Transcriptome analysis reveals candidate genes related to phosphorus starvation tolerance in sorghum

Low phosphorus impact on Moso bamboo (Phyllostachys edulis) root morphological polymorphism and expression pattern of the related genes

Moso bamboo typically grows in phosphorus (P)-deficient soil that limits its growth and development. In this study, 10 Moso bamboo genotypes (Ph-1 to Ph-10) were evaluated for their responses to P deficiency during the seedling stage by growing them in both P-sufficient and P-deficient conditions. Adaptive responses to low P (LP) conditions were observed in the majority of genotypes. Under P deficiency conditions, the total biomass decreased in several genotypes, but at the same time, the root-to-shoot ratio increased. Principal component analysis identified two main comprehensive traits (PC1 and PC2) related to the root volume and surface area and P concentration and accumulation. Based on the analysis, two genotypes (Ph-6 and Ph-10) were identified with significantly different levels of tolerance to P deficiency. The results revealed that the genotype Ph-10 responded to P deficiency by significantly increasing the root surface area and volume, while simultaneously reducing the number of root cortex cells when compared with the genotype Ph-6, which showed the lowest tolerance (intolerant). The genotype Ph-10 exhibited a robust response to external LP conditions, marked by elevated expression levels of PHOSPHATE TRANSPORTERs and SYG1/PHO81/XPR1s. In situ Polymerase Chain Reaction (PCR) analysis also revealed distinct tissue-specific expression patterns of the genes in the roots, particularly highlighting the differences between Ph-6 and Ph-10. The results provide a foundation for elucidating the mechanism of LP tolerance, thus potentially contributing to developing high P-use efficiency in Moso bamboo species.

Current advances in the molecular regulation of abiotic stress tolerance in sorghum via transcriptomic, proteomic, and metabolomic approaches

Sorghum (Sorghum bicolor L. Moench), a monocot C4 crop, is an important staple crop for many countries in arid and semi-arid regions worldwide. Because sorghum has outstanding tolerance and adaptability to a variety of abiotic stresses, including drought, salt, and alkaline, and heavy metal stressors, it is valuable research material for better understanding the molecular mechanisms of stress tolerance in crops and for mining new genes for their genetic improvement of abiotic stress tolerance. Here, we compile recent progress achieved using physiological, transcriptome, proteome, and metabolome approaches; discuss the similarities and differences in how sorghum responds to differing stresses; and summarize the candidate genes involved in the process of responding to and regulating abiotic stresses. More importantly, we exemplify the differences between combined stresses and a single stress, emphasizing the necessity to strengthen future studies regarding the molecular responses and mechanisms of combined abiotic stresses, which has greater practical significance for food security. Our review lays a foundation for future functional studies of stress-tolerance-related genes and provides new insights into the molecular breeding of stress-tolerant sorghum genotypes, as well as listing a catalog of candidate genes for improving the stress tolerance for other key monocot crops, such as maize, rice, and sugarcane.

Transcriptome analysis provides insights into the response of Lotus corniculatus roots to low-phosphorus stress

INTRODUCTION

A lack of soil phosphorus (P) is a principal factor restricting the normal growth of Lotus corniculatus in the karst area of Guizhou Province, China, but the response mechanism of L. corniculatus under low-phosphorus stress remains unclear.

METHODS

Therefore, we treated two selected L. corniculatus lines (low-P-intolerant line 08518 and low-P-tolerant line 01549) from 13 L. corniculatus lines with normal phosphorus (0.5 mmol/L KH₂PO₄, NP) and low phosphorus (0.005 mmol/L KH₂PO₄, LP) concentrations to study changes in morphological, physiological and transcriptome data under low-phosphorus stress.

