atmospheric water vapor under partial caryopsis-soil contact conditions. To absorb atmospheric moisture, grass embryos developed profuse and highly elongated hairs on the embryo surface. These hairs, classically known as coleorhiza hairs, developed only on the embryo surface exposed to humid air, and submergence of the embryo surface inhibited their development. In addition to humid air-dependent development, almost all other developmental features of coleorhiza hairs were substantially different from root hairs. However, coleorhiza hair development was regulated by ROOTHAIRLESS 1. Besides the genetic control of coleorhiza hair development, we also identified how caryopses manage to keep the hairs turgid in natural open environments as the hairs were highly sensitive to dry air exposure. Moreover, we video-documented the regulation of developmental processes. The unique humid air-dependent coleorhiza hair development and their ability to absorb water from water vapor present in microsites or soil air give grasses advantages in germination and seedling establishment. Ultimately, coleorhiza hairs may have contributed to the ecological success of the grass family.

Tissue-specific enhancement of OsRNS1 with root-preferred expression is required for the increase of crop yield

INTRODUCTION

Root development is a fundamental process that supports plant survival and crop productivity. One of the essential factors to consider when developing biotechnology crops is the selection of a promoter that can optimize the spatial-temporal expression of introduced genes. However, there are insufficient cases of suitable promoters in crop plants, including rice.

OBJECTIVES

This study aimed to verify the usefulness of a new rice root-preferred promoter to optimize the function of a target gene with root-preferred expression in rice.

METHODS

osrns1 mutant had defects in root development based on T-DNA insertional mutant screening and CRISPR technology. To optimize the function of OsRNS1, we generated OsRNS1-overexpression plants under two different promoters: a whole-plant expression promoter and a novel root-preferred expression promoter. Root growth, yield-related agronomic traits, RNA-seq, and reactive oxygen species (ROS) accumulation were analyzed for comparison.

RESULTS

OsRNS1 was found to be involved in root development through T-DNA insertional mutant analysis and gene editing mutant analysis. To understand the gain of function of OsRNS1, pUbi1::OsRNS1 was generated for the whole-plant expression, and both root growth defects and overall growth defects were found. To overcome this problem, a root-preferential overexpression line using Os1-CysPrxB promoter (Per) was generated and showed an increase in root length, plant height, and grain yield compared to wild-type (WT). RNA-seq analysis revealed that the response to oxidative stress-related genes was significantly up-regulated in both overexpression lines but was more obvious in pPer::OsRNS1. Furthermore, ROS levels in the roots were drastically decreased in pPer::OsRNS1 but were increased in the osrns1 mutants compared to WT.

CONCLUSION

The results demonstrated that the use of a root-preferred promoter effectively optimizes the function of OsRNS1 and is a useful strategy for improving root-related agronomic traits as well as ROS regulation.

Significance of root hairs in developing stress-resilient plants for sustainable crop production

Root hairs represent a beneficial agronomic trait to potentially reduce fertilizer and irrigation inputs. Over the past decades, research in the plant model Arabidopsis thaliana has provided insights into root hair development, the underlying genetic framework and the integration of environmental cues within this framework. Recent years have seen a paradigm shift, where studies are now highlighting conservation and diversification of root hair developmental programs in other plant species and the agronomic relevance of root hairs in a wider ecological context. In this review, we specifically discuss the molecular evolution of the RSL (RHD Six-Like) pathway that controls root hair development and growth in land plants. We also discuss how root hairs contribute to plant performance as an active physiological rooting structure by performing resource acquisition, providing anchorage and constructing the rhizosphere with desirable physical, chemical and biological properties. Finally, we outline future research directions that can help achieve the potential of root hairs in developing sustainable agroecosystems.

Genome-wide association study reveals the genetic architecture of root hair length in maize

Background

Root hair, a special type of tubular-shaped cell, outgrows from root epidermal cell and plays important roles in the acquisition of nutrients and water, as well as interactions with biotic and abiotic stress. Although many genes involved in root hair development have been identified, genetic basis of natural variation in root hair growth has never been explored.

