Search

Efficient utilization of agricultural wastes and reduction of chemical fertilizer inputs are crucial for sustainable development of agriculture. Plant growth promoting rhizobacteria (PGPR) are widely used as biofertilizers to partially replace chemical fertilizers in agricultural production. The functional performance of PGPR strains is closely related to their root colonization capacity. Some organic acids from root exudates can recruit PGPR to colonize the root. In this study, agricultural organic wastes such as mushroom bran and tobacco waste materials were used to produce organic acids through the hypoxic hydrolysis process. The hydrolysis conditions were optimized to maximize the production of a mixture of complex organic acids from the hypoxic hydrolysis of these materials, employing both single-factor and orthogonal experimental methods. The diluted hydrolysates were tested for their effects on the rhizosphere colonization of the PGPR strain Bacillus amyloliquefaciens SQR9 using fluorogenic quantitative PCR in greenhouse pot experiments. The results demonstrated that hypoxic hydrolysates from tobacco waste and mushroom bran significantly enhanced the colonization of SQR9 in the maize rhizosphere. Specifically, a 2000-fold dilution of tobacco waste hydrolysate yielded the most effective result, while a 5000-fold dilution of mushroom bran hydrolysate provided the best outcome. All treatments combining these hydrolysates with SQR9 significantly increased maize stem dry weight, indicating that with appropriate treatment, such as anaerobic fermentation, these agricultural organic wastes can serve as synergistic agents of microbial fertilizers, contributing to agricultural sustainability. [ABSTRACT FROM AUTHOR]

Introduction: Low ground temperature is a major factor limiting overwintering in cucumber cultivation facilities in northern alpine regions. Lower temperatures in the root zone directly affect the physiological function of the root system, which in turn affects the normal physiological activity of plants. However, the importance of the ground temperature in facilities has not attracted sufficient attention. Methods: Therefore, this study tested the cucumber variety Jinyou 35 under three root zone temperatures (room temperature, 20-22°C; suboptimal temperature, 13-15°C; and low temperature, 8-10°C) to investigated possible cold resistance mechanisms in the root of cucumber seedlings through hormone, metabolomics, and transcriptomics analyses. Results and discussion: The results showed that cucumber roots were subjected to chilling stress at different temperatures. Hormone analysis indicated that auxin content was highest in the roots. Jasmonic acid and strigolactone participated in the low-temperature stress response. Auxin and jasmonate are key hormones that regulate the response of cucumber roots to low temperatures. Phenolic acid was the most abundant metabolite in cucumber roots under chilling stress. Additionally, triterpenes may play an important role in chilling resistance. Differentially expressed genes and metabolites were significantly enriched in benzoxazinoid biosynthesis in the room temperature vs. suboptimal temperature groups and the room temperature vs. low temperature groups. Most differentially expressed transcription factor genes in AP2/ERF were strongly induced in cucumber roots by both suboptimal and low-temperature stress conditions. These results provide guidance for the cultivation of cucumber in facilities. [ABSTRACT FROM AUTHOR]

Background: The plant root system is critical for the absorption of water and nutrients, and have a direct influence on growth and yield. In cucumber, a globally consumed crop, the molecular mechanism of root development remains unclear, and this has implications for developing stress tolerant varieties. This study sought to determine the genetic patterns and related genes of cucumber root weight. A core cucumber germplasms population was used to do the GWAS analysis in three environments. Results: Here, we investigated four root-weight related traits including root fresh weight (RFW), root dry weight (RDW), ratio of root dry weight to root fresh weight (RDFW) and the comprehensive evaluation index, D-value of root weight (DRW) deduced based on the above three traits for the core germplasm of the cucumber global repository. According to the D-value, we identified 21 and 16 accessions with light and heavy-root, respectively. We also found that the East Asian ecotype accessions had significantly heavier root than other three ecotypes. The genome-wide association study (GWAS) for these four traits reveals that 4 of 10 significant loci (gDRW3.1, gDRW3.2, gDRW4.1 and gDRW5.1) were repeatedly detected for at least two traits. Further haplotype and expression analysis for protein-coding genes positioned within these 4 loci between light and heavy-root accessions predicted five candidate genes (i.e., Csa3G132020 and Csa3G132520 both encoding F-box protein PP2-B1 for gDRW3.1, Csa3G629240 encoding a B-cell receptor-associated protein for gDRW3.2, Csa4G499330 encodes a GTP binding protein for gDRW4.1, and Csa5G286040 encodes a proteinase inhibitor for gDRW5.1). Conclusions: We conducted a systematic analysis of the root genetic basis and characteristics of cucumber core germplasms population. We detected four novel loci, which regulate the root weight in cucumber. Our study provides valuable candidate genes and haplotypes for the improvement of root system in cucumber breeding. [ABSTRACT FROM AUTHOR]

Tobacco cembranoids, known for their anti-insect and antifungal properties, were shown to be mainly present on the surface of leaves and flowers, being biosynthesized by their trichomes. It remains unclear whether they could be biosynthesized in other organs without trichomes. Cembratrien-ol synthases (CBTSs) catalyze the conversion of GGPP to CBT-ols and thus play an important role in cembranoid biosynthesis. This study identified the CBTS family genes in tobacco and examined their spatiotemporal expression patterns. The CBTS genes showed diverse expression patterns in tobacco organs, with the majority highly expressed in leaves and a few highly expressed in flowers. The expression of CBTS genes were also correlated with the development of tobacco plants, and most of them showed the highest expression level at the budding stage. Furthermore, their expression is mediated by the JA (jasmonate) signaling in all tobacco organs. Several CBTS genes were found to be highly expressed in tobacco roots that have no trichomes, which prompted us to determine the cembranoid production in roots and other organs. GC-MS and UPLC assays revealed that cembranoids were produced in all tobacco organs, which was supported by the bioactivity assay results that almost all these CBTS enzymes could catalyze CBT-ol biosyntheis in yeast, and that the content ratio of CBT-ols and CBT-diols in tobacco roots was different to that in leaves. This work sheds insights into the expression profiles of tobacco CBTS genes and provides a feasibility to engineer tobacco roots for industrial production of cembranoids. [ABSTRACT FROM AUTHOR]

Ultraviolet (UV)-B radiation is considered one of the major detrimental rays coming from the Sun. UV-B radiation has a harmful impact on plant growth and development. The effect of UV-B radiation was studied on 64 rice (Oryza sativa L.) genotypes during the vegetative season. An equal number of genotypes from the japonica (50%) and indica (50%) subspecies were phenotyped using the Soil-Plant-Atmosphere-Research (SPAR) units. The 10 kJ UV-B was imposed 12 days after planting (DAP) and continued for three weeks (21 d). Based on the combined ultraviolet-B radiation response index (CUVBRI) for each genotype, the 64 rice genotypes were classified into sensitive, moderately sensitive, moderately tolerant, and tolerant. Various shoot traits, such as plant height, tiller, and leaf numbers, were measured. We also studied critical root phenological traits like root volume, diameter, tips, and forks. Out of all the studied shoot traits, leaf area showed maximum reduction for both indica (54%) and japonica (48%). Among the root traits, root length decreased by negligible (1%) for indica as compared to japonica (5%), while root crossing and forks showed a maximum decline for japonica (37 and 42%), respectively. This study is timely, meaningful, and required because it will help breeders select a tolerant or sensitive rice line for better yield and production under abiotic stresses. [ABSTRACT FROM AUTHOR]

The biotic release of nitric oxide (NO), a greenhouse gas, into the atmosphere contributes to climate change. In plants, NO plays a significant role in metabolic and signaling processes. However, little attention has been paid to the plantborne portion of global NO emissions. Owing to the growing significance of global flooding events caused by climate change, the extent of plant NO emissions has been assessed under low-oxygen conditions for the roots of intact plants. Each examined plant species (tomato, tobacco, and barley) exhibited NO emissions in a highly oxygen-dependent manner. The transfer of data obtained under laboratory conditions to the global area of farmland was used to estimate possible plant NO contribution to greenhouse gas budgets. Plant-derived and stress-induced NO emissions were estimated to account for the equivalent of 1 to 9% of global annual NO emissions from agricultural land. Because several stressors induce NO formation in plants, the actual impact may be even higher. [ABSTRACT FROM AUTHOR]

Ultraviolet (UV)-B radiation is considered one of the major detrimental rays coming from the Sun. UV-B radiation has a harmful impact on plant growth and development. The effect of UV-B radiation was studied on 64 rice (Oryza sativa L.) genotypes during the vegetative season. An equal number of genotypes from the japonica (50%) and indica (50%) subspecies were phenotyped using the Soil-Plant-Atmosphere-Research (SPAR) units. The 10 kJ UV-B was imposed 12 days after planting (DAP) and continued for three weeks (21 d). Based on the combined ultraviolet-B radiation response index (CUVBRI) for each genotype, the 64 rice genotypes were classified into sensitive, moderately sensitive, moderately tolerant, and tolerant. Various shoot traits, such as plant height, tiller, and leaf numbers, were measured. We also studied critical root phenological traits like root volume, diameter, tips, and forks. Out of all the studied shoot traits, leaf area showed maximum reduction for both indica (54%) and japonica (48%). Among the root traits, root length decreased by negligible (1%) for indica as compared to japonica (5%), while root crossing and forks showed a maximum decline for japonica (37 and 42%), respectively. This study is timely, meaningful, and required because it will help breeders select a tolerant or sensitive rice line for better yield and production under abiotic stresses.