RESULTS

The low-P-tolerant line 01549 exhibited better performance under low-phosphorus stress. Compared with the NP treatment, all root morphological indicators of the low-P-tolerant line 01549 increased, and those of the low-P-intolerant line 08518 decreased under low-P stress. Compared with the NP treatment, acid phosphatase (ACP), catalase (CAT), superoxide dismutase (SOD), and peroxidase (POD) activities, and the malondialdehyde (MDA), soluble sugar (SS), soluble protein (SP) and proline (Pro) contents of the two L. corniculatus lines increased under low-P stress. A transcriptome analysis of L. corniculatus showed that a total of 656 and 2243 differentially expressed genes (DEGs) were identified in line 01549 and line 08518, respectively. Meanwhile, the main pathways, such as carbohydrate metabolism, acid phosphatases, phosphate transporters and biosynthesis of secondary metabolites, as well as related genes were also screened by performing a KEGG enrichment analysis.

DISCUSSION

The findings provide an essential point of reference for studying the physiological and molecular mechanism of the response to low-P stress in L. corniculatus.

SbPHO2, a conserved Pi starvation signalling gene, is involved in the regulation of the uptake of multiple nutrients in sorghum

Sorghum is one of the five most productive crops worldwide, but its yield is seriously limited by phosphate (Pi) availability. Although inorganic Pi signalling is well studied in Arabidopsis and rice, it remains largely unknown in sorghum. The sorghum sbpho2 mutant was identified, showing leaf necrosis and short roots. Map-based cloning identified SbPHO2 as Sobic.009G228100, an E2 conjugase gene that is a putative orthologue of the PHO2 genes in rice and Arabidopsis, which play important roles in Pi signalling. Pi starvation experiments and transformation of SbPHO2 into the rice ospho2 mutant further revealed that SbPHO2 is likely involved in Pi accumulation and root architecture alteration in sorghum. qRTPCR results showed that SbPHO2 was expressed in almost the entire plant, especially in the leaves. Furthermore, some typical Pi starvation-induced genes were induced in sbpho2 even under Pi-sufficient conditions, including Pi transporters, SPXs, phosphatases and lipid composition alteration-related genes. In addition to P accumulation in the shoots of sbpho2, concentrations of N, K, and other metal elements were also altered significantly in the sbpho2 plants. Nitrate uptake was also suppressed in the sbpho2 mutant. Consistent with this finding, the expression of several nitrate-, potassium- and other metal element-related genes was also altered in sbpho2. Furthermore, the results indicated that N-dependent control of the P starvation response is regulated via SbPHO2 in sorghum. Our results suggest that SbPHO2 participates in the regulation of the absorption of multiple nutrients, although PHO2 is a crucial and conserved component of Pi starvation signalling.

Global transcriptomic analysis reveals candidate genes associated with different phosphorus acquisition strategies among soybean varieties

Introduction

Soybean adapts to phosphorus-deficient soils through three important phosphorus acquisition strategies, namely altered root conformation, exudation of carboxylic acids, and symbiosis with clumping mycorrhizal fungi. However, the trade-offs and regulatory mechanisms of these three phosphorus acquisition strategies in soybean have not been researched.

Methods

In this study, we investigated the responses of ten different soybean varieties to low soil phosphorus availability by determining biomass, phosphorus accumulation, root morphology, exudation, and mycorrhizal colonization rate. Furthermore, the molecular regulatory mechanisms underlying root phosphorus acquisition strategies were examined among varieties with different low-phosphorus tolerance using transcriptome sequencing and weighted gene co-expression network analysis.

Results and discussion

The results showed that two types of phosphorus acquisition strategies-"outsourcing" and "do-it-yourself"-were employed by soybean varieties under low phosphorus availability. The "do-it-yourself" varieties, represented by QD11, Zh30, and Sd, obtained sufficient phosphorus by increasing their root surface area and secreting carboxylic acids. In contrast, the "outsourcing" varieties, represented by Zh301, Zh13, and Hc6, used increased symbiosis with mycorrhizae to obtain phosphorus owing to their large root diameters. Transcriptome analysis showed that the direction of acetyl-CoA metabolism could be the dividing line between the two strategies of soybean selection. ERF1 and WRKY1 may be involved in the regulation of phosphorus acquisition strategies for soybeans grown under low P environments. These findings will enhance our understanding of phosphorus acquisition strategies in soybeans. In addition, they will facilitate the development of breeding strategies that are more flexible to accommodate a variety of production scenarios in agriculture under low phosphorus environments.

