OsPTF1, a novel transcription factor involved in tolerance to phosphate starvation in rice

Root Adaptation via Common Genetic Factors Conditioning Tolerance to Multiple Stresses for Crops Cultivated on Acidic Tropical Soils

Crop tolerance to multiple abiotic stresses has long been pursued as a Holy Grail in plant breeding efforts that target crop adaptation to tropical soils. On tropical, acidic soils, aluminum (Al) toxicity, low phosphorus (P) availability and drought stress are the major limitations to yield stability. Molecular breeding based on a small suite of pleiotropic genes, particularly those with moderate to major phenotypic effects, could help circumvent the need for complex breeding designs and large population sizes aimed at selecting transgressive progeny accumulating favorable alleles controlling polygenic traits. The underlying question is twofold: do common tolerance mechanisms to Al toxicity, P deficiency and drought exist? And if they do, will they be useful in a plant breeding program that targets stress-prone environments. The selective environments in tropical regions are such that multiple, co-existing regulatory networks may drive the fixation of either distinctly different or a smaller number of pleiotropic abiotic stress tolerance genes. Recent studies suggest that genes contributing to crop adaptation to acidic soils, such as the major Arabidopsis Al tolerance protein, AtALMT1, which encodes an aluminum-activated root malate transporter, may influence both Al tolerance and P acquisition via changes in root system morphology and architecture. However, trans-acting elements such as transcription factors (TFs) may be the best option for pleiotropic control of multiple abiotic stress genes, due to their small and often multiple binding sequences in the genome. One such example is the C2H2-type zinc finger, AtSTOP1, which is a transcriptional regulator of a number of Arabidopsis Al tolerance genes, including AtMATE and AtALMT1, and has been shown to activate AtALMT1, not only in response to Al but also low soil P. The large WRKY family of transcription factors are also known to affect a broad spectrum of phenotypes, some of which are related to acidic soil abiotic stress responses. Hence, we focus here on signaling proteins such as TFs and protein kinases to identify, from the literature, evidence for unifying regulatory networks controlling Al tolerance, P efficiency and, also possibly drought tolerance. Particular emphasis will be given to modification of root system morphology and architecture, which could be an important physiological "hub" leading to crop adaptation to multiple soil-based abiotic stress factors.

The MYB transcription factor TaPHR3-A1 is involved in phosphate signaling and governs yield-related traits in bread wheat

Improved inorganic phosphate (Pi) use efficiency in crops will be important for sustainable agriculture. Exploring molecular mechanisms that regulate Pi uptake could provide useful information for breeding wheat with improved Pi use efficiency. Here, a TaPHR3-A1 (Gene ID: TraesCS7A02G415800) ortholog of rice OsPHR3 that functions in transcriptional regulation of Pi signaling was cloned from wheat chromosome 7A. Ectopic expression of TaPHR3-A1 in Arabidopsis and rice produced enhanced vegetative growth and more seeds. Overexpression in transgenic rice led to increased biomass, grain number, and primary panicle branching by 61.23, 42.12, and 36.34% compared with the wild type. Transgenic wheat lines with down-regulation of TaPHR3-A1 exhibited retarded growth and root hair development at the seedling stage, and showed yield-related effects at the adult stage when grown in both low- and sufficient Pi conditions, indicating that TaPHR3-A1 positively regulated tolerance to low Pi. Introgression lines further confirmed the effect of TaPHR3-A1 in improving grain number. The Chinese wheat mini core collection and a recombinant inbred line analysis demonstrated that the favorable allele TaPHR3-A1-A associated with higher grain number was positively selected in breeding. A TaPHR3-A1-derived cleaved amplified polymorphic sequence marker effectively identified haplotype TaPHR3-A1-A. Our results suggested that TaPHR3-A1 was a functional regulatory factor for Pi uptake and provided useful information for marker-assisted selection for high yield in wheat.

Systemic induction of phosphatidylinositol-based signaling in leaves of arbuscular mycorrhizal rice plants

Most land plants form beneficial associations with arbuscular mycorrhizal (AM) fungi which improves mineral nutrition, mainly phosphorus, in the host plant in exchange for photosynthetically fixed carbon. Most of our knowledge on the AM symbiosis derives from dicotyledonous species. We show that inoculation with the AM fungus Funneliformis mosseae stimulates growth and increases Pi content in leaves of rice plants (O. sativa, cv Loto, ssp japonica). Although rice is a host for AM fungi, the systemic transcriptional responses to AM inoculation, and molecular mechanisms underlying AM symbiosis in rice remain largely elusive. Transcriptomic analysis identified genes systemically regulated in leaves of mycorrhizal rice plants, including genes with functions associated with the biosynthesis of phospholipids and non-phosphorus lipids (up-regulated and down-regulated, respectively). A coordinated regulation of genes involved in the biosynthesis of phospholipids and inositol polyphosphates, and genes involved in hormone biosynthesis and signaling (jasmonic acid, ethylene) occurs in leaves of mycorrhizal rice. Members of gene families playing a role in phosphate starvation responses and remobilization of Pi were down-regulated in leaves of mycorrhizal rice. These results demonstrated that the AM symbiosis is accompanied by systemic transcriptional responses, which are potentially important to maintain a stable symbiotic relationship in rice plants.

OsCYCP4s coordinate phosphate starvation signaling with cell cycle progression in rice

Phosphate starvation leads to a strong reduction in shoot growth and yield in crops. The reduced shoot growth is caused by extensive gene expression reprogramming triggered by phosphate deficiency, which is not itself a direct consequence of low levels of shoot phosphorus. However, how phosphate starvation inhibits shoot growth in rice is still unclear. In this study, we determined the role of OsCYCP4s in the regulation of shoot growth in response to phosphate starvation in rice. We demonstrate that the expression levels of OsCYCP4s, except OsCYCP4;3, were induced by phosphate starvation. Overexpression of the phosphate starvation induced OsCYCP4s could compete with the other cyclins for the binding with cyclin-dependent kinases, therefore suppressing growth by reducing cell proliferation. The phosphate starvation induced growth inhibition in the loss-of-function mutants cycp4;1, cycp4;2, and cycp4;4 is partially compromised. Furthermore, the expression of some phosphate starvation inducible genes is negatively modulated by these cyclins, which indicates that these OsCYCP4s may also be involved in phosphate starvation signaling. We conclude that phosphate starvation induced OsCYCP4s might coordinate phosphate starvation signaling and cell cycle progression under phosphate starvation stress.