The biotic release of nitric oxide (NO), a greenhouse gas, into the atmosphere contributes to climate change. In plants, NO plays a significant role in metabolic and signaling processes. However, little attention has been paid to the plant-borne portion of global NO emissions. Owing to the growing significance of global flooding events caused by climate change, the extent of plant NO emissions has been assessed under low-oxygen conditions for the roots of intact plants. Each examined plant species (tomato, tobacco, and barley) exhibited NO emissions in a highly oxygen-dependent manner. The transfer of data obtained under laboratory conditions to the global area of farmland was used to estimate possible plant NO contribution to greenhouse gas budgets. Plant-derived and stress-induced NO emissions were estimated to account for the equivalent of 1 to 9% of global annual NO emissions from agricultural land. Because several stressors induce NO formation in plants, the actual impact may be even higher.

Due to drought stress, durum wheat production in the Mediterranean basin will be severely affected in the coming years. Durum wheat cultivation relies on a few genetically uniform "modern" varieties, more productive but less tolerant to stresses, and "traditional" varieties, still representing a source of genetic biodiversity for drought tolerance. Root architecture plasticity is crucial for plant adaptation to drought stress and the relationship linking root structures to drought is complex and still largely under-explored. In this study, we examined the effect of drought stress on the roots’ characteristics of the “traditional” Saragolla cultivar and the “modern” Svevo. By means of “SmartRoot” software, we demonstrated that drought stress affected primary and lateral roots as well as root hair at different extents in Saragolla and Svevo cultivars. Indeed, we observed that under drought stress Saragolla possibly revamped its root architecture, by significantly increasing the length of lateral roots, and the length/density of root hairs compared to the Svevo cultivar. Scanning Electron Microscopy analysis of root anatomical traits demonstrated that under drought stress a greater stele area and an increase of the xylem lumen size vessel occurred in Saragolla, indicating that the Saragolla variety had a more efficient adaptive response to osmotic stress than the Svevo. Furthermore, for the analysis of root structural data, Artificial Intelligence (AI) algorithms have been used: Their application allowed to predict from root structural traits modified by the osmotic stress the type of cultivar observed and to infer the relationship stress-cultivar type, thus demonstrating that root structural traits are clear and incontrovertible indicators of the higher tolerance to osmotic stress of the Saragolla cultivar. Finally, to obtain an integrated view of root morphogenesis, phytohormone levels were investigated. According to the phenotypic effects, under drought stress,a larger increase in IAA and ABA levels, as well as a more pronounced reduction in GA levels occurred in Saragolla as compared to Svevo. In conclusion, these results show that the root growth and hormonal profile of Saragolla are less affected by osmotic stress than those of Svevo, demonstrating the great potential of ancient varieties as reservoirs of genetic variability for improving crop responses to environmental stresses. [ABSTRACT FROM AUTHOR]

Drought is a major environmental factor that limits agricultural crop productivity and threatens food security. Foxtail millet is a model crop with excellent abiotic stress tolerance and is consequently an important subject for obtaining a better understanding of the molecular mechanisms underlying plant responses to drought and recovery. Here the physiological and proteomic responses of foxtail millet (cultivar Yugu1) leaves and roots to drought treatments and recovery were evaluated. Drought-treated foxtail millet exhibited increased relative electrolyte leakage and decreased relative water content and chlorophyll content compared to control and rewatering plants. A global analysis of protein profiles was evaluated for drought-treated and recovery treatment leaves and roots. We also identified differentially abundant proteins in drought and recovery groups, enabling comparisons between leaf and root tissue responses to the conditions. The principal component analysis suggested a clear distinction between leaf and root proteomes for the drought-treated and recovery treatment plants. Gene Ontology enrichment and co-expression analyses indicated that the biological responses of leaves differed from those in roots after drought and drought recovery. These results provide new insights and data resources to investigate the molecular basis of tissue-specific functional responses of foxtail millet during drought and recovery, thereby significantly informing crop breeding. [ABSTRACT FROM AUTHOR]

Due to drought stress, durum wheat production in the Mediterranean basin will be severely affected in the coming years. Durum wheat cultivation relies on a few genetically uniform "modern" varieties, more productive but less tolerant to stresses, and "traditional" varieties, still representing a source of genetic biodiversity for drought tolerance. Root architecture plasticity is crucial for plant adaptation to drought stress and the relationship linking root structures to drought is complex and still largely under-explored. In this study, we examined the effect of drought stress on the roots’ characteristics of the “traditional” Saragolla cultivar and the “modern” Svevo. By means of “SmartRoot” software, we demonstrated that drought stress affected primary and lateral roots as well as root hair at different extents in Saragolla and Svevo cultivars. Indeed, we observed that under drought stress Saragolla possibly revamped its root architecture, by significantly increasing the length of lateral roots, and the length/density of root hairs compared to the Svevo cultivar. Scanning Electron Microscopy analysis of root anatomical traits demonstrated that under drought stress a greater stele area and an increase of the xylem lumen size vessel occurred in Saragolla, indicating that the Saragolla variety had a more efficient adaptive response to osmotic stress than the Svevo. Furthermore, for the analysis of root structural data, Artificial Intelligence (AI) algorithms have been used: Their application allowed to predict from root structural traits modified by the osmotic stress the type of cultivar observed and to infer the relationship stress-cultivar type, thus demonstrating that root structural traits are clear and incontrovertible indicators of the higher tolerance to osmotic stress of the Saragolla cultivar. Finally, to obtain an integrated view of root morphogenesis, phytohormone levels were investigated. According to the phenotypic effects, under drought stress,a larger increase in IAA and ABA levels, as well as a more pronounced reduction in GA levels occurred in Saragolla as compared to Svevo. In conclusion, these results show that the root growth and hormonal profile of Saragolla are less affected by osmotic stress than those of Svevo, demonstrating the great potential of ancient varieties as reservoirs of genetic variability for improving crop responses to environmental stresses.

Root system architecture (RSA) is the primary predictor of nutrient intake and significantly influences potassium utilization efficiency (KUE). Uncertainty persists regarding the genetic factors governing root growth in rapeseed. The root transcriptome analysis reveals the genetic basis driving crop root growth. In this study, RNA-seq was used to profile the overall transcriptome in the root tissue of 20 Brassica napus accessions with high and low KUE. 71,437 genes in the roots displayed variable expression profiles between the two contrasting genotype groups. The 212 genes that had varied expression levels between the high and low KUE lines were found using a pairwise comparison approach. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) functional classification analysis revealed that the DEGs implicated in hormone and signaling pathways, as well as glucose, lipid, and amino acid metabolism, were all differently regulated in the rapeseed root system. Additionally, we discovered 33 transcription factors (TFs) that control root development were differentially expressed. By combining differential expression analysis, weighted gene co-expression network analysis (WGCNA), and recent genome-wide association study (GWAS) results, four candidate genes were identified as essential hub genes. These potential genes were located fewer than 100 kb from the peak SNPs of QTL clusters, and it was hypothesized that they regulated the formation of the root system. Three of the four hub genes' homologs--BnaC04G0560400ZS, BnaC04G0560400ZS, and BnaA03G0073500ZS--have been shown to control root development in earlier research. The information produced by our transcriptome profiling could be useful in revealing the molecular processes involved in the growth of rapeseed roots in response to KUE. [ABSTRACT FROM AUTHOR]