Systematic Identification and Expression Analysis of the Sorghum Pht1 Gene Family Reveals Several New Members Encoding High-Affinity Phosphate Transporters

Sorghum (Sorghum bicolor) is known to have a more robust capability of phosphorus uptake than many other cereal plants, which could be attributed to its phosphate transporter 1 (Pht1) that has a high phosphorus affinity. There are eleven SbPht1 genes in the sorghum genome, nine of which are expressed in sorghum roots or shoots in response to phosphorus deficiency (low-P). The molecular features of these nine genes were investigated by gene expression analysis, subcellular localization, and a yeast mutant complementation growth assay. They were found to be induced in response to low-P stress in root or shoot. All these SbPht1 proteins were found to be localized on the cell membrane, and SbPht1;8 was also detected in the endoplasmic reticulum. These SbPht1s were able to complement the yeast mutant EY917 that lacks all the functional phosphate transporters, and, among them, SbPht1;5, SbPht1;6 and SbPht1;8 could partially complement the yeast mutant strain EY917 in low-P conditions. Overall, these findings demonstrate that SbPht1;5, SbPht1;6, and SbPht1;8 are high-affinity phosphate transporters. SbPht1;5, in particular, is specifically involved in phosphorus uptake in the roots, whilst SbPht1;6 and SbPht1;8 are key players in both P uptake and P transport in response to low-P stress in sorghum.

Transcriptome Analysis Reveals Contrasting Plant Responses of Sorghum bicolor upon Colonization by Two Formae Speciales of Sporisorium reilianum

The biotrophic fungus Sporisorium reilianum exists in two host-adapted formae speciales that cause head smut in maize (S. reilianum f. sp. zeae; SRZ) and sorghum (S. reilianum f. sp. reilianum; SRS). In sorghum, the spread of SRZ is limited to the leaves. To understand the plant responses to each forma specialis, we determined the transcriptome of sorghum leaves inoculated either with SRS or SRZ. Fungal inoculation led to gene expression rather than suppression in sorghum. SRZ induced a much greater number of genes than SRS. Each forma specialis induced a distinct set of plant genes. The SRZ-induced genes were involved in plant defense mainly at the plasma membrane and were associated with the Molecular Function Gene Ontology terms chitin binding, abscisic acid binding, protein phosphatase inhibitor activity, terpene synthase activity, chitinase activity, transmembrane transporter activity and signaling receptor activity. Specifically, we found an upregulation of the genes involved in phospholipid degradation and sphingolipid biosynthesis, suggesting that the lipid content of the plant plasma membrane may contribute to preventing the systemic spread of SRZ. In contrast, the colonization of sorghum with SRS increased the expression of the genes involved in the detoxification of cellular oxidants and in the unfolded protein response at the endoplasmic reticulum, as well as of the genes modifying the cuticle wax and lipid composition through the generation of alkanes and phytosterols. These results identified plant compartments that may have a function in resistance against SRZ (plasma membrane) and susceptibility towards SRS (endoplasmic reticulum) that need more attention in the future.

Transcriptome analysis of a near-isogenic line and its recurrent parent reveals the role of Pup1 QTL in phosphorus deficiency tolerance of rice at tillering stage