Results

Here, we utilized a maize association panel including 281 inbred lines with tropical, subtropical, and temperate origins to decipher the phenotypic diversity and genetic basis of root hair length. We demonstrated significant associations of root hair length with many metabolic pathways and other agronomic traits. Combining root hair phenotypes with 1.25 million single nucleotide polymorphisms (SNPs) via genome-wide association study (GWAS) revealed several candidate genes implicated in cellular signaling, polar growth, disease resistance and various metabolic pathways.

Conclusions

These results illustrate the genetic basis of root hair length in maize, offering a list of candidate genes predictably contributing to root hair growth, which are invaluable resource for the future functional investigation.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07961-z.

Recognizing the hidden half in wheat: root system attributes associated with drought tolerance

Improving drought tolerance in wheat is crucial for maintaining productivity and food security. Roots are responsible for the uptake of water from soil, and a number of root traits are associated with drought tolerance. Studies have revealed many quantitative trait loci and genes controlling root development in plants. However, the genetic dissection of root traits in response to drought in wheat is still unclear. Here, we review crop root traits associated with drought, key genes governing root development in plants, and quantitative trait loci and genes regulating root system architecture under water-limited conditions in wheat. Deep roots, optimal root length density and xylem diameter, and increased root surface area are traits contributing to drought tolerance. In view of the diverse environments in which wheat is grown, the balance among root and shoot traits, as well as individual and population performance, are discussed. The known functions of key genes provide information for the genetic dissection of root development of wheat in a wide range of conditions, and will be beneficial for molecular marker development, marker-assisted selection, and genetic improvement in breeding for drought tolerance.

Interaction of OsRopGEF3 Protein With OsRac3 to Regulate Root Hair Elongation and Reactive Oxygen Species Formation in Rice (Oryza sativa)

Root hairs are tip-growing cells that emerge from the root epidermis and play a role in water and nutrient uptake. One of the key signaling steps for polar cell elongation is the formation of Rho-GTP by accelerating the intrinsic exchange activity of the Rho-of-plant (ROP) or the Rac GTPase protein; this step is activated through the interaction with the plant Rho guanine nucleotide exchange factor (RopGEFs). The molecular players involved in root hair growth in rice are largely unknown. Here, we performed the functional analysis of OsRopGEF3, which is highly expressed in the root hair tissues among the OsRopGEF family genes in rice. To reveal the role of OsRopGEF3, we analyzed the phenotype of loss-of-function mutants of OsRopGEF3, which were generated using the CRISPR-Cas9 system. The mutants had reduced root hair length and increased root hair width. In addition, we confirmed that reactive oxygen species (ROS) were highly reduced in the root hairs of the osropgef3 mutant. The pairwise yeast two-hybrid experiments between OsRopGEF3 and OsROP/Rac proteins in rice revealed that the OsRopGEF3 protein interacts with OsRac3. This interaction and colocalization at the same subcellular organelles were again verified in tobacco leaf cells and rice root protoplasts via bimolecular functional complementation (BiFC) assay. Furthermore, among the three respiratory burst oxidase homolog (OsRBOH) genes that are highly expressed in rice root hair cells, we found that OsRBOH5 can interact with OsRac3. Our results demonstrate an interaction network model wherein OsRopGEF3 converts the GDP of OsRac3 into GTP, and OsRac3-GTP then interacts with the N-terminal of OsRBOH5 to produce ROS, thereby suggesting OsRopGEF3 as a key regulating factor in rice root hair growth.

CAFRI-Rice: CRISPR applicable functional redundancy inspector to accelerate functional genomics in rice