Introduction: With the warming global climate, drought stress has become an important abiotic stress factor limiting plant growth and crop yield. As the most rapidly drought-sensing organs of plants, roots undergo a series of changes to enhance their ability to absorb water, but the molecular mechanism is unclear. Results and methods: In this study, we found that PLT1 and PLT2, two important transcription factors of root development in Arabidopsis thaliana, are involved in the plant response to drought and are inhibited by BR signaling. PLT1- and PLT2-overexpressing plants showed greater drought tolerance than wild-type plants. Furthermore, we found that BZR1 could bind to the promoter of PLT1 and inhibit its transcriptional activity in vitro and in vivo. PLT1 and PLT2 were regulated by BR signaling in root development and PLT2 could partially rescue the drought sensitivity of bes1-D. In addition, RNA-seq data analysis showed that BR-regulated root genes and PLT1/2 target genes were also regulated by drought; for example, CIPK3, RCI2A, PCaP1, PIP1;5, ERF61 were downregulated by drought and PLT1/2 but upregulated by BR treatment; AAP4, WRKY60, and AT5G19970 were downregulated by PLT1/2 but upregulated by drought and BR treatment; and RGL2 was upregulated by drought and PLT1/2 but downregulated by BR treatment. Discussion: Our findings not only reveal the mechanism by which BR signaling coordinates root growth and drought tolerance by suppressing the expression of PLT1 and PLT2 but also elucidates the relationship between drought and root development. The current study thus provides an important theoretical basis for the improvement of crop yield under drought conditions. [ABSTRACT FROM AUTHOR]

The 14-3-3 protein is a kind of evolutionary ubiquitous protein family highly conserved in eukaryotes. Initially, 14-3-3 proteins were reported in mammalian nervous tissues, but in the last decade, their role in various metabolic pathways in plants established the importance of 14-3-3 proteins. In the present study, a total of 22 14-3-3 genes, also called general regulatory factors (GRF), were identified in the peanut (Arachis hypogaea) genome, out of which 12 belonged to the ε group, whereas 10 of them belonged to the non-ε-group. Tissue-specific expression of identified 14-3-3 genes were studied using transcriptome analysis. The peanut AhGRFi gene was cloned and transformed into Arabidopsis thaliana. The investigation of subcellular localization indicated that AhGRFi is localized in the cytoplasm. Overexpression of the AhGRFi gene in transgenic Arabidopsis showed that under exogenous 1-naphthaleneacetic acid (NAA) treatment, root growth inhibition in transgenic plants was enhanced. Further analysis indicated that the expression of auxin-responsive genes IAA3, IAA7, IAA17, and SAUR-AC1 was upregulated and GH3.2 and GH3.3 were downregulated in transgenic plants, but the expression of GH3.2, GH3.3, and SAUR-AC1 showed opposite trends of change under NAA treatment. These results suggest that AhGRFi may be involved in auxin signaling during seedling root development. An in-depth study of the molecular mechanism of this process remains to be further explored. [ABSTRACT FROM AUTHOR]

Phytohormones play an important role in regulating the plant behavior to drought. In previous studies, NIBER® pepper rootstock showed tolerance to drought in terms of production and fruit quality compared to ungrafted plants. In this study, our hypothesis was that short-term exposure to water stress in young, grafted pepper plants would shed light on tolerance to drought in terms of modulation of the hormonal balance. To validate this hypothesis, fresh weight, water use efficiency (WUE) and the main hormone classes were analyzed in self-grafted pepper plants (variety onto variety, V/V) and variety grafted onto NIBER® (V/N) at 4, 24, and 48h after severe water stress was induced by PEG addition. After 48h, WUE in V/N was higher than in V/V, due to major stomata closure to maintain water retention in the leaves. This can be explained by the higher abscisic acid (ABA) levels observed in the leaves of V/N plants. Despite the interaction between ABA and the ethylene precursor, 1-aminocyclopropane-1-carboxylic acid (ACC), in relation to stomata closure is controversial, we observed an important increase of ACC at the end of the experiment in V/N plants coinciding with an important rise of the WUE and ABA. The maximum concentration of jasmonic acid and salicylic acid after 48h was found in the leaves of V/N, associated with their role in abiotic stress signaling and tolerance. Respect to auxins and cytokinins, the highest concentrations were linked to water stress and NIBER®, but this effect did not occur for gibberellins. These results show that hormone balance was affected by water stress and rootstock genotype, where NIBER® rootstock displayed a better ability to overcome short-term water stress. [ABSTRACT FROM AUTHOR]

Excess boron (B) is toxic to plants and thereby causes DNA damage and cell death in root meristems. However, the underlying mechanisms which link boron and DNA damage remain unclear. It has been reported that the rpt5a-6 mutant of the 26S proteasome is sensitive to excess boron, resulting in more frequent cell death in root meristem and reduced root elongation. In this study, we showed that a reduction in root growth in the rpt5a mutant in the presence of high boron levels is repressed by a mutation in NAC domain containing transcription factor NAC103, a substrate of the proteasome, which functions in the unfolded protein response pathway. The mutation in NAC103 alleviated excess-B-induced DNA damage and cell death in root meristems of the rpt5a mutant. Superoxide (O−2 ) staining with nitroblue tetrazolium revealed that boron stress causes O−2 accumulation in root tips, which was higher in the rpt5a-6 mutant, whereas the accumulation was lower in the rpt5a-6 nac103-3 double mutant. Our work demonstrates the overall involvement of NAC103 in maintaining healthy root meristem under excess boron conditions in the absence of RPT5A proteasome subunit. [ABSTRACT FROM AUTHOR]

Verticillium wilt (VW) is often referred to as the cancer of cotton and it has a detrimental effect on cotton yield and quality. Since the root system is the first to be infested, it is feasible to detect VW by root analysis in the early stages of the disease. In recent years, with the update of computing equipment and the emergence of large-scale high-quality data sets, deep learning has achieved remarkable results in computer vision tasks. However, in some specific areas, such as cotton root MRI image task processing, it will bring some challenges. For example, the data imbalance problem (there is a serious imbalance between the cotton root and the background in the segmentation task) makes it difficult for existing algorithms to segment the target. In this paper, we proposed two new methods to solve these problems. The effectiveness of the algorithms was verified by experimental results. The results showed that the new segmentation model improved the Dice and mIoU by 46% and 44% compared with the original model. And this model could segment MRI images of rapeseed root cross-sections well with good robustness and scalability. The new classification model improved the accuracy by 34.9% over the original model. The recall score and F1 score increased by 59% and 42%, respectively. The results of this paper indicate that MRI and deep learning have the potential for non-destructive early detection of VW diseases in cotton. [ABSTRACT FROM AUTHOR]

Infection by the Japanese soil-borne wheat mosaic virus (JSBWMV) can lead to substantial losses in the grain yield of barley and wheat crops. While genetically based resistance to this virus has been documented, its mechanistic basis remains obscure. In this study, the deployment of a quantitative PCR assay showed that the resistance acts directly against the virus rather than by inhibiting the colonization of the roots by the virus' fungal vector Polymyxa graminis. In the susceptible barley cultivar (cv.) Tochinoibuki, the JSBWMV titre was maintained at a high level in the roots during the period December--April, and the virus was translocated from the root to the leaf from January onwards. In contrast, in the roots of both cv. Sukai Golden and cv. Haruna Nijo, the titre was retained at a low level, and translocation of the virus to the shoot was strongly suppressed throughout the host's entire life cycle. The roots of wild barley (Hordeum vulgare ssp. spontaneum) accession H602 responded in the early stages of infection similarly to those of the resistant cultivated forms, but the host was unable to suppress the translocation of the virus to the shoot from March onwards. The virus titre in the root was presumed to have been restricted by the action of the gene product of Jmv1 (on chromosome 2H), while the stochastic nature of the infection was suppressed by the action of that of Jmv2 (on chromosome 3H), a gene harbored by cv. Sukai Golden but not by either cv. Haruna Nijo or accession H602. [ABSTRACT FROM AUTHOR]

Root system architecture (RSA) is the primary predictor of nutrient intake and significantly influences potassium utilization efficiency (KUE). Uncertainty persists regarding the genetic factors governing root growth in rapeseed. The root transcriptome analysis reveals the genetic basis driving crop root growth. In this study, RNA-seq was used to profile the overall transcriptome in the root tissue of 20 Brassica napus accessions with high and low KUE. 71,437 genes in the roots displayed variable expression profiles between the two contrasting genotype groups. The 212 genes that had varied expression levels between the high and low KUE lines were found using a pairwise comparison approach. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) functional classification analysis revealed that the DEGs implicated in hormone and signaling pathways, as well as glucose, lipid, and amino acid metabolism, were all differently regulated in the rapeseed root system. Additionally, we discovered 33 transcription factors (TFs) that control root development were differentially expressed. By combining differential expression analysis, weighted gene co-expression network analysis (WGCNA), and recent genome-wide association study (GWAS) results, four candidate genes were identified as essential hub genes. These potential genes were located fewer than 100 kb from the peak SNPs of QTL clusters, and it was hypothesized that they regulated the formation of the root system. Three of the four hub genes’ homologs—BnaC04G0560400ZS, BnaC04G0560400ZS, and BnaA03G0073500ZS—have been shown to control root development in earlier research. The information produced by our transcriptome profiling could be useful in revealing the molecular processes involved in the growth of rapeseed roots in response to KUE.