Phosphorus (P) is essential for cellular processes like respiration, photosynthesis, biosynthesis of membrane phospholipids, etc. To cope with P deficiency stress, plants adopt reprograming of the expression of genes involved in different metabolic/signaling pathways for survival, growth, and development. Plants use transcriptional, post-transcriptional, and/or post-translational machinery to achieve P homeostasis. Several transcription factors (TFs), miRNAs, and P transporters play important roles in P deficiency tolerance; however, the underlying mechanisms responsible for P deficiency tolerance remain poorly understood. Studies on P starvation/deficiency responses in plants at early (seedling) stage of growth have been reported but only a few of them focused on molecular responses of the plant at advanced (tillering or reproductive) stage of growth. To decipher the strategies adopted by rice at tillering stage under P deficiency stress, a pair of contrasting genotypes [Pusa-44 (a high-yielding, P deficiency sensitive cultivar) and its near-isogenic line (NIL-23, P deficiency tolerant) for Pup1 QTL] was used for morphophysiological, biochemical, and molecular analyses. Comparative analyses of shoot and root tissues from 45-day-old plants grown hydroponically under P sufficient (16 ppm) or P deficient (4 ppm) medium confirmed some of the known morphophysiological responses. Moreover, RNA-seq analysis revealed the important roles of phosphate transporters, TFs, auxin-responsive proteins, modulation in the cell wall, fatty acid metabolism, and chromatin architecture/epigenetic modifications in providing P deficiency tolerance to NIL-23, which were brought in due to the introgression of the Pup1 QTL in Pusa-44. This study provides insights into the molecular functions of Pup1 for P deficiency tolerance, which might be utilized to improve P-use efficiency of rice for better productivity in P deficient soils. KEY MESSAGE: Introgression of Pup1 QTL in high-yielding rice cultivar modulates mainly phosphate transporters, TFs, auxin-responsive proteins, cell wall structure, fatty acid metabolism, and chromatin architecture/epigenetic modifications at tillering stage of growth under phosphorus deficiency stress.

Remodeling and protecting the membrane system to resist phosphorus deficiency in wild soybean (Glycine soja) seedling leaves

MAIN CONCLUSION

The poor-soil-tolerant wild soybean resist phosphorus deficiency by remodeling membrane lipids to reuse phosphorus. The plants synthesize phenolic acids and flavonoids to remove reactive oxygen species and protect membrane stability. Poor soil largely limits plant yields, and the development and utilization of high-quality wild plant resources is an effective approach to resolving this problem. Two ecotypes of wild soybean were used as experimental materials in this experiment. We integrated metabolomics and transcriptomics to determine whether wild soybean (Glycine soja) could resist phosphorus deficiency by remodeling and protecting its membrane system. Under phosphorus-deficient conditions, the plant height and aboveground fresh and dry weight of poor-soil-tolerant wild soybean seedlings were less inhibited than those in common wild soybean. In poor-soil-tolerant wild soybean seedling leaves, the glycerol-3-phosphate content decreased significantly, while caffeic acid, ferulic acid, shikimic acid, phenylalanine, tyrosine, and tryptophan increased significantly. β-Glucosidase and chalcone synthase genes and those that encode SQD2, a crucial enzyme in thiolipid biosynthesis, were specifically up-regulated, whereas the glucosyltransferase UGT74B1 gene was down-regulated. The poor-soil-tolerant wild soybean enhanced glycerolipid metabolism to decompose phospholipids and release phosphorus for reuse to improve resistance to phosphorus deficiency. The plants synthesized thiolipids to replace phospholipids and maintain membrane structure integrity and inhibited glucosinolate biosynthesis to promote phenylpropanoid biosynthesis, leading to the production of phenolic acids and flavonoids that removed reactive oxygen species and protected membrane system stability. The experiments evaluated and provided insight into the innovative utilization of wild soybean germplasm resources.