Understanding the heat resistance of cucumber through leaf transcriptomics

Heat stress is a major environmental factor limiting plant productivity and quality in agriculture. Cucumber, one of the most important vegetables among cucurbitaceae, prefers to grow in a warm environment. Until now the molecular knowledge of heat stress in cucumber remained unclear. In this study, we performed transcriptome analysis using two diverse genetic cucumber cultivars, L-9 and A-16 grown under normal and heat stress. L-9 displayed heat-tolerance phenotype with higher superoxide dismutase enzyme (SOD) enzyme activity and lower malondialdehyde (MDA) content than A-16 under heat stress. RNA-sequencing revealed that a total of 963 and 2778 genes are differentially expressed between L-9 and A-16 under normal and heat stress respectively. In addition, we found that differentially expressed genes (DEGs) associated with plant hormones signally pathway, transcription factors, and secondary metabolites showed significantly change in expression level after heat stress, which were confirmed by quantitative real-time PCR assay. Our results not only explored several crucial genes involved in cucumber heat resistance, but also provide a new insight into studying heat stress.

Indel marker analysis of putative stress-related genes reveals genetic diversity and differentiation of rice landraces in peninsular Thailand

Genetic assessment of rice landraces is important for germplasm evaluation and genetic resource utilization. Rice landraces in peninsular Thailand have adapted to unique environmental stresses over time and have great significance as a genetic resource for crop improvement. In this study, rice landraces derived from rice research centers and farmers from different areas of peninsular Thailand were genetically assessed using 16 polymorphic InDel markers from putative stress-related genes. A total of 36 alleles were obtained. The average PIC value was 0.27/marker. The F_ST varied from 0.46 to 1.00. Genetic diversity was observed both within and between populations. AMOVA indicated that genetic variations occurred mainly between populations (70%) rather than within populations (30%). The dendrogram, population structure, and PCoA scatter plot clearly demonstrated the differentiation of the two major groups, i.e., landraces from upland and lowland rice ecosystems. The unique alleles of Indel1922, -2543, -6746, -7447 and -8538, which lie in genes encoding putative WAX2, heavy metal-associated domain-containing protein, GA20ox2, PTF1, and PLETHORA2, respectively, were only found in rice from upland ecosystems. Putative WAX2, GA20ox2, and PLETHORA2 are likely related to drought and salt stress. Our findings demonstrate the diversity of landraces in peninsular Thailand. The preservation of these landraces should be facilitated with effective markers to maintain all variant alleles and to protect the genetic diversity. Indel1922, -2543, -6746, -7447 and -8538 have the potential to differentiate upland rice from lowland rice. Furthermore, Indel1922, -6746 and -8538 might be effective markers for drought and salt tolerance.

Improvement of nutrient use efficiency in rice: current toolbox and future perspectives

Modern agriculture relies heavily on chemical fertilizers, especially in terms of cereal production. The excess application of fertilizers not only increases production cost, but also causes severe environmental problems. As one of the major cereal crops, rice (Oryza sativa L.) provides the staple food for nearly half of population worldwide, especially in developing countries. Therefore, improving rice yield is always the priority for rice breeding. Macronutrients, especially nitrogen (N) and phosphorus (P), are two most important players for the grain yield of rice. However, with economic development and improved living standard, improving nutritional quality such as micronutrient contents in grains has become a new goal in order to solve the "hidden hunger." Micronutrients, such as iron (Fe), zinc (Zn), and selenium (Se), are critical nutritional elements for human health. Therefore, breeding the rice varieties with improved nutrient use efficiency (NUE) is thought to be one of the most feasible ways to increase both grain yield and nutritional quality with limited fertilizer input. In this review, we summarized the progresses in molecular dissection of genes for NUE by reverse genetics on macronutrients (N and P) and micronutrients (Fe, Zn, and Se), exploring natural variations for improving NUE in rice; and also, the current genetic toolbox and future perspectives for improving rice NUE are discussed.

Same same, but different: growth responses of primary and lateral roots

The root system architecture describes the shape and spatial arrangement of roots within the soil. Its spatial distribution depends on growth and branching rates as well as directional organ growth. The embryonic primary root gives rise to lateral (secondary) roots, and the ratio of both root types changes over the life span of a plant. Most studies have focused on the growth of primary roots and the development of lateral root primordia. Comparably less is known about the growth regulation of secondary root organs. Here, we review similarities and differences between primary and lateral root organ growth, and emphasize particularly how external stimuli and internal signals differentially integrate root system growth.

The bHLH family member ZmPTF1 regulates drought tolerance in maize by promoting root development and abscisic acid synthesis

Drought stress is the most important environmental stress limiting maize production. ZmPTF1, a phosphate starvation-induced basic helix-loop-helix (bHLH) transcription factor, contributes to root development and low-phosphate tolerance in maize. Here, ZmPTF1 expression, drought tolerance, and the underlying mechanisms were studied by using maize ZmPTF1 overexpression lines and mutants. ZmPTF1 was found to be a positive regulator of root development, ABA synthesis, signalling pathways, and drought tolerance. ZmPTF1 was also found to bind to the G-box element within the promoter of 9-cis-epoxycarotenoid dioxygenase (NCED), C-repeat-binding factor (CBF4), ATAF2/NAC081, NAC30, and other transcription factors, and to act as a positive regulator of the expression of those genes. The dramatically upregulated NCEDs led to increased abscisic acid (ABA) synthesis and activation of the ABA signalling pathway. The up-regulated transcription factors hierarchically regulate the expression of genes involved in root development, stress responses, and modifications of transcriptional regulation. The improved root system, increased ABA content, and activated ABA-, CBF4-, ATAF2-, and NAC30-mediated stress responses increased the drought tolerance of the ZmPTF1 overexpression lines, while the mutants showed opposite trends. This study describes a useful gene for transgenic breeding and helps us understand the role of a bHLH protein in plant root development and stress responses.

The potential application of genome editing by using CRISPR/Cas9, and its engineered and ortholog variants for studying the transcription factors involved in the maintenance of phosphate homeostasis in model plants

Phosphorus (P), an essential macronutrient, is pivotal for growth and development of plants. Availability of phosphate (Pi), the only assimilable P, is often suboptimal in rhizospheres. Pi deficiency triggers an array of spatiotemporal adaptive responses including the differential regulation of several transcription factors (TFs). Studies on MYB TF PHR1 in Arabidopsis thaliana (Arabidopsis) and its orthologs OsPHRs in Oryza sativa (rice) have provided empirical evidence of their significant roles in the maintenance of Pi homeostasis. Since the functional characterization of PHR1 in 2001, several other TFs have now been identified in these model plants. This raised a pertinent question whether there are any likely interactions across these TFs. Clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein 9 (Cas9) system has provided an attractive paradigm for editing genome in plants. Here, we review the applications and challenges of this technique for genome editing of the TFs for deciphering the function and plausible interactions across them. This technology could thus provide a much-needed fillip towards engineering TFs for generating Pi use efficient plants for sustainable agriculture. Furthermore, we contemplate whether this technology could be a viable alternative to the controversial genetically modified (GM) rice or it may also eventually embroil into a limbo.