Phytohormones play an important role in regulating the plant behavior to drought. In previous studies, NIBER® pepper rootstock showed tolerance to drought in terms of production and fruit quality compared to ungrafted plants. In this study, our hypothesis was that short-term exposure to water stress in young, grafted pepper plants would shed light on tolerance to drought in terms of modulation of the hormonal balance. To validate this hypothesis, fresh weight, water use efficiency (WUE) and the main hormone classes were analyzed in self-grafted pepper plants (variety onto variety, V/V) and variety grafted onto NIBER® (V/N) at 4, 24, and 48h after severe water stress was induced by PEG addition. After 48h, WUE in V/N was higher than in V/V, due to major stomata closure to maintain water retention in the leaves. This can be explained by the higher abscisic acid (ABA) levels observed in the leaves of V/N plants. Despite the interaction between ABA and the ethylene precursor, 1-aminocyclopropane-1-carboxylic acid (ACC), in relation to stomata closure is controversial, we observed an important increase of ACC at the end of the experiment in V/N plants coinciding with an important rise of the WUE and ABA. The maximum concentration of jasmonic acid and salicylic acid after 48h was found in the leaves of V/N, associated with their role in abiotic stress signaling and tolerance. Respect to auxins and cytokinins, the highest concentrations were linked to water stress and NIBER®, but this effect did not occur for gibberellins. These results show that hormone balance was affected by water stress and rootstock genotype, where NIBER® rootstock displayed a better ability to overcome short-term water stress.

Ammonium absorbed by roots is assimilated into amino acids. The glutamine synthetase/glutamate synthase (glutamine 2-oxoglutarate aminotransferase) (GS/GOGAT) cycle is essential to this biological process. In Arabidopsis thaliana, GLN1;2 and GLT1 are the GS and GOGAT isoenzymes induced in response to ammonium supply and playing key roles in ammonium utilization. Although recent studies suggest gene regulatory networks involved in transcriptional regulation of ammonium-responsive genes, direct regulatory mechanisms for ammonium-induced expression of GS/GOGAT remain unclear. In this study, we revealed that the expression of GLN1;2 and GLT1 in Arabidopsis is not directly induced by ammonium but is regulated by glutamine or post-glutamine metabolites produced by ammonium assimilation. Previously, we identified a promoter region required for ammonium-responsive expression of GLN1;2. In this study, we further dissected the ammonium-responsive region of the GLN1;2 promoter and also performed a deletion analysis of the GLT1 promoter, which led to the identification of a conserved ammonium-responsive region. Yeast one-hybrid screening using the ammonium-responsive region of the GLN1;2 promoter as a decoy sequence revealed a trihelix family transcription factor DF1 that binds to this region. A putative DF1 binding site was also found in the ammonium-responsive region of the GLT1 promoter. [ABSTRACT FROM AUTHOR]

High concentrations of heavy metals in the environment will cause serious harm to ecosystems and human health. It is urgent to develop effective methods to control soil heavy metal pollution. Phytoremediation has advantages and potential for soil heavy metal pollution control. However, the current hyperaccumulators have the disadvantages of poor environmental adaptability, single enrichment species and small biomass. Based on the concept of modularity, synthetic biology makes it possible to design a wide range of organisms. In this paper, a comprehensive strategy of "microbial biosensor detection - phytoremediation - heavy metal recovery" for soil heavy metal pollution control was proposed, and the required steps were modified by using synthetic biology methods. This paper summarizes the new experimental methods that promote the discovery of synthetic biological elements and the construction of circuits, and combs the methods of producing transgenic plants to facilitate the transformation of constructed synthetic biological vectors. Finally, the problems that should be paid more attention to in the remediation of soil heavy metal pollution based on synthetic biology were discussed. [ABSTRACT FROM AUTHOR]

Phosphate deprivation compromises plant productivity and modulates immunity. DAMP signalling by extracellular ATP (eATP) could be compromised under phosphate deprivation by the lowered production of cytosolic ATP and the need to salvage eATP as a nutritional phosphate source. Phosphate-starved roots of Arabidopsis can still sense eATP, indicating robustness in receptor function. However, the resultant cytosolic free Ca2+ signature is impaired, indicating modulation of downstream components. This perspective on DAMP signalling by extracellular ATP (eATP) addresses the salvage of eATP under phosphate deprivation and its promotion of immunity, how Ca2+ signals are generated and how the Ca2+ signalling pathway could be overcome to allow beneficial fungal root colonization to fulfill phosphate demands. Safe passage for an endophytic fungus allowing root colonization could be achieved by its down-regulation of the Ca2+ channels that act downstream of the eATP receptors and by also preventing ROS accumulation, thus further impairing DAMP signalling. [ABSTRACT FROM AUTHOR]

One sentence summary: Bi-directional-dual-flow-RootChip to track calcium signatures in Arabidopsis primary roots responding to osmotic stress. Plant growth and survival is fundamentally linked with the ability to detect and respond to abiotic and biotic factors. Cytosolic free calcium (Ca2+) is a key messenger in signal transduction pathways associated with a variety of stresses, including mechanical, osmotic stress and the plants’ innate immune system. These stresses trigger an increase in cytosolic Ca2+ and thus initiate a signal transduction cascade, contributing to plant stress adaptation. Here we combine fluorescent G-CaMP3 Arabidopsis thaliana sensor lines to visualise Ca2+ signals in the primary root of 9-day old plants with an optimised dual-flow RootChip (dfRC). The enhanced polydimethylsiloxane (PDMS) bi-directionaldual- flow-RootChip (bi-dfRC) reported here adds two adjacent inlet channels at the base of the observation chamber, allowing independent or asymmetric chemical stimulation at either the root differentiation zone or tip. Observations confirm distinct early spatio-temporal patterns of salinity (sodium chloride, NaCl) and drought (polyethylene glycol, PEG)-induced Ca2+ signals throughout different cell types dependent on the first contact site. Furthermore, we show that the primary signal always dissociates away from initially stimulated cells. The observed early signaling events induced by NaCl and PEG are surprisingly complex and differ from long-term changes in cytosolic Ca2+ reported in roots. Bi-dfRC microfluidic devices will provide a novel approach to challenge plant roots with different conditions simultaneously, while observing bi-directionality of signals. Future applications include combining the bi-dfRC with H2O2 and redox sensor lines to test root systemic signaling responses to biotic and abiotic factors. [ABSTRACT FROM AUTHOR]

One sentence summary: Bi-directional-dual-flow-RootChip to track calcium signatures in Arabidopsis primary roots responding to osmotic stress.Plant growth and survival is fundamentally linked with the ability to detect and respond to abiotic and biotic factors. Cytosolic free calcium (Ca2+) is a key messenger in signal transduction pathways associated with a variety of stresses, including mechanical, osmotic stress and the plants’ innate immune system. These stresses trigger an increase in cytosolic Ca2+ and thus initiate a signal transduction cascade, contributing to plant stress adaptation. Here we combine fluorescent G-CaMP3 Arabidopsis thaliana sensor lines to visualise Ca2+ signals in the primary root of 9-day old plants with an optimised dual-flow RootChip (dfRC). The enhanced polydimethylsiloxane (PDMS) bi-directional-dual-flow-RootChip (bi-dfRC) reported here adds two adjacent inlet channels at the base of the observation chamber, allowing independent or asymmetric chemical stimulation at either the root differentiation zone or tip. Observations confirm distinct early spatio-temporal patterns of salinity (sodium chloride, NaCl) and drought (polyethylene glycol, PEG)-induced Ca2+ signals throughout different cell types dependent on the first contact site. Furthermore, we show that the primary signal always dissociates away from initially stimulated cells. The observed early signaling events induced by NaCl and PEG are surprisingly complex and differ from long-term changes in cytosolic Ca2+ reported in roots. Bi-dfRC microfluidic devices will provide a novel approach to challenge plant roots with different conditions simultaneously, while observing bi-directionality of signals. Future applications include combining the bi-dfRC with H2O2 and redox sensor lines to test root systemic signaling responses to biotic and abiotic factors.