Integrative analysis of the metabolome and transcriptome reveal the phosphate deficiency response pathways of alfalfa

Understanding the mechanisms underlying the responses to inorganic phosphate (Pi) deficiency in alfalfa will help enhance Pi acquisition efficiency and the sustainable use of phosphorous resources. Integrated global metabolomic and transcriptomic analyses of mid-vegetative alfalfa seedlings under 12-day Pi deficiency were conducted. Limited seedling growth were found, including 13.24%, 16.85% and 33.36% decreases in height, root length and photosynthesis, and a 24.10% increase in root-to-shoot ratio on day 12. A total of 322 and 448 differentially abundant metabolites and 1199 and 1061 differentially expressed genes were identified in roots and shoots. Increased (>3.68-fold) inorganic phosphate transporter 1;4 and SPX proteins levels in the roots (>2.15-fold) and shoots (>2.50-fold) were related to Pi absorption and translocation. The levels of phospholipids and Pi-binding carbohydrates and nucleosides were decreased, while those of phosphatases and pyrophosphatases in whole seedlings were induced under reduced Pi. In addition, nitrogen assimilation was affected by inhibiting high-affinity nitrate transporters (NRT2.1 and NRT3.1), and nitrate reductase. Increased delphinidin-3-glucoside might contribute to the gray-green leaves induced by Pi limitation. Stress-induced MYB, WRKY and ERF transcription factors were identified. The responses of alfalfa to Pi deficiency were summarized as local systemic signaling pathways, including root growth, stress-related responses consisting of enzymatic and nonenzymatic systems, and hormone signaling and systemic signaling pathways including Pi recycling and Pi sensing in the whole plant, as well as Pi recovery, and nitrate and metal absorption in the roots. This study provides important information on the molecular mechanism of the response to Pi deficiency in alfalfa.

Starve to Sustain-An Ancient Syrian Landrace of Sorghum as Tool for Phosphorous Bio-Economy?

Phosphorus (P) is an essential macronutrient, playing a role in developmental and metabolic processes in plants. To understand the local and systemic responses of sorghum to inorganic phosphorus (P_i) starvation and the potential of straw and ash for reutilisation in agriculture, we compared two grain (Razinieh) and sweet (Della) sorghum varieties with respect to their morpho-physiological and molecular responses. We found that P_i starvation increased the elongation of primary roots, the formation of lateral roots, and the accumulation of anthocyanin. In Razinieh, lateral roots were promoted to a higher extent, correlated with a higher expression of SbPht1 phosphate transporters. Infrared spectra of straw from mature plants raised to maturity showed two prominent bands at 1371 and 2337 cm⁻¹, which could be assigned to P-H(H₂) stretching vibration in phosphine acid and phosphinothious acid, and their derivates, whose abundance correlated with phosphate uptake of the source plant and genotype (with a higher intensity in Razinieh). The ash generated from these straws stimulated the shoot elongation and root development of the rice seedlings, especially for the material derived from Razinieh raised under P_i starvation. In conclusion, sorghum growing on marginal lands has potential as a bio-economy alternative for mineral phosphorus recycling.

Gm6PGDH1, a Cytosolic 6-Phosphogluconate Dehydrogenase, Enhanced Tolerance to Phosphate Starvation by Improving Root System Development and Modifying the Antioxidant System in Soybean

Phosphorus plays an important role in plant growth and development, and is an important limiting factor for crop yield. Although previous studies have shown that 6-phosphogluconate dehydrogenase (6PGDH) plays an important role in plant resistance to adversity, its response to low phosphorus (P) stress remains unknown. In this study, we reported the cloning and characterization of a cytosolic 6PGDH gene, Gm6PGDH1, which enhanced the tolerance to phosphate (Pi) starvation by improving root system development and modifying the antioxidant system in transgenic plants. Gm6PGDH1 was highly expressed in the root at full bloom stage, and strongly induced by Pi starvation. The results from intact soybean composite plant and soybean plant, both containing a Gm6PGDH1-overexpressing construct, showed that Gm6PGDH1 was involved in root system development, and subsequently affected P uptake under Pi-deficient conditions. Meanwhile, the accumulation of reactive oxygen species (ROS) in the root tip of transgenic soybean was reduced, and the activity of ROS-scavenging enzymes was enhanced compared with those of the wild type under Pi-deficient conditions. Interestingly, we found that the overexpression of Gm6PGDH1 weakened the response of several other important Pi-answer genes to Pi starvation, such as some purple acid phosphatases (PAPs) and redox-related genes. In addition, the results from a virus-induced gene silencing (VIGS) indicated that Gm6PGDH1 might have functional redundancy in soybean, and the results from a heterogeneous transformation system showed that overexpressing Gm6PGDH1 also enhanced tolerance to Pi starvation in transgenic Arabidopsis. Together, these results suggested the great potential of Gm6PGDH1 in crop breeding for low Pi tolerance.