Rice (Oryza sativa L.) is a staple crop with agricultural traits that have been intensively investigated. However, despite the variety of mutant population and multi-omics data that have been generated, rice functional genomic research has been bottlenecked due to the functional redundancy in the genome. This phenomenon has masked the phenotypes of knockout mutants by functional compensation and redundancy. Here, we present an intuitive tool, CRISPR applicable functional redundancy inspector to accelerate functional genomics in rice (CAFRI-Rice; cafri-rice.khu.ac.kr). To create this tool, we generated a phylogenetic heatmap that can estimate the similarity between protein sequences and expression patterns, based on 2,617 phylogenetic trees and eight tissue RNA-sequencing datasets. In this study, 33,483 genes were sorted into 2,617 families, and about 24,980 genes were tested for functional redundancy using a phylogenetic heatmap approach. It was predicted that 7,075 genes would have functional redundancy, according to the threshold value validated by an analysis of 111 known genes functionally characterized using knockout mutants and 5,170 duplicated genes. In addition, our analysis demonstrated that an anther/pollen-preferred gene cluster has more functional redundancy than other clusters. Finally, we showed the usefulness of the CAFRI-Rice-based approach by overcoming the functional redundancy between two root-preferred genes via loss-of-function analyses as well as confirming the functional dominancy of three genes through a literature search. This CAFRI-Rice-based target selection for CRISPR/Cas9-mediated mutagenesis will not only accelerate functional genomic studies in rice but can also be straightforwardly expanded to other plant species.

Arabidopsis JAZ Proteins Interact with and Suppress RHD6 Transcription Factor to Regulate Jasmonate-Stimulated Root Hair Development

Root hairs arise from trichoblasts and are crucial for plant anchorage, nutrient acquisition, and environmental interactions. The phytohormone jasmonate is known to regulate root hair development in Arabidopsis (Arabidopsis thaliana), but little is known about the molecular mechanism underlying jasmonate modulation in this process. Here, we show that the application of exogenous jasmonate significantly stimulated root hair elongation, but, on the contrary, blocking the perception or signaling of jasmonate resulted in defective root hairs. Jasmonate consistently elevated the expression levels of several crucial genes positively involved in root hair growth. Mechanistic investigation revealed that JASMONATE ZIM-DOMAIN (JAZ) proteins, critical repressors of jasmonate signaling, physically interacted with ROOT HAIR DEFECTIVE 6 (RHD6) and RHD6 LIKE1 (RSL1), two transcription factors that are essential for root hair development. JAZ proteins inhibited the transcriptional function of RHD6 and interfered with the interaction of RHD6 with RSL1. Genetic analysis indicated that jasmonate promoted root hair growth in a RHD6/RSL1-dependent manner. Moreover, overexpression of RHD6 largely rescued the root hair defects of JAZ-accumulating plants. Collectively, our study reveals a key signaling module in which JAZ repressors of the jasmonate pathway directly modulate RHD6 and RSL1 transcription factors to integrate jasmonate signaling and the root hair developmental process.

Overexpression of OsPIN2 Regulates Root Growth and Formation in Response to Phosphate Deficiency in Rice

The response of root architecture to phosphate (P) deficiency is critical in plant growth and development. Auxin is a key regulator of plant root growth in response to P deficiency, but the underlying mechanisms are unclear. In this study, phenotypic and genetic analyses were undertaken to explore the role of OsPIN2, an auxin efflux transporter, in regulating the growth and development of rice roots under normal nutrition condition (control) and low-phosphate condition (LP). Higher expression of OsPIN2 was observed in rice plants under LP compared to the control. Meanwhile, the auxin levels of roots were increased under LP relative to control condition in wild-type (WT) plants. Compared to WT plants, two overexpression (OE) lines had higher auxin levels in the roots under control and LP. LP led to increased seminal roots (SRs) length and the root hairs (RHs) density, but decreased lateral roots (LRs) density in WT plants. However, overexpression of OsPIN2 caused a loss of sensitivity in the root response to P deficiency. The OE lines had a shorter SR length, lower LR density, and greater RH density than WT plants under control. However, the LR and RH densities in the OE lines were similar to those in WT plants under LP. Compared to WT plants, overexpression of OsPIN2 had a shorter root length through decreased root cell elongation under control and LP. Surprisingly, overexpression of OsPIN2 might increase auxin distribution in epidermis of root, resulting in greater RH formation but less LR development in OE plants than in WT plants in the control condition but levels similar of these under LP. These results suggest that higher OsPIN2 expression regulates rice root growth and development maybe by changing auxin distribution in roots under LP condition.