AtMBD4: A methylated DNA binding protein negatively regulates a subset of phosphate starvation genes

DNA methylation is an important epigenetic modification that governs transcriptional regulation. The methylation mark is read by a special class of proteins called methyl-CpG-binding domain proteins. The role of DNA methylation has been found in X-chromosome inactivation, genomic imprinting, transposon silencing, and self-incompatibility. Recently, remodeling of global DNA methylation was demonstrated in Arabidopsis during low phosphate availability. The present study reports that AtMBD4 gene of Arabidopsis negatively regulates phosphate starvation. The T-DNA insertion mutation at the AtMBD4 locus exhibited altered root architecture as compared to wild-type plants. Using microarray hybridization and analysis, an increased transcript accumulation of 242 genes was observed in the mutant. Many of these genes were related to phosphate transporters and transcription factors, involved in phosphate starvation response. Comparison of data of atmbd4 mutant with publicly available microarray data of phosphate starvation response indicated the role of AtMBD4 protein in phosphate starvation response. Further, promoter analysis of up-regulated genes suggested that cis-regulatory elements like MBS, W-box, and B1BS are more prominent in the promoters of up-regulated genes. Upon performing a methylation-specific PCR, a decreased DNA methylation in the promoter regions of up-regulated genes was observed. The accumulation of anthocyanin and inorganic phosphate in the atmbd4 mutant was found to be higher than the wild-type plant. Altered root morphology, up-regulation of phosphate starvation-induced genes in atmbd4 mutant suggests that AtMBD4 negatively regulates the phosphate starvation response.

Identification of Quantitative Trait Loci Associated with Nutrient Use Efficiency Traits, Using SNP Markers in an Early Backcross Population of Rice (Oryza sativa L.)

The development of rice cultivars with nutrient use efficiency (NuUE) is highly crucial for sustaining global rice production in Asia and Africa. However, this requires a better understanding of the genetics of NuUE-related traits and their relationship to grain yield. In this study, simultaneous efforts were made to develop nutrient use efficient rice cultivars and to map quantitative trait loci (QTLs) governing NuUE-related traits in rice. A total of 230 BC₁F₅ introgression lines (ILs) were developed from a single early backcross population involving Weed Tolerant Rice 1, as the recipient parent, and Hao-an-nong, as the donor parent. The ILs were cultivated in field conditions with a different combination of fertilizer schedule under six nutrient conditions: minus nitrogen (–N), minus phosphorus (–P), (–NP), minus nitrogen phosphorus and potassium (–NPK), 75% of recommended nitrogen (75N), and NPK. Analysis of variance revealed that significant differences (p < 0.01) were noted among ILs and treatments for all traits. A high-density linkage map was constructed by using 704 high-quality single nucleotide polymorphism (SNP) markers. A total of 49 main-effect QTLs were identified on all chromosomes, except on chromosome 7, 11 and 12, which are showing 20.25% to 34.68% of phenotypic variation. With further analysis of these QTLs, we refined them to four top hotspot QTLs (QTL harbor-I to IV) located on chromosomes 3, 5, 9, and 11. However, we identified four novel putative QTLs for agronomic efficiency (AE) and 22 QTLs for partial factor productivity (PFP) under –P and 75N conditions. These interval regions of QTLs, several transporters and genes are located that were involved in nutrient uptake from soil to plant organs and tolerance to biotic and abiotic stresses. Further, the validation of these potential QTLs, genes may provide remarkable value for marker-aided selection and pyramiding of multiple QTLs, which would provide supporting evidence for the enhancement of grain yield and cloning of NuUE tolerance-responsive genes in rice.

Transcriptome Analyses Provide Novel Insights into Heat Stress Responses in Chieh-Qua (Benincasa hispida Cogn. var. Chieh-Qua How)

Temperature rising caused by global warming has imposed significant negative effects on crop qualities and yields. To get the well-known molecular mechanism upon the higher temperature, we carefully analyzed the RNA sequencing-based transcriptomic responses of two contrasting chieh-qua genotypes: A39 (heat-tolerant) and H5 (heat-sensitive). In this study, twelve cDNA libraries generated from A39 and H5 were performed with a transcriptome assay under normal and heat stress conditions, respectively. A total of 8705 differentially expressed genes (DEGs) were detected under normal conditions (3676 up-regulated and 5029 down-regulated) and 1505 genes under heat stress (914 up-regulated and 591 down-regulated), respectively. A significant positive correlation between RNA-Seq data and qRT-PCR results was identified. DEGs related to heat shock proteins (HSPs), ubiquitin-protein ligase, transcriptional factors, and pentatricopeptide repeat-containing proteins were significantly changed after heat stress. Several genes, which encoded HSPs (CL2311.Contig3 and CL6612.Contig2), cytochrome P450 (CL4517.Contig4 and CL683.Contig7), and bHLH TFs (CL914.Contig2 and CL8321.Contig1) were specifically induced after four days of heat stress. DEGs detected in our study between these two contrasting cultivars would provide a novel basis for isolating useful candidate genes of heat stress responses in chieh-qua.

Comparative functional genomics analysis of bHLH gene family in rice, maize and wheat

BACKGROUND

The basic helix-loop-helix transcription factors play important roles in diverse cellular and molecular processes. Comparative functional genomics can provide powerful approaches to draw inferences about gene function and evolution among species. The comprehensive comparison of bHLH gene family in different gramineous plants has not yet been reported.