Sorghum breeding in the genomic era: opportunities and challenges

The importance and potential of the multi-purpose crop sorghum in global food security have not yet been fully exploited, and the integration of the state-of-art genomics and high-throughput technologies into breeding practice is required. Sorghum, a historically vital staple food source and currently the fifth most important major cereal, is emerging as a crop with diverse end-uses as food, feed, fuel and forage and a model for functional genetics and genomics of tropical grasses. Rapid development in high-throughput experimental and data processing technologies has significantly speeded up sorghum genomic researches in the past few years. The genomes of three sorghum lines are available, thousands of genetic stocks accessible and various genetic populations, including NAM, MAGIC, and mutagenised populations released. Functional and comparative genomics have elucidated key genetic loci and genes controlling agronomical and adaptive traits. However, the knowledge gained has far away from being translated into real breeding practices. We argue that the way forward is to take a genome-based approach for tailored designing of sorghum as a multi-functional crop combining excellent agricultural traits for various end uses. In this review, we update the new concepts and innovation systems in crop breeding and summarise recent advances in sorghum genomic researches, especially the genome-wide dissection of variations in genes and alleles for agronomically important traits. Future directions and opportunities for sorghum breeding are highlighted to stimulate discussion amongst sorghum academic and industrial communities.

Characterization of contrasting rice (Oryza sativa L.) genotypes reveals the Pi-efficient schema for phosphate starvation tolerance

BACKGROUND

Phosphorus (P), being one of the essential components of nucleic acids, cell membranes and enzymes, indispensable for diverse cellular processes like photosynthesis/carbohydrate metabolism, energy production, redox homeostasis and signaling. Crop yield is severely affected due to Phosphate (Pi) deficiency; and to cope with Pi-deficiency, plants have evolved several strategies. Some rice genotypes are compatible with low Pi availability, whereas others are sensitive to Pi deficiency. However, the underlying molecular mechanism for low Pi tolerance remains largely unexplored.

RESULT

Several studies were carried out to understand Pi-deficiency responses in rice at seedling stage, but few of them targeted molecular aspects/responses of Pi-starvation at the advanced stage of growth. To delineate the molecular mechanisms for low Pi tolerance, a pair of contrasting rice (Oryza sativa L.) genotypes [viz. Pusa-44 (Pi-deficiency sensitive) and its near isogenic line (NIL-23, Pi-deficiency tolerant) harboring Phosphorus uptake 1 (Pup1) QTL from an aus landrace Kasalath] were used. Comparative morphological, physiological, and biochemical analyses confirmed some of the well-known findings. Transcriptome analysis of shoot and root tissues from 45-day-old rice plants grown hydroponically under P-sufficient (16 ppm Pi) or P-starved (0 ppm Pi) medium revealed that Pi-starvation stress causes global transcriptional reprogramming affecting several transcription factors, signaling pathways and other regulatory genes. We could identify several significantly up-regulated genes in roots of NIL-23 under Pi-starvation which might be responsible for the Pi starvation tolerance. Pathway enrichment analysis indicated significant role of certain phosphatases, transporters, transcription factors, carbohydrate metabolism, hormone-signaling, and epigenetic processes in improving P-starvation stress tolerance in NIL-23.

CONCLUSION

We report the important candidate mechanisms for Pi acquisition/solubilization, recycling, remobilization/transport, sensing/signalling, genetic/epigenetic regulation, and cell wall structural changes to be responsible for P-starvation tolerance in NIL-23. The study provides some of the novel information useful for improving phosphorus-use efficiency in rice cultivars.