Tomato is a horticultural crop of high economic and nutritional value. Suboptimal environmental conditions, such as limited water and nutrient availability, cause severe yield reductions. Thus, selection of genotypes requiring lower inputs is a goal for the tomato breeding sector. We screened 10 tomato varieties exposed to water deficit, low nitrate or a combination of both. Biometric, physiological and molecular analyses revealed different stress responses among genotypes, identifying T270 as severely affected, and T250 as tolerant to the stresses applied. Investigation of transcriptome changes caused by combined stress in roots and leaves of these two genotypes yielded a low number of differentially expressed genes (DEGs) in T250 compared to T270, suggesting that T250 tailors changes in gene expression to efficiently respond to combined stress. By contrast, the susceptible tomato activated approximately one thousand and two thousand genes in leaves and roots respectively, indicating a more generalized stress response in this genotype. In particular, developmental and stress-related genes were differentially expressed, such as hormone responsive factors and transcription factors. Analysis of differential alternative splicing (DAS) events showed that combined stress greatly affects the splicing landscape in both genotypes, highlighting the important role of AS in stress response mechanisms. In particular, several stress and growth-related genes as well as transcription and splicing factors were differentially spliced in both tissues. Taken together, these results reveal important insights into the transcriptional and posttranscriptional mechanisms regulating tomato adaptation to growth under reduced water and nitrogen inputs. [ABSTRACT FROM AUTHOR]

Cell wall proteins perform diverse cellular functions in response to abiotic and biotic stresses. To elucidate the possible mechanisms of salt-stress tolerance in tomato. The 30 d seedlings of two tomato genotypes with contrasting salt tolerances were transplanted to salt stress (200 mM NaCl) for three days, and then, the cell wall proteins of seedling roots were analyzed by isobaric tags for relative and absolute quantification (iTRAQ). There were 82 and 81 cell wall proteins that changed significantly in the salt-tolerant tomato IL8-3 and the salt-sensitive tomato M82, respectively. The proteins associated with signal transduction and alterations to cell wall polysaccharides were increased in both IL8-3 and M82 cells wall in response to salt stress. In addition, many different or even opposite metabolic changes occurred between IL8-3 and M82 in response to salt stress. The salt-tolerant tomato IL8-3 experienced not only significantly decreased in Na+ accumulation but also an obviously enhanced in regulating redox balance and cell wall lignification in response to salt stress. Taken together, these results provide novel insight for further understanding the molecular mechanism of salt tolerance in tomato. [ABSTRACT FROM AUTHOR]

Breeding cultivars that can maintain high production and water productivity (WP) under various growing conditions would be important for mitigating freshwater shortage problems. Experiments were carried out to assess the changes in yield and WP of different cultivars by breeding and traits related to the changes using tubes with 1.05 m depth and 19.2 cm inner diameter buried in the field located in the North China Plain. Six winter wheat cultivars released from the 1970s to 2010s were assessed under three water levels for three seasons. The results indicated that yield was on average improved by 19.9% and WP by 21.5% under the three water levels for the three seasons for the cultivar released in the 2010s as compared with that released in the 1970s. The performance of the six cultivars was relatively stable across the experimental duration. The improvement in yield was mainly attributed to the maintenance of higher photosynthetic capacity during the reproductive growth stage and greater above-ground biomass accumulation. These improvements were larger under wet conditions than that under dry conditions, indicating that the yield potential was increased by cultivar renewal. Traits related to yield and WP improvements included the increased harvest index and reduced root: shoot ratio. New cultivars reduced the redundancy in root proliferation in the topsoil layer, which did not compromise the efficient utilization of soil moisture but reduced the metabolic input in root growth. Balanced above- and below-ground growth resulted in a significant improvement in root efficiency at grain yield level up to 40% from the cultivars released in the 1970s to those recently released. The results from this study indicated that the improved efficiency in both the above- and below-parts played important roles in enhancing crop production and resource use efficiency. [ABSTRACT FROM AUTHOR]

Climate change-related drought stress is expected to shift carbon partitioning toward volatile organic compound (VOC) biosynthesis. The effect of drought stress on VOC synthesis remains unknown in several tree species. Therefore, we exposed eastern white pine (Pinus strobus) plants to severe drought for 32 days and performed physiological analysis (chlorophyll content, leaf water content, and root/shoot index), biochemical analysis (non-structural carbohydrates, proline, lipid peroxidation, and antioxidant assay), and total root VOC analysis. Drought stress decreased the relative water and soil moisture contents. Root proline accumulation and antioxidant activity increased significantly, whereas leaf chlorophyll synthesis and fresh weight decreased significantly in drought-treated plants. A non-significant increase in sugar accumulation (leaves and roots), proline accumulation (leaves), antioxidant activity (leaves), and lipid peroxidation (leaves and roots) was observed in drought-treated plants. Drought stress caused a non-significant decline in root/shoot ratio and starch accumulation (leaves and roots) and caused a significant increase in root abscisic acid content. Drought-treated plants showed an increase in overall monoterpene synthesis (16%) and decline in total sesquiterpene synthesis (3%). Our findings provide an overall assessment of the different responses of VOC synthesis to severe water deficit that may help unravel the molecular mechanisms underlying drought tolerance in P. strobus. [ABSTRACT FROM AUTHOR]

Dioecious plant species have a high genetic variation that is important for coping with or adapting to environmental stress through natural selection. Intensive studies have reported dimorphism morphism in morphology, physiology, as well as biotic and abiotic stress responses in dioecious plants. Here, we demonstrated the dimorphism of metabolic profile and the preference of some microorganisms in the roots and rhizosphere soils of male and female papaya. The metabolic composition of roots were significantly different between the males and females. Some sex hormones occurred in the differential metabolites in roots and rhizosphere soils. For example, testosterone was up-regulated in male papaya roots and rhizosphere soils, whereas norgestrel was up-regulated in the female papaya roots, indicating a possible balance in papaya roots to control the sexual differentiation. Plant hormones such as BRs, JAs, SA and GAs were also detected among the differential metabolites in the roots and rhizosphere soils of dioecious papaya. In addition, some metabolites that have medicinal values, such as ecliptasaponin A, crocin, berberine and sapindoside A were also expressed differentially between the two sexes. Numerous differential metabolites from the papaya roots were secreted in the soil, resulting in the differences in microbial community structure in the roots and rhizosphere soils. Some nitrogen-fixing bacteria such as Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium, Brevundimonas and Microvirga were enriched in the male papaya roots or rhizosphere soils. While Candidatus Solibacter and Tumebacillus, which utilize organic matters, were enriched in the roots or rhizosphere soils of the female papaya. Some differences in the fungi abundance were also observed in both male and female papaya roots. These findings uncovered the effect of sex types on the metabolic and microbiota differences in roots and rhizosphere soils in papaya and will lead to investigations of underlining genomic and molecular mechanisms. [ABSTRACT FROM AUTHOR]

The ER (endoplasmic reticulum) is the largest membrane-bound multifunctional organelle in eukaryotic cells, serving particularly important in protein synthesis, modification, folding and transport. UPR (unfolded protein response) is one of the systematized strategies that eukaryotic cells employ for responding to ER stress, a condition represents the processing capability of ER is overwhelmed and stressed. UPR is usually triggered when the protein folding capacity of ER is overloaded, and indeed, mounting studies were focused on the stress responding side of UPR. In plants, beyond stress response, accumulating evidence suggests that UPR is essential for growth and development, and more importantly, the necessity of UPR in this regard requires its endogenous basal activation even without stress. Then plants must have to fine tune the activation level of UPR pathway for balancing growth and stress response. In this review, we summarized the recent progresses in plant UPR, centering on its role in controlling plant reproduction and root growth, and lay out some outstanding questions to be addressed in the future. [ABSTRACT FROM AUTHOR]