RESULTS

In this study, a total of 183, 231 and 571 bHLHs were identified in rice, maize and wheat genomes respectively, and 1154 bHLH genes from the three species and Arabidopsis were classified into 36 subfamilies. Of the identified genes, 110 OsbHLHs, 188 ZmbHLHs and 209 TabHLHs with relatively high mRNA abundances were detected in one or more tissues during development, and some of them exhibited tissue-specific expression such as TabHLH454-459, ZmbHLH099-101 and OsbHLH037 in root, TabHLH559-562, - 046, - 047 and ZmbHLH010, - 072, - 226 in leaf, TabHLH216-221, - 333, - 335, - 340 and OsbHLH005, - 141 in inflorescence, TabHLH081, ZmbHLH139 and OsbHLH144 in seed. Forty five, twenty nine and thirty one differentially expressed bHLHs were respectively detected in wheat, maize and rice under drought stresses using RNA-seq technology. Among them, the expressions of TabHLH046, - 047, ZmbHLH097, - 098, OsbHLH006 and - 185 were strongly induced, whereas TabHLH303, - 562, ZmbHLH155, - 154, OsbHLH152 and - 113 showed significant down-regulation. Twenty two TabHLHs were induced after stripe rust infection at 24 h and nine of them were suppressed at 72 hpi, whereas 28 and 6 TabHLHs exhibited obviously down- and up-regulation after powdery mildew attack respectively. Forty one ZmbHLHs were differentially expressed in response to F. verticillioides infection. Twenty two co-expression modules were identified by the WGCNA, some of which were associated with particular tissue types. And GO enrichment analysis for the modules showed that some TabHLHs were involved in the control of several biological processes, such as tapetal PCD, lipid metabolism, iron absorption, stress responses and signal regulation.

CONCLUSION

The present study identifies the bHLH family in rice, maize and wheat genomes, and detailedly discusses the evolutionary relationships, expression and function of bHLHs. This study provides some novel and detail information about bHLHs, and may facilitate understanding the molecular basis of the plant growth, development and stress physiology.

Overexpression of a Phosphate Starvation Response AP2/ERF Gene From Physic Nut in Arabidopsis Alters Root Morphological Traits and Phosphate Starvation-Induced Anthocyanin Accumulation

Physic nut (Jatropha curcas L.) is highly tolerant of barren environments and a significant biofuel plant. To probe mechanisms of its tolerance mechanisms, we have analyzed genome-wide transcriptional profiles of 8-week-old physic nut seedlings subjected to Pi deficiency (P-) for 2 and 16 days, and Pi-sufficient conditions (P+) controls. We identified several phosphate transporters, purple acid phosphatases, and enzymes of membrane lipid metabolism among the 272 most differentially expressed genes. Genes of the miR399/PHO2 pathway (IPS, miR399, and members of the SPX family) showed alterations in expression. We also found that expression of several transcription factor genes was modulated by phosphate starvation stress in physic nut seedlings, including an AP2/ERF gene (JcERF035), which was down-regulated in both root and leaf tissues under Pi-deprivation. In JcERF035-overexpressing Arabidopsis lines both numbers and lengths of first-order lateral roots were dramatically reduced, but numbers of root hairs on the primary root tip were significantly elevated, under both P+ and P- conditions. Furthermore, the transgenic plants accumulated less anthocyanin but had similar Pi contents to wild-type plants under P-deficiency conditions. Expression levels of the tested genes related to anthocyanin biosynthesis and regulation, and genes induced by low phosphate, were significantly lower in shoots of transgenic lines than in wild-type plants under P-deficiency. Our data show that down-regulation of the JcERF035 gene might contribute to the regulation of root system architecture and both biosynthesis and accumulation of anthocyanins in aerial tissues of plants under low Pi conditions.

Early Transcriptomic Response to Phosphate Deprivation in Soybean Leaves as Revealed by RNA-Sequencing

Low phosphate (Pi) availability is an important limiting factor affecting soybean production. However, the underlying molecular mechanisms responsible for low Pi stress response and tolerance remain largely unknown, especially for the early signaling events under low Pi stress. Here, a genome-wide transcriptomic analysis in soybean leaves treated with a short-term Pi-deprivation (24 h) was performed through high-throughput RNA sequencing (RNA-seq) technology. A total of 533 loci were found to be differentially expressed in response to Pi deprivation, including 36 mis-annotated loci and 32 novel loci. Among the differentially expressed genes (DEGs), 303 were induced and 230 were repressed by Pi deprivation. To validate the reliability of the RNA-seq data, 18 DEGs were randomly selected and analyzed by quantitative RT-PCR (reverse transcription polymerase chain reaction), which exhibited similar fold changes with RNA-seq. Enrichment analyses showed that 29 GO (Gene Ontology) terms and 8 KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways were significantly enriched in the up-regulated DEGs and 25 GO terms and 16 KEGG pathways were significantly enriched in the down-regulated DEGs. Some DEGs potentially involved in Pi sensing and signaling were up-regulated by short-term Pi deprivation, including five SPX-containing genes. Some DEGs possibly associated with water and nutrient uptake, hormonal and calcium signaling, protein phosphorylation and dephosphorylation and cell wall modification were affected at the early stage of Pi deprivation. The cis-elements of PHO (phosphatase) element, PHO-like element and P responsive element were present more frequently in promoter regions of up-regulated DEGs compared to that of randomly-selected genes in the soybean genome. Our transcriptomic data showed an intricate network containing transporters, transcription factors, kinases and phosphatases, hormone and calcium signaling components is involved in plant responses to early Pi deprivation.

Are we ready to improve phosphorus homeostasis in rice?

Phosphorus (P) is an essential macronutrient which often limits plant growth, but the phosphate rock used for fertilizer production is a finite resource. On the other hand, large amounts of P compounds are entering surface waters, leading to eutrophication. Therefore, improvement of phosphate use efficiency of crop plants is a major task for plant science. Rice as a staple crop has recently been a focus of such efforts with several major discoveries. New transporters controlling phosphate homeostasis in rice have been discovered. Manipulation of expression of the corresponding genes improves different components of phosphate use efficiency, such as delivery of phosphate to the developing seeds and synthesis of phytic acid. Here these new findings are discussed in the context of general P nutrition and with the aim of finding out how far we can optimize P homeostasis in rice.