Comparative transcriptome analysis reveals novel insights into transcriptional responses to phosphorus starvation in oil palm (Elaeis guineensis) root

BACKGROUND

Phosphorus (P), in its orthophosphate form (Pi) is an essential macronutrient for oil palm early growth development in which Pi deficiency could later on be reflected in lower biomass production. Application of phosphate rock, a non-renewable resource has been the common practice to increase Pi accessibility and maintain crop productivity in Malaysia. However, high fixation rate of Pi in the native acidic tropical soils has led to excessive utilization of P fertilizers. This has caused serious environmental pollutions and cost increment. Even so, the Pi deficiency response mechanism in oil palm as one of the basic prerequisites for crop improvement remains largely unknown.

RESULTS

Using total RNA extracted from young roots as template, we performed a comparative transcriptome analysis on oil palm responding to 14d and 28d of Pi deprivation treatment and under adequate Pi supply. By using Illumina HiSeq4000 platform, RNA-Seq analysis was successfully conducted on 12 paired-end RNA-Seq libraries and generated more than 1.2 billion of clean reads in total. Transcript abundance estimated by fragments per kilobase per million fragments (FPKM) and differential expression analysis revealed 36 and 252 genes that are differentially regulated in Pi-starved roots at 14d and 28d, respectively. Genes possibly involved in regulating Pi homeostasis, nutrient uptake and transport, hormonal signaling and gene transcription were found among the differentially expressed genes.

CONCLUSIONS

Our results showed that the molecular response mechanism underlying Pi starvation in oil palm is complexed and involved multilevel regulation of various sensing and signaling components. This contribution would generate valuable genomic resources in the effort to develop oil palm planting materials that possess Pi-use efficient trait through molecular manipulation and breeding programs.

Response of Soybean Root to Phosphorus Deficiency under Sucrose Feeding: Insight from Morphological and Metabolome Characterizations

Phosphorus (P) is one the least available essential plant macronutrients in soils that is a major constraint on plant growth. Soybean (Glycine max L.) production is often limited due to low P availability. The better management of P deficiency requires improvement of soybean's P use efficiency. Sugars are implicated in P starvation responses, and a complete understanding of the role of sucrose together with P in coordinating P starvation responses is missing in soybean. This study explored global metabolomic changes in previously screened low-P-tolerant (Liaodou, L13) and low-P-sensitive (Tiefeng 3, T3) soybean genotypes by liquid chromatography coupled mass spectrometry. We also studied the root morphological response to sucrose application (1%) in P-starved soybean genotypes against normal P supply. Root morphology in L13 genotype has significantly improved P starvation responses as compared to the T3 genotype. Exogenous sucrose application greatly affected root length, root volume, and root surface area in L13 genotype while low-P-sensitive genotype, i.e., T3, only responded by increasing number of lateral roots. Root : shoot ratio increased after sucrose treatment regardless of P conditions, in both genotypes. T3 showed a relatively higher number of differentially accumulated metabolites between P-starved and normal P conditions as compared to L13 genotype. Common metabolites accumulated under the influence of sucrose were 5-O-methylembelin, D-glucuronic acid, and N-acetyl-L-phenylalanine. We have discussed the possible roles of the pathways associated with these metabolites. The differentially accumulated metabolites between both genotypes under the influence of sucrose are also discussed. These results are important to further explore the role of sucrose in the observed pathways. Especially, our results are relevant to formulate strategies for improving P efficiency of soybean genotypes with different P efficiencies.

Phylogenomic Analysis of R2R3 MYB Transcription Factors in Sorghum and their Role in Conditioning Biofuel Syndrome

Background

Large scale cultivation of sorghum for food, feed, and biofuel requires concerted efforts for engineering multipurpose cultivars with optimised agronomic traits. Due to their vital role in regulating the biosynthesis of phenylpropanoid-derived compounds, biomass composition, biotic, and abiotic stress response, R2R3-MYB family transcription factors are ideal targets for improving environmental resilience and economic value of sorghum.