Pogostemon cablin (patchouli) cultivation is challenged by serious soil sickness, of which autotoxins accumulation is a major cause. p-hydroxybenzoic acid (p-HBA) is one of the main autotoxins of patchouli. However, the molecular mechanism underlying the response of patchouli to p-HBA remains unclear. In this study, RNA-sequencing combined with physiological analysis was used to monitor the dynamic transcriptomic and physiological changes in patchouli seedlings 0, 6, 12, 24, 48, and 96 h after p-HBA treatment. p-HBA stress inhibited root biomass accumulation, induced excessive hydrogen peroxide accumulation and lipid peroxidation, and activated most antioxidant enzymes. Compared with that of the control, the osmotic adjustment substance content was elevated with treatment. Subsequently, 15,532, 8,217, 8,946, 2,489, and 5,843 differentially expressed genes (DEGs) at 6, 12, 24, 48, and 96 h after p-HBA treatment, respectively, were identified in patchouli roots. GO functional enrichment analysis showed that the DEGs were enriched mainly in plasma membrane, defense response, response to chitin, DNA-binding transcription factor activity and abscisic acid-activated signaling pathway. The upregulated genes were involved in glycolysis/gluconeogenesis, cysteine and methionine metabolism, starch and sucrose metabolism, biosynthesis of unsaturated fatty acids, and linoleic acid metabolism. Genes associated with MAPK signaling pathway-plant, plantpathogen interaction, plant hormone signal transduction were downregulated with p-HBA treatment. These pathways are related to root browning and rotting, leading to plant death. [ABSTRACT FROM AUTHOR]

Efficient utilization of agricultural wastes and reduction of chemical fertilizer inputs are crucial for sustainable development of agriculture. Plant growth promoting rhizobacteria (PGPR) are widely used as biofertilizers to partially replace chemical fertilizers in agricultural production. The functional performance of PGPR strains is closely related to their root colonization capacity. Some organic acids from root exudates can recruit PGPR to colonize the root. In this study, agricultural organic wastes such as mushroom bran and tobacco waste materials were used to produce organic acids through the hypoxic hydrolysis process. The hydrolysis conditions were optimized to maximize the production of a mixture of complex organic acids from the hypoxic hydrolysis of these materials, employing both single-factor and orthogonal experimental methods. The diluted hydrolysates were tested for their effects on the rhizosphere colonization of the PGPR strain Bacillus amyloliquefaciens SQR9 using fluorogenic quantitative PCR in greenhouse pot experiments. The results demonstrated that hypoxic hydrolysates from tobacco waste and mushroom bran significantly enhanced the colonization of SQR9 in the maize rhizosphere. Specifically, a 2000-fold dilution of tobacco waste hydrolysate yielded the most effective result, while a 5000-fold dilution of mushroom bran hydrolysate provided the best outcome. All treatments combining these hydrolysates with SQR9 significantly increased maize stem dry weight, indicating that with appropriate treatment, such as anaerobic fermentation, these agricultural organic wastes can serve as synergistic agents of microbial fertilizers, contributing to agricultural sustainability., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2024 Xu, Wang, Wang, Tian, Yue, Li, Wang, Zhang and Zhang.)

Introduction: Low ground temperature is a major factor limiting overwintering in cucumber cultivation facilities in northern alpine regions. Lower temperatures in the root zone directly affect the physiological function of the root system, which in turn affects the normal physiological activity of plants. However, the importance of the ground temperature in facilities has not attracted sufficient attention., Methods: Therefore, this study tested the cucumber variety Jinyou 35 under three root zone temperatures (room temperature, 20-22°C; suboptimal temperature, 13- 15°C; and low temperature, 8-10°C) to investigated possible cold resistance mechanisms in the root of cucumber seedlings through hormone, metabolomics, and transcriptomics analyses., Results and Discussion: The results showed that cucumber roots were subjected to chilling stress at different temperatures. Hormone analysis indicated that auxin content was highest in the roots. Jasmonic acid and strigolactone participated in the low-temperature stress response. Auxin and jasmonate are key hormones that regulate the response of cucumber roots to low temperatures. Phenolic acid was the most abundant metabolite in cucumber roots under chilling stress. Additionally, triterpenes may play an important role in chilling resistance. Differentially expressed genes and metabolites were significantly enriched in benzoxazinoid biosynthesis in the room temperature vs. suboptimal temperature groups and the room temperature vs. low temperature groups. Most differentially expressed transcription factor genes in AP2/ERF were strongly induced in cucumber roots by both suboptimal and low-temperature stress conditions. These results provide guidance for the cultivation of cucumber in facilities., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2024 Sun, Yang, Hao, Liu, Zhang, Yang, Zhang and Luo.)

Tomato is a horticultural crop of high economic and nutritional value. Suboptimal environmental conditions, such as limited water and nutrient availability, cause severe yield reductions. Thus, selection of genotypes requiring lower inputs is a goal for the tomato breeding sector. We screened 10 tomato varieties exposed to water deficit, low nitrate or a combination of both. Biometric, physiological and molecular analyses revealed different stress responses among genotypes, identifying T270 as severely affected, and T250 as tolerant to the stresses applied. Investigation of transcriptome changes caused by combined stress in roots and leaves of these two genotypes yielded a low number of differentially expressed genes (DEGs) in T250 compared to T270, suggesting that T250 tailors changes in gene expression to efficiently respond to combined stress. By contrast, the susceptible tomato activated approximately one thousand and two thousand genes in leaves and roots respectively, indicating a more generalized stress response in this genotype. In particular, developmental and stress-related genes were differentially expressed, such as hormone responsive factors and transcription factors. Analysis of differential alternative splicing (DAS) events showed that combined stress greatly affects the splicing landscape in both genotypes, highlighting the important role of AS in stress response mechanisms. In particular, several stress and growth-related genes as well as transcription and splicing factors were differentially spliced in both tissues. Taken together, these results reveal important insights into the transcriptional and post-transcriptional mechanisms regulating tomato adaptation to growth under reduced water and nitrogen inputs.

Climate change-related drought stress is expected to shift carbon partitioning toward volatile organic compound (VOC) biosynthesis. The effect of drought stress on VOC synthesis remains unknown in several tree species. Therefore, we exposed eastern white pine (Pinus strobus) plants to severe drought for 32 days and performed physiological analysis (chlorophyll content, leaf water content, and root/shoot index), biochemical analysis (non-structural carbohydrates, proline, lipid peroxidation, and antioxidant assay), and total root VOC analysis. Drought stress decreased the relative water and soil moisture contents. Root proline accumulation and antioxidant activity increased significantly, whereas leaf chlorophyll synthesis and fresh weight decreased significantly in drought-treated plants. A non-significant increase in sugar accumulation (leaves and roots), proline accumulation (leaves), antioxidant activity (leaves), and lipid peroxidation (leaves and roots) was observed in drought-treated plants. Drought stress caused a non-significant decline in root/shoot ratio and starch accumulation (leaves and roots) and caused a significant increase in root abscisic acid content. Drought-treated plants showed an increase in overall monoterpene synthesis (16%) and decline in total sesquiterpene synthesis (3%). Our findings provide an overall assessment of the different responses of VOC synthesis to severe water deficit that may help unravel the molecular mechanisms underlying drought tolerance in P. strobus.