Functional characterization of the gene promoter for an Elaeis guineensis phosphate starvation-inducible, high affinity phosphate transporter in both homologous and heterologous model systems

Oil palm is grown in tropical soils with low bioavailability of Pi. A cDNA clone specifically expressed under phosphate-starvation condition in oil palm roots was identified as a high-affinity phosphate transporter (EgPHT1). The deduced amino acid sequence has 6 transmembrane domains each at the N- and C-termini separated by a hydrophilic linker. Comparison of promoter motifs within 1500 bp upstream of ATG of 10 promoters from high- and low-affinity phosphate transporter from both dicots and monocots including EgPHT1 was performed. The EgPHT1 promoter was fused to β-glucuronidase (GUS) reporter gene and its activity was analysed by histochemical and fluorometric GUS assays in transiently transformed oil palm tissues and T₃ homozygous transgenic Arabidopsis plants. In response to Pi-starvation, no GUS activity was detected in oil palm leaves, but a strong inducible activity was observed in the roots (1.4 times higher than the CaMV35S promoter). GUS was specifically expressed in transgenic Arabidopsis roots under Pi deficiency and starvation of the other macronutrients (N and K) did not induce GUS activity. Eight motifs including ABRERATCAL (abscisic-acid responsive), RHERPATEXPA7 (root hair-specific), SURECOREATSULTR11 (sulfur-deficiency response), LTRECOREATCOR15 (temperature-stress response), MYB2CONSENSUSAT and ACGTATERD1 (water-stress response) as well as two novel motifs, 3 (TAAAAAAA) and 26 (TTTTATGT) identified through pattern discovery, occur at significantly higher frequency (p < 0.05) in the high-than the low-affinity phosphate transporter promoters. The Pi deficiency-responsive elements in EgPHT1 includes the P1BS, W-box, E-box and the G-box. Thus, EgPHT1 is important for improving Pi uptake in oil palm with potential for engineering efficient Pi acquisition.

Characterization of the basic helix-loop-helix gene family and its tissue-differential expression in response to salt stress in poplar

The basic helix–loop–helix (bHLH) transcription factor gene family is one of the largest gene families and extensively involved in plant growth, development, and stress responses. However, limited studies are available on the gene family in poplar. In this study, we focused on 202 bHLH genes, exploring their DNA and protein sequences and physicochemical properties. According to their protein sequence similarities, we classified the genes into 25 groups with specific motif structures. In order to explore their expressions, we performed gene expression profiling using RNA-Seq and identified 19 genes that display tissue-differential expression patterns without treatment. Furthermore, we also performed gene expression profiling under salt stress. We found 74 differentially expressed genes (DEGs), which are responsive to the treatment. A total of 18 of the 19 genes correspond well to the DEGs. We validated the results using reverse transcription quantitative real-time PCR. This study lays the foundation for future studies on gene cloning, transgenes, and biological mechanisms.

Do longer root hairs improve phosphorus uptake? Testing the hypothesis with transgenic Brachypodium distachyon lines overexpressing endogenous RSL genes

Mutants without root hairs show reduced inorganic orthophosphate (Pi) uptake and compromised growth on soils when Pi availability is restricted. What is less clear is whether root hairs that are longer than wild-type provide an additional benefit to phosphorus (P) nutrition. This was tested using transgenic Brachypodium lines with longer root hairs. The lines were transformed with the endogenous BdRSL2 and BdRSL3 genes using either a constitutive promoter or a root hair-specific promoter. Plants were grown for 32 d in soil amended with various Pi concentrations. Plant biomass and P uptake were measured and genotypes were compared on the basis of critical Pi values and P uptake per unit root length. Ectopic expression of RSL2 and RSL3 increased root hair length three-fold but decreased plant biomass. Constitutive expression of BdRSL2, but not expression of BdRSL3, consistently improved P nutrition as measured by lowering the critical Pi values and increasing Pi uptake per unit root length. Increasing root hair length through breeding or biotechnology can improve P uptake efficiency if the pleotropic effects on plant biomass are avoided. Long root hairs, alone, appear to be insufficient to improve Pi uptake and need to be combined with other traits to benefit P nutrition.

Transcription Factors and Their Roles in Signal Transduction in Plants under Abiotic Stresses

In agricultural production, abiotic stresses are known as the main disturbance leading to negative impacts on crop performance. Research on elucidating plant defense mechanisms against the stresses at molecular level has been addressed for years in order to identify the major contributors in boosting the plant tolerance ability. From literature, numerous genes from different species, and from both functional and regulatory gene categories, have been suggested to be on the list of potential candidates for genetic engineering. Noticeably, enhancement of plant stress tolerance by manipulating expression of Transcription Factors (TFs) encoding genes has emerged as a popular approach since most of them are early stress-responsive genes and control the expression of a set of downstream target genes. Consequently, there is a higher chance to generate novel cultivars with better tolerance to either single or multiple stresses. Perhaps, the difficult task when deploying this approach is selecting appropriate gene(s) for manipulation. In this review, on the basis of the current findings from molecular and post-genomic studies, our interest is to highlight the current understanding of the roles of TFs in signal transduction and mediating plant responses towards abiotic stressors. Furthermore, interactions among TFs within the stress-responsive network will be discussed. The last section will be reserved for discussing the potential applications of TFs for stress tolerance improvement in plants.

Ecophysiological responses to excess iron in lowland and upland rice cultivars

Iron (Fe) is an essential nutrient for plants but under high concentrations, such as that found naturally in clay and waterlogged soils, its toxic effect can limit production. This study aimed to investigate the stress tolerance responses exhibited by different rice cultivars. Both lowland and upland cultivars were grown under excess Fe and hypoxic conditions. Lowland cultivars showed higher Fe accumulation in roots compared with upland cultivars suggesting the use of different strategies to tolerate excess Fe. The upland Canastra cultivar displayed a mechanism to limit iron translocation from roots to the shoots, minimizing leaf oxidative stress induced by excess Fe. Conversely, the cultivar Curinga invested in the increase of R1/A, as an alternative drain of electrons. However, the higher iron accumulation in the leaves, was not necessarily related to high toxicity. Nutrient uptake and/or utilization mechanisms in rice plants are in accordance with their needs, which may be defined in relation to crop environments. Alterations in the biochemical parameters of photosynthesis suggest that photosynthesis in rice under excess Fe is primarily limited by biochemical processes rather than by diffusional limitations, particularly in the upland cultivars. The electron transport rate, carboxylation efficiency and electron excess dissipation by photorespiration demonstrate to be good indicators of iron tolerance. Altogether, these chemical and molecular patterns suggests that rice plants grown under excess Fe exhibit gene expression reprogramming in response to the Fe excess per se and in response to changes in photosynthesis and nutrient levels to maintain growth under stress.

Transcription Factors and Their Roles in Signal Transduction in Plants under Abiotic Stresses

In agricultural production, abiotic stresses are known as the main disturbance leading to negative impacts on crop performance. Research on elucidating plant defense mechanisms against the stresses at molecular level has been addressed for years in order to identify the major contributors in boosting the plant tolerance ability. From literature, numerous genes from different species, and from both functional and regulatory gene categories, have been suggested to be on the list of potential candidates for genetic engineering. Noticeably, enhancement of plant stress tolerance by manipulating expression of Transcription Factors (TFs) encoding genes has emerged as a popular approach since most of them are early stress-responsive genes and control the expression of a set of downstream target genes. Consequently, there is a higher chance to generate novel cultivars with better tolerance to either single or multiple stresses. Perhaps, the difficult task when deploying this approach is selecting appropriate gene(s) for manipulation. In this review, on the basis of the current findings from molecular and post-genomic studies, our interest is to highlight the current understanding of the roles of TFs in signal transduction and mediating plant responses towards abiotic stressors. Furthermore, interactions among TFs within the stress-responsive network will be discussed. The last section will be reserved for discussing the potential applications of TFs for stress tolerance improvement in plants.