Methods

We used diverse computational biology tools to survey the sorghum genome to identify R2R3-MYB transcription factors followed by their structural and phylogenomic analysis. We used in-house generated as well as publicly available high throughput expression data to analyse the R2R3 expression patterns in various sorghum tissue types.

Results

We have identified a total of 134 R2R3-MYB genes from sorghum and developed a framework to predict gene functions. Collating information from the physical location, duplication, structural analysis, orthologous sequences, phylogeny, and expression patterns revealed the role of duplications in clade-wise expansion of the R2R3-MYB family as well as intra-clade functional diversification. Using publicly available and in-house generated RNA sequencing data, we provide MYB candidates for conditioning biofuel syndrome by engineering phenylpropanoid biosynthesis and sugar signalling pathways in sorghum.

Conclusion

The results presented here are pivotal to prioritize MYB genes for functional validation and optimize agronomic traits in sorghum.

Interaction between Humic Substances and Plant Hormones for Phosphorous Acquisition

Phosphorus (P) deficiency is a major constraint in highly weathered tropical soils. Although phosphorous rock reserves may last for several hundred years, there exists an urgent need to research efficient P management for sustainable agriculture. Plant hormones play an important role in regulating plant growth, development, and reproduction. Humic substances (HS) are not only considered an essential component of soil organic carbon (SOC), but also well known as a biostimulant which can perform phytohormone-like activities to induce nutrient uptake. This review paper presents an overview of the scientific outputs in the relationship between HS and plant hormones. Special attention will be paid to the interaction between HS and plant hormones for nutrient uptake under P-deficient conditions.

Transcriptome Changes Induced by Different Potassium Levels in Banana Roots

Potassium plays an important role in enhancing plant resistance to biological and abiotic stresses and improving fruit quality. To study the effect of potassium nutrient levels on banana root growth and its regulation mechanism, four potassium concentrations were designed to treat banana roots from no potassium to high potassium. The results indicated that K2 (3 mmol/L K2SO4) treatment was a relatively normal potassium concentration for the growth of banana root, and too high or too low potassium concentration was not conducive to the growth of banana root. By comparing the transcriptome data in each treatment in pairs, 4454 differentially expressed genes were obtained. There were obvious differences in gene function enrichment in root systems treated with different concentrations of potassium. Six significant expression profiles (profile 0, 1, 2, 7, 9 and 13) were identified by STEM analysis. The hub genes were FKF1, HsP70-1, NRT1/PTR5, CRY1, and ZIP11 in the profile 0; CYP51 in profile 1; SOS1 in profile 7; THA, LKR/SDH, MCC, C4H, CHI, F3'H, 2 PR1s, BSP, TLP, ICS, RO, chitinase and peroxidase in profile 9. Our results provide a comprehensive and systematic analysis of the gene regulation network in banana roots under different potassium stress.

Plant PHR Transcription Factors: Put on A Map

The phosphate starvation response (PHR) protein family exhibits the MYB and coiled-coil domains. In plants, within the either 5' untranslated regions (UTRs) or promoter regions of phosphate starvation-induced (PSI) genes are characteristic cis-regulatory elements, namely PHR1 binding sequence (P1BS). The most widely studied PHR protein family members, such as AtPHR1 in Arabidopsis thaliana (L.) and OsPHR2 in Oryza sativa (L.), may activate the gene expression of a broad range of PSI genes by binding to such elements in a phosphate (Pi) dependent manner. In Pi signaling, PHR transcription factors (TFs) can be selectively activated or deactivated by other proteins to execute the final step of signal transduction. Several new proteins have been associated with the AtPHR1/OsPHR2 signaling cascade in the last few years. While the PHR TF transcriptional role has been studied intensively, here we highlight the recent findings of upstream molecular components and other signaling pathways that may interfere with the PHR final mode of action in plants. Detailed information about transcriptional regulation of the AtPHR1 gene itself and its upstream molecular events has been reviewed.