Plant nutrition, growth, and response to environmental stresses are pH-dependent processes that are regulated at the apoplastic and subcellular levels. The root apoplastic pH is especially sensitive to external cues and can also be modified by intracellular inputs, such as hormonal signaling. Optimal crosstalk of the mechanisms involved in the extent and span of the apoplast pH fluctuations promotes plant resilience to detrimental biotic and abiotic factors. The fact that variations in local pHs are a standard mechanism in different signaling pathways indicates that the pH itself can be the pivotal element to provide a physiological context to plant cell regions, allowing a proportional reaction to different situations. This review brings a collective vision of the causes that initiate root apoplastic pHs variations, their interaction, and how they influence root response outcomes. [ABSTRACT FROM AUTHOR]

Phosphate (Pi) stress is an important environmental factor that limits plant growth and development. Of various posttranslational modifications (PTMs), protein phosphorylation and succinylation are the two most important PTMs that regulate multiple biological processes in response to Pi stress. However, these PTMs have been investigated individually but their interactions with proteins in response to Pi stress remain poorly understood. In this study, to elucidate the underlying mechanisms of protein phosphorylation and succinylation in response to Pi stress, we performed a global analysis of the barley root phosphorylome and succinylome in Pi starvation and recovery stages, respectively. A total of 3,634 and 884 unique phosphorylated and succinylated proteins, respectively, corresponding to 11,538 and 2,840 phospho- and succinyl-sites, were identified; of these, 275 proteins were found to be simultaneously phosphorylated and succinylated. Gene Set Enrichment Analysis was performed with a Kyoto Encyclopedia of Genes and Genomes pathway database revealing pathways that significantly enriched in the phosphorylome and succinylome. Such pathways, were dynamically regulated by Pi starvation and recovery treatments, and could be partitioned into distinct metabolic processes. In particular, phosphorylated proteins related to purine, the mitogen-activated protein kinase (MAPK) signaling pathway, pyrimidine, and ATP-binding cassette (ABC) transporters were upregulated in both Pi deprivation and recovery stages. Succinylated proteins, significantly upregulated by both Pi starvation and recovery, were enriched in nitrogen metabolism and phenylpropanoid biosynthesis. Meanwhile, succinylated proteins that were significantly downregulated by both Pi starvation and recovery were enriched in lysine degradation and tryptophan metabolism. This highlighted the importance of these metabolic pathways in regulating Pi homeostasis. Furthermore, protein-protein interaction network analyses showed that the response of central metabolic pathways to Pi starvation and recovery was significantly modulated by phosphorylation or succinylation, both individually and together. In addition, we discovered relevant proteins involved in MAPK signaling and phenylpropanoid biosynthetic pathways existing in interactions between phosphorylated and succinylated proteins in response to Pi recovery. The current study not only provides a comprehensive analysis of phosphorylated and succinylated proteins in plant responses to Pi starvation and recovery, but also reveals detailed interactions between phosphorylated and succinylated proteins in barley roots. [ABSTRACT FROM AUTHOR]

Numerous papers studied the relations between nitrogen rate and rice yield in saline soils, whereas the rice root morphological and physiological characteristics mediating nitrogen rates in yield formation under varied salinity levels remain less concerns. Through a field experiment applied with five nitrogen rates (0, 210, 255, 300, 345, and 390 kg ha-1) in saline land, we found that rice yield peaked at 7.7 t ha-1 under 300 kg ha-1 nitrogen, and excessive N was not conductive for increasing yield. To further elucidate its internal physiological mechanism, a pot experiment was designed with three N rates (210 [N1], 300 [N2], 390 [N3] kg ha-1) and three salt concentrations (0 [S0], 1.5 [S1], 3.0 [S2] g kg-1 NaCl). Results showed that the average grain yield was decreased by 19.1 and 51.1% under S1 and S2, respectively, while notably increased by 18.5 and 14.5% under N2 and N3, respectively. Salinity stress significantly inhibited root biomass, root length and surface area, root oxidation capacity (ROC), K+ and K+/Na+ ratio, and nitrogen metabolism-related enzyme activities, whereas root Na+ and antioxidant enzyme activities were notably increased. The mechanism of how insufficient N supply (N1) affected rice yield formation was consistent at different salinity levels, which displayed adverse impacts on root morphological and physiological traits, thereby significantly inhibiting leaf photosynthesis and grain yield of rice. However, the mechanism thorough which excessive N (N3) affected yield formation was quite different under varied salinity levels. Under lower salinity (S0 and S1), no significant differences on root morphological traits and grain yield were observed except the significantly decline in activities of NR and GS between N3 and N2 treatments. Under higher salinity level (S2), the decreased ROC, K+/Na+ ratio due to increased Na+, antioxidant enzyme activities, and NR and GS activities were the main reason leading to undesirable root morphological traits and leaf photosynthesis, which further triggered decreased grain yield under N3 treatment, compared to that under N2 treatment. Overall, our results suggest that improved physiological and morphological traits of root synergistically enhanced salinity tolerance in rice under appropriate nitrogen application rate. [ABSTRACT FROM AUTHOR]

The Arabidopsis ABC transporter ABCG11 transports lipidic precursors of surface coating polymers at the plasma membrane of epidermal cells. Mutants in ABCG11 exhibit severe developmental defects, suggesting that ABCG11 might also participate in phytohormone-mediated development. Here, we report that ABCG11 is involved in cytokinin-mediated development. The roots of abcg11 mutant seedlings failed to respond to cytokinins and accumulated more cytokinins than wild-type roots. When grown under short-day conditions, abcg11 exhibited longer roots and shorter hypocotyls compared to wild type, similar to abcg14, a knockout mutant in a cytokinin transporter. Treatment with exogenous trans-zeatin, which inhibits primary root elongation in the wild type, enhanced abcg11 primary root elongation. It also increased the expression of cytokinin-responsive Arabidopsis response regulator (ARR) genes, and the signal of the TCS::GFP reporter in abcg11 roots compared to wild-type roots, suggesting that cytokinin signaling was enhanced in abcg11 roots. When we treated only the roots of abcg11 with trans-zeatin, their shoots showed lower ARR induction than the wild type. The abcg14 abcg11 double mutant did not have additional root phenotypes compared to abcg11. Together, these results suggest that ABCG11 is necessary for normal cytokinin-mediated root development, likely because it contributes to cytokinin transport, either directly or indirectly. [ABSTRACT FROM AUTHOR]

Water and land resources have been aggressively exploited in the recent decades to meet the growing demands for food. The changing climate has prompted rice scientists and farmers of the tropics and subtropics to adopt the direct seeded rice (DSR) system. DSR system of rice cultivation significantly reduces freshwater consumption and labor requirements, while increasing system productivity, resource use efficiency, and reducing greenhouse gas emissions. Early root vigor is an essential trait required in an ideal DSR system of rice cultivation to ensure a good crop stand, adequate uptake of water, nutrients and compete with weeds. The aus subpopulation which is adapted for DSR was evaluated to understand the biology of early root growth under limited nitrogen conditions over two seasons under two-time points (14 and 28 days). The correlation study identified a positive association between shoot dry weight and root dry weight. The genome-wide association study was conducted on root traits of 14 and 28 days with 2 million single-nucleotide polymorphisms (SNPs) using an efficient mixed model. QTLs over a significant threshold of p < 0.0001 and a 10% false discovery rate were selected to identify genes involved in root growth related to root architecture and nutrient acquisition from 97 QTLs. Candidate genes under these QTLs were explored. On chromosome 4, around 30 Mbp are two important peptide transporters (PTR5 and PTR6) involved in mobilizing nitrogen in the root during the early vegetative stage. In addition, several P transporters and expansin genes with superior haplotypes are discussed. A novel QTL from 21.12 to 21.46 Mb on chromosome 7 with two linkage disequilibrium (LD) blocks governing root length at 14 days were identified. The QTLs/candidate genes with superior haplotype for early root vigor reported here could be explored further to develop genotypes for DSR conditions. [ABSTRACT FROM AUTHOR]

Understanding the mechanism of crop response to nitrogen (N) deficiency is very important for developing sustainable agriculture. In addition, it is unclear if the microRNA-mediated mechanism related to root growth complies with a common mechanism in monocots and dicots under N deficiency. Therefore, the root morpho-physiological characteristics and microRNA-mediated mechanisms were studied under N deficiency in wheat (Triticum aestivum L.) and cotton (Gossypium hirsutum L.). For both crops, shoot dry weight, plant dry weight and total leaf area as well as some physiological traits, i.e., the oxygen consuming rate in leaf and root, the performance index based on light energy absorption were significantly decreased after 8 days of N deficiency. Although N deficiency did not significantly impact the root biomass, an obvious change on the root morphological traits was observed in both wheat and cotton. After 8 days of treatment with N deficiency, the total root length, root surface area, root volume of both crops showed an opposite trend with significantly decreasing in wheat but significantly increasing in cotton, while the lateral root density was significantly increased in wheat but significantly decreased in cotton. At the same time, the seminal root length in wheat and the primary root length in cotton were increased after 8 days of N deficiency treatment. Additionally, the two crops had different root regulatory mechanisms of microRNAs (miRNAs) to N deficiency. In wheat, the expressions of miR167, miR319, miR390, miR827, miR847, and miR165/166 were induced by N treatment; these miRNAs inhibited the total root growth but promoted the seminal roots growth and lateral root formation to tolerate N deficiency. In cotton, the expressions of miR156, miR167, miR171, miR172, miR390, miR396 were induced and the expressions of miR162 and miR393 were inhibited; which contributed to increasing in the total root length and primary root growth and to decreasing in the lateral root formation to adapt the N deficiency. In conclusion, N deficiency significantly affected the morpho-physiological characteristics of roots that were regulated by miRNAs, but the miRNA-mediated mechanisms were different in wheat and cotton. [ABSTRACT FROM AUTHOR]