Identification of putative QTLs for seedling stage phosphorus starvation response in finger millet (Eleusine coracana L. Gaertn.) by association mapping and cross species synteny analysis

A germplasm assembly of 128 finger millet genotypes from 18 countries was evaluated for seedling-stage phosphorus (P) responses by growing them in P sufficient (Psuf) and P deficient (Pdef) treatments. Majority of the genotypes showed adaptive responses to low P condition. Based on phenotype behaviour using the best linear unbiased predictors for each trait, genotypes were classified into, P responsive, low P tolerant and P non-responsive types. Based on the overall phenotype performance under Pdef, 10 genotypes were identified as low P tolerants. The low P tolerant genotypes were characterised by increased shoot and root length and increased root hair induction with longer root hairs under Pdef, than under Psuf. Association mapping of P response traits using mixed linear models revealed four quantitative trait loci (QTLs). Two QTLs (qLRDW.1 and qLRDW.2) for low P response affecting root dry weight explained over 10% phenotypic variation. In silico synteny analysis across grass genomes for these QTLs identified putative candidate genes such as Ser-Thr kinase and transcription factors such as WRKY and basic helix-loop-helix (bHLH). The QTLs for response under Psuf were mapped for traits such as shoot dry weight (qHSDW.1) and root length (qHRL.1). Putative associations of these QTLs over the syntenous regions on the grass genomes revealed proximity to cytochrome P450, phosphate transporter and pectin methylesterase inhibitor (PMEI) genes. This is the first report of the extent of phenotypic variability for P response in finger millet genotypes during seedling-stage, along with the QTLs and putative candidate genes associated with P starvation tolerance.

Genome-wide analysis of basic helix-loop-helix (bHLH) transcription factors in Brachypodium distachyon

BACKGROUND

As a superfamily of transcription factors (TFs), the basic helix-loop-helix (bHLH) proteins have been characterized functionally in many plants with a vital role in the regulation of diverse biological processes including growth, development, response to various stresses, and so on. However, no systemic analysis of the bHLH TFs has been reported in Brachypodium distachyon, an emerging model plant in Poaceae.

RESULTS

A total of 146 bHLH TFs were identified in the Brachypodium distachyon genome and classified into 24 subfamilies. BdbHLHs in the same subfamily share similar protein motifs and gene structures. Gene duplication events showed a close relationship to rice, maize and sorghum, and segment duplications might play a key role in the expansion of this gene family. The amino acid sequence of the bHLH domains were quite conservative, especially Leu-27 and Leu-54. Based on the predicted binding activities, the BdbHLHs were divided into DNA binding and non-DNA binding types. According to the gene ontology (GO) analysis, BdbHLHs were speculated to function in homodimer or heterodimer manner. By integrating the available high throughput data in public database and results of quantitative RT-PCR, we found the expression profiles of BdbHLHs were different, implying their differentiated functions.

CONCLUSION

One hundred fourty-six BdbHLHs were identified and their conserved domains, sequence features, phylogenetic relationship, chromosomal distribution, GO annotations, gene structures, gene duplication and expression profiles were investigated. Our findings lay a foundation for further evolutionary and functional elucidation of BdbHLH genes.

Piriformospora indica Reprograms Gene Expression in Arabidopsis Phosphate Metabolism Mutants But Does Not Compensate for Phosphate Limitation

Piriformospora indica is an endophytic fungus of Sebacinaceae which colonizes the roots of many plant species and confers benefits to the hosts. We demonstrate that approximately 75% of the genes, which respond to P. indica in Arabidopsis roots, differ among seedlings grown on normal phosphate (Pi) or Pi limitation conditions, and among wild-type and the wrky6 mutant impaired in the regulation of the Pi metabolism. Mapman analyses suggest that the fungus activates different signaling, transport, metabolic and developmental programs in the roots of wild-type and wrky6 seedlings under normal and low Pi conditions. Under low Pi, P. indica promotes growth and Pi uptake of wild-type seedlings, and the stimulatory effects are identical for mutants impaired in the PHOSPHATE TRANSPORTERS1;1, -1;2 and -1;4. The data suggest that the fungus does not stimulate Pi uptake, but adapts the expression profiles to Pi limitation in Pi metabolism mutants.

AtbHLH68 transcription factor contributes to the regulation of ABA homeostasis and drought stress tolerance in Arabidopsis thaliana

Basic helix-loop-helix (bHLH) transcription factors are involved in a wide range of developmental processes and in response to biotic and abiotic stresses. They represent one of the biggest families of transcription factors but only few of them have been functionally characterized. Here we report the characterization of AtbHLH68 and show that, although the knock out mutant did not have an obvious development phenotype, it was slightly more sensitive to drought stress than the Col-0, and AtbHLH68 overexpressing lines displayed defects in lateral root (LR) formation and a significant increased tolerance to drought stress, likely related to an enhanced sensitivity to abscisic acid (ABA) and/or increased ABA content. AtbHLH68 was expressed in the vascular system of Arabidopsis and its expression was modulated by exogenously applied ABA in an organ-specific manner. We showed that the expression of genes involved in ABA metabolism [AtAAO3 (AtALDEHYDE OXIDASE 3) and AtCYP707A3 (AtABSCISIC ACID 8'HYDROXYLASE 3)], in ABA-related response to drought-stress (AtMYC2, AtbHLH122 and AtRD29A) or during LRs development (AtMYC2 and AtABI3) was de-regulated in the overexpressing lines. We propose that AtbHLH68 has a function in the regulation of LR elongation, and in the response to drought stress, likely through an ABA-dependent pathway by regulating directly or indirectly components of ABA signaling and/or metabolism.