Calcium-dependent protein kinases (CPK) are key components of a wide array of signaling pathways, translating stress and nutrient signaling into the modulation of cellular processes such as ion transport and transcription. However, not much is known about CPKs in endomembrane trafficking. Here, we screened for CPKs that impact on root growth and gravitropism, by overexpressing constitutively active forms of CPKs under the control of an inducible promoter in Arabidopsis thaliana. We found that inducible overexpression of an constitutive active CPK30 (CA-CPK30) resulted in a loss of root gravitropism and ectopic auxin accumulation in the root tip. Immunolocalization revealed that CA-CPK30 roots have reduced PIN protein levels, PIN1 polarity defects and impaired Brefeldin A (BFA)-sensitive trafficking. Moreover, FM4-64 uptake was reduced, indicative of a defect in endocytosis. The effects on BFA-sensitive trafficking were not specific to PINs, as BFA could not induce aggregation of ARF1- and CHC-labeled endosomes in CA-CPK30. Interestingly, the interference with BFA-body formation, could be reverted by increasing the extracellular pH, indicating a pH-dependence of this CA-CPK30 effect. Altogether, our data reveal an important role for CPK30 in root growth regulation and endomembrane trafficking in Arabidopsis thaliana. [ABSTRACT FROM AUTHOR]

Plant nutrition, growth, and response to environmental stresses are pH-dependent processes that are regulated at the apoplastic and subcellular levels. The root apoplastic pH is especially sensitive to external cues and can also be modified by intracellular inputs, such as hormonal signaling. Optimal crosstalk of the mechanisms involved in the extent and span of the apoplast pH fluctuations promotes plant resilience to detrimental biotic and abiotic factors. The fact that variations in local pHs are a standard mechanism in different signaling pathways indicates that the pH itself can be the pivotal element to provide a physiological context to plant cell regions, allowing a proportional reaction to different situations. This review brings a collective vision of the causes that initiate root apoplastic pHs variations, their interaction, and how they influence root response outcomes.

Water and land resources have been aggressively exploited in the recent decades to meet the growing demands for food. The changing climate has prompted rice scientists and farmers of the tropics and subtropics to adopt the direct seeded rice (DSR) system. DSR system of rice cultivation significantly reduces freshwater consumption and labor requirements, while increasing system productivity, resource use efficiency, and reducing greenhouse gas emissions. Early root vigor is an essential trait required in an ideal DSR system of rice cultivation to ensure a good crop stand, adequate uptake of water, nutrients and compete with weeds. The aus subpopulation which is adapted for DSR was evaluated to understand the biology of early root growth under limited nitrogen conditions over two seasons under two-time points (14 and 28 days). The correlation study identified a positive association between shoot dry weight and root dry weight. The genome-wide association study was conducted on root traits of 14 and 28 days with 2 million single-nucleotide polymorphisms (SNPs) using an efficient mixed model. QTLs over a significant threshold of p < 0.0001 and a 10% false discovery rate were selected to identify genes involved in root growth related to root architecture and nutrient acquisition from 97 QTLs. Candidate genes under these QTLs were explored. On chromosome 4, around 30 Mbp are two important peptide transporters (PTR5 and PTR6) involved in mobilizing nitrogen in the root during the early vegetative stage. In addition, several P transporters and expansin genes with superior haplotypes are discussed. A novel QTL from 21.12 to 21.46 Mb on chromosome 7 with two linkage disequilibrium (LD) blocks governing root length at 14 days were identified. The QTLs/candidate genes with superior haplotype for early root vigor reported here could be explored further to develop genotypes for DSR conditions.

Understanding the mechanism of crop response to nitrogen (N) deficiency is very important for developing sustainable agriculture. In addition, it is unclear if the microRNA-mediated mechanism related to root growth complies with a common mechanism in monocots and dicots under N deficiency. Therefore, the root morpho-physiological characteristics and microRNA-mediated mechanisms were studied under N deficiency in wheat (Triticum aestivum L.) and cotton (Gossypium hirsutum L.). For both crops, shoot dry weight, plant dry weight and total leaf area as well as some physiological traits, i.e., the oxygen consuming rate in leaf and root, the performance index based on light energy absorption were significantly decreased after 8 days of N deficiency. Although N deficiency did not significantly impact the root biomass, an obvious change on the root morphological traits was observed in both wheat and cotton. After 8 days of treatment with N deficiency, the total root length, root surface area, root volume of both crops showed an opposite trend with significantly decreasing in wheat but significantly increasing in cotton, while the lateral root density was significantly increased in wheat but significantly decreased in cotton. At the same time, the seminal root length in wheat and the primary root length in cotton were increased after 8 days of N deficiency treatment. Additionally, the two crops had different root regulatory mechanisms of microRNAs (miRNAs) to N deficiency. In wheat, the expressions of miR167, miR319, miR390, miR827, miR847, and miR165/166 were induced by N treatment; these miRNAs inhibited the total root growth but promoted the seminal roots growth and lateral root formation to tolerate N deficiency. In cotton, the expressions of miR156, miR167, miR171, miR172, miR390, miR396 were induced and the expressions of miR162 and miR393 were inhibited; which contributed to increasing in the total root length and primary root growth and to decreasing in the lateral root formation to adapt the N deficiency. In conclusion, N deficiency significantly affected the morpho-physiological characteristics of roots that were regulated by miRNAs, but the miRNA-mediated mechanisms were different in wheat and cotton.

Calcium-dependent protein kinases (CPK) are key components of a wide array of signaling pathways, translating stress and nutrient signaling into the modulation of cellular processes such as ion transport and transcription. However, not much is known about CPKs in endomembrane trafficking. Here, we screened for CPKs that impact on root growth and gravitropism, by overexpressing constitutively active forms of CPKs under the control of an inducible promoter in Arabidopsis thaliana. We found that inducible overexpression of an constitutive active CPK30 (CA-CPK30) resulted in a loss of root gravitropism and ectopic auxin accumulation in the root tip. Immunolocalization revealed that CA-CPK30 roots have reduced PIN protein levels, PIN1 polarity defects and impaired Brefeldin A (BFA)-sensitive trafficking. Moreover, FM4-64 uptake was reduced, indicative of a defect in endocytosis. The effects on BFA-sensitive trafficking were not specific to PINs, as BFA could not induce aggregation of ARF1- and CHC-labeled endosomes in CA-CPK30. Interestingly, the interference with BFA-body formation, could be reverted by increasing the extracellular pH, indicating a pH-dependence of this CA-CPK30 effect. Altogether, our data reveal an important role for CPK30 in root growth regulation and endomembrane trafficking in Arabidopsis thaliana.

The plant nutrient acquisition strategies are diverse, such as root nutrient acquisition and leaf nutrient resorption, playing important roles in driving soil processes, vegetation performance as well as ecosystem nutrient cycling. However, it is still in a debate whether there is a synergy or tradeoff between above- and below-ground nutrient acquisition strategy under nitrogen (N) and phosphorus (P) addition, or with stand age. Herein, this study investigated the responses of root-soil accumulation factor (RSAF) and leaf nutrient resorption efficiency (NuRE) to long-term N and P fertilization, and further explored the trade-off between them in Metasequoia glyptostroboides plantations with different stand age. Results showed that under N fertilization in young plantations, leaf N resorption efficiency (NRE) increased, and root-soil accumulation factor for P (RSAF-P) decreased. For young forests under P fertilization, the NRE increased whereas RSAF-P decreased. For middle-aged forests under P fertilization, the NRE and leaf P resorption efficiency (PRE) increased and the RSAF-P decreased. Under P fertilization in young and middle-aged plantations, PRE had a significant positive correlation with RSAF-P. Under N fertilization in young plantations, NRE was significantly positive correlated with root-soil accumulation factor for N (RSAF-N). The covariance-based structural equation modeling (CB-SEM) analysis indicated that stand age had positive effects on PRE whether under N or P fertilization, as well as on RSAF-P under N fertilization, whereas had no effects on the NRE or RSAF-N. Overall, our results can shed light on the nutrient acquisition strategies of M. glyptostroboides plantations under future environmental changes and the results could be applied to the nutrient management practices. [ABSTRACT FROM AUTHOR]