Molecular mechanisms of phosphate transport and signaling in higher plants

Phosphorus (P) is an essential macronutrient for plant growth and development. To adapt to low inorganic-phosphate (P_i) environments, plants have evolved complex mechanisms and pathways that regulate the acquisition and remobilization of P_i and maintain P homeostasis. These mechanisms are regulated by complex gene regulatory networks through the functions of P_i transporters (PTs) and P_i starvation-induced (PSI) genes. This review summarizes recent progress in determining the molecular regulatory mechanisms of phosphate transporters and the P_i signaling network in the dicot Arabidopsis (Arabidopsis thaliana) and the monocot rice (Oryza sativa L.). Recent advances in this field provide a reference for understanding plant P_i signaling and specific mechanisms that mediate plant adaptation to environments with limited P_i availability. We propose potential biotechnological applications of known genes to develop plant cultivars with improved P_i uptake and use efficiency.

Maintenance of phosphate homeostasis and root development are coordinately regulated by MYB1, an R2R3-type MYB transcription factor in rice

The adaptive responses of plants to phosphate (Pi) starvation stress are fine-tuned by an elaborate regulatory network. In this study, we identified and characterized a novel Pi starvation-responsive gene, MYB1, encoding an R2R3-type transcription factor in rice. MYB1 was transcriptionally induced in leaf sheaths and old leaf blades. It was localized to the nucleus and expressed mainly in vascular tissues. Mutation of MYB1 led to an increase in Pi uptake and accumulation, accompanied by altered expression of a subset of Pi transporters and several genes involved in Pi starvation signaling. Furthermore, MYB1 affected the elongation of the primary root in a Pi-dependent manner and lateral roots in a Pi-independent manner. Moreover, gibberellic acid (GA)-triggered lateral root elongation was largely suppressed in wild-type plants under Pi starvation conditions, whereas this suppression was partially rescued in myb1 mutant lines, correlating with the up-regulation of a GA biosynthetic gene upon MYB1 mutation. Taken together, the findings of this study highlight the role of MYB1 as a regulator involved in both Pi starvation signaling and GA biosynthesis. Such a co-regulator might have broad implications for the study of cross-talk between nutrient stress and other signaling pathways.

Improving phosphorus use efficiency: a complex trait with emerging opportunities

Phosphorus (P) is one of the essential nutrients for plants, and is indispensable for plant growth and development. P deficiency severely limits crop yield, and regular fertilizer applications are required to obtain high yields and to prevent soil degradation. To access P from the soil, plants have evolved high- and low-affinity Pi transporters and the ability to induce root architectural changes to forage P. Also, adjustments of numerous cellular processes are triggered by the P starvation response, a tightly regulated process in plants. With the increasing demand for food as a result of a growing population, the demand for P fertilizer is steadily increasing. Given the high costs of fertilizers and in light of the fact that phosphate rock, the source of P fertilizer, is a finite natural resource, there is a need to enhance P fertilizer use efficiency in agricultural systems and to develop plants with enhanced Pi uptake and internal P-use efficiency (PUE). In this review we will provide an overview of continuing relevant research and highlight different approaches towards developing crops with enhanced PUE. In this context, we will summarize our current understanding of root responses to low phosphorus conditions and will emphasize the importance of combining PUE with tolerance of other stresses, such as aluminum toxicity. Of the many genes associated with Pi deficiency, this review will focus on those that hold promise or are already at an advanced stage of testing (OsPSTOL1, AVP1, PHO1 and OsPHT1;6). Finally, an update is provided on the progress made exploring alternative technologies, such as phosphite fertilizer.

Root transcriptomes of two acidic soil adapted Indica rice genotypes suggest diverse and complex mechanism of low phosphorus tolerance

Low phosphorus (P) tolerance in rice is a biologically and agronomically important character. Low P tolerant Indica-type rice genotypes, Sahbhagi Dhan (SD) and Chakhao Poreiton (CP), are adapted to acidic soils and show variable response to low P levels. Using RNAseq approach, transcriptome data was generated from roots of SD and CP after 15 days of low P treatment to understand differences and similarities at molecular level. In response to low P, number of genes up-regulated (1318) was more when compared with down-regulated genes (761). Eight hundred twenty-one genes found to be significantly regulated between SD and CP in response to low P. De novo assembly using plant database led to further identification of 1535 novel transcripts. Functional annotation of significantly expressed genes suggests two distinct methods of low P tolerance. While root system architecture in SD works through serine-threonine kinase PSTOL1, suberin-mediated cell wall modification seems to be key in CP. The transcription data indicated that CP relies more on releasing its internally bound Pi and coping with low P levels by transcriptional and translational modifications and using dehydration response-based signals. Role of P transporters seems to be vital in response to low P in CP while sugar- and auxin-mediated pathway seems to be preferred in SD. At least six small RNA clusters overlap with transcripts highly expressed under low P, suggesting role of RNA super clusters in nutrient response in plants. These results help us to understand and thereby devise better strategy to enhance low P tolerance in Indica-type rice.

StMYB44 negatively regulates phosphate transport by suppressing expression of PHOSPHATE1 in potato

Phosphorus is an important macronutrient for plant growth, but often deficient in soil. To understand the molecular basis of the complex responses of potato (Solanum tuberosum L.) to phosphate (Pi) deficiency stress, the RNA-Seq approach was taken to identify genes responding to Pi starvation in potato roots. A total of 359 differentially expressed genes were identified, among which the Solanum tuberosum transcription factor gene MYB44 (StMYB44) was found to be down-regulated by Pi starvation. StMYB44 was ubiquitously expressed in potato tissues and organs, and StMYB44 protein was exclusively localized in the nucleus. Overexpression of StMYB44 in potato resulted in lower accumulation of Pi in shoots. Transcriptomic analysis indicated that the abundance of S. tuberosum PHOSPHATE1 (StPHO1), a Pi transport-related gene, was reduced in StMYB44 overexpression lines. In contrast, knock-out of StMYB44 by a CRISPR/Cas9 system failed to increase transcription of StPHO1. Moreover, StMYB44 was found to interact in the nucleus with AtWRKY6, a known Arabidopsis transcription factor directly regulating PHO1 expression, and StWRKY6, indicating that StMYB44 could be a member of the regulatory complex controlling transcription of StPHO1. Taken together, our study demonstrates that StMYB44 negatively regulates Pi transport in potato by suppressing StPHO1 expression.

Growth Stimulatory Effects and Genome-Wide Transcriptional Changes Produced by Protein Hydrolysates in Maize Seedlings

Protein hydrolysates are an emerging class of crop management products utilized for improving nutrient assimilation and mitigating crop stress. They generally consist of a mixture of peptides and free amino acids derived from the hydrolysis of plant or animal sources. The present work was aimed at studying the effects and the action mechanisms of a protein hydrolysate derived from animal residues on maize root growth and physiology in comparison with the effects induced by either free amino acids or inorganic N supply. The application of the protein hydrolysate caused a remarkable enhancement of root growth. In particular, in the protein hydrolysate-treated plants the length and surface area of lateral roots were about 7 and 1.5 times higher than in plants treated with inorganic N or free amino acids, respectively. The root growth promoting effect of the protein hydrolysate was associated with an increased root accumulation of K, Zn, Cu, and Mn when compared with inorganic N and amino acids treatments. A microarray analysis allowed to dissect the transcriptional changes induced by the different treatments demonstrating treatment-specific effects principally on cell wall organization, transport processes, stress responses and hormone metabolism.

Defense-Related Transcriptional Reprogramming in Vitamin E-Deficient Arabidopsis Mutants Exposed to Contrasting Phosphate Availability

Vitamin E inhibits the propagation of lipid peroxidation and helps protecting photosystem II from photoinhibition, but little is known about its possible role in plant response to Pi availability. Here, we aimed at examining the effect of vitamin E deficiency in Arabidopsis thaliana vte mutants on phytohormone contents and the expression of transcription factors in plants exposed to contrasting Pi availability. Plants were subjected to two doses of Pi, either unprimed (controls) or previously exposed to low Pi (primed). In the wild type, α-tocopherol contents increased significantly in response to repeated periods of low Pi, which was paralleled by increased growth, indicative of a priming effect. This growth-stimulating effect was, however, abolished in vte mutants. Hormonal profiling revealed significant effects of Pi availability, priming and genotype on the contents of jasmonates and salicylates; remarkably, vte mutants showed enhanced accumulation of both hormones under low Pi. Furthermore, expression profiling of 1,880 transcription factors by qRT-PCR revealed a pronounced effect of priming on the transcript levels of 45 transcription factors mainly associated with growth and stress in wild-type plants in response to low Pi availability; while distinct differences in the transcriptional response were detected in vte mutants. We conclude that α-tocopherol plays a major role in the response of plants to Pi availability not only by protecting plants from photo-oxidative stress, but also by exerting a control over growth- and defense-related transcriptional reprogramming and hormonal modulation.

Root transcriptome of two contrasting indica rice cultivars uncovers regulators of root development and physiological responses

The huge variation in root system architecture (RSA) among different rice (Oryza sativa) cultivars is conferred by their genetic makeup and different growth or climatic conditions. Unlike model plant Arabidopsis, the molecular basis of such variation in RSA is very poorly understood in rice. Cultivars with stable variation are valuable resources for identification of genes involved in RSA and related physiological traits. We have screened for RSA and identified two such indica rice cultivars, IR-64 (OsAS83) and IET-16348 (OsAS84), with stable contrasting RSA. OsAS84 produces robust RSA with more crown roots, lateral roots and root hairs than OsAS83. Using comparative root transcriptome analysis of these cultivars, we identified genes related to root development and different physiological responses like abiotic stress responses, hormone signaling, and nutrient acquisition or transport. The two cultivars differ in their response to salinity/dehydration stresses, phosphate/nitrogen deficiency, and different phytohormones. Differential expression of genes involved in salinity or dehydration response, nitrogen (N) transport, phosphate (Pi) starvation signaling, hormone signaling and root development underlies more resistance of OsAS84 towards abiotic stresses, Pi or N deficiency and its robust RSA. Thus our study uncovers gene-network involved in root development and abiotic stress responses in rice.

TaZAT8, a C2H2-ZFP type transcription factor gene in wheat, plays critical roles in mediating tolerance to Pi deprivation through regulating P acquisition, ROS homeostasis and root system establishment

Transcription factors (TFs) play critical roles in mediating defense of plants to abiotic stresses through regulating downstream defensive genes. In this study, a wheat C2H2-ZFP (zinc finger protein) type TF gene designated as TaZAT8 was functionally characterized in mediating tolerance to the inorganic phosphate (Pi)-starvation stress. TaZAT8 bears conserved motifs harboring in the C2H2-ZFP type counterparts across vascular plant species. The expression of TaZAT8 was shown to be induced in roots upon Pi deprivation, with a Pi concentration- and temporal-dependent manner. Overexpression of TaZAT8 in tobacco conferred plants improved tolerance to Pi deprivation; the transgenic lines exhibited enlarged phenotype and elevated biomass and phosphorus (P) accumulation relative to wild-type (WT) after Pi-starvation treatment. NtPT1 and NtPT2, the tobacco phosphate transporter (PT) genes, showed increased transcripts in the Pi-deprived transgenic lines, indicative of their transcriptional regulation by TaZAT8. Overexpression analysis of these PT genes validated their function in mediating Pi acquisition under the Pi deprivation conditions. Additionally, the TaZAT8-overexpressing lines also behaved enhanced antioxidant enzyme (AE) activities and enlarged root system architecture (RSA) with respect to WT. Evaluation of the transcript abundance of tobacco genes encoding AE and PIN proteins, including NtMnSOD1, NtSOD1, NtPOD1;2, NtPOD1;5, NtPOD1;6, and NtPOD1;9, and NtPIN1 and NtPIN4 are upregulated in the TaZAT8-overexpressing lines. Overexpression of NtPIN1 and NtPIN4 conferred plants to enlarged RSA and elevated biomass under the Pi-starvation stress conditions. Our investigation provides insights into plant adaptation to the Pi-starvation stress mediated by distinct ZFP TFs through modulation of Pi acquisition and cellular ROS detoxicity.

Strand-specific RNA-Seq transcriptome analysis of genotypes with and without low-phosphorus tolerance provides novel insights into phosphorus-use efficiency in maize

BACKGROUND

Phosphorus (P) stress is a global problem in maize production. Although macro/microarray technologies have greatly increased our general knowledge of maize responses to P stress, a greater understanding of the diversity of responses in maize genotypes is still needed.

RESULTS

In this study, we first evaluated the tolerance to low P of 560 accessions under field conditions, and selected the low P-tolerant line CCM454 and the low P-sensitive line 31778 for further research. We then generated 24 strand-specific RNA libraries from shoots and roots of CCM454 and 31778 that had been subjected to P stress for 2 and 8 days. The P deficiency-responsive genes common to CCM454 and 31778 were involved in various metabolic processes, including acid phosphatase (APase) activity. Determination of root-secretory APase activities showed that the induction of APase by P stress occurred much earlier in CCM454 than that in 31778. Gene Ontology analysis of differentially expressed genes (DEGs) and CAT/POD activities between CCM454 and 31778 under P-sufficient and -deficient conditions demonstrated that CCM454 has a greater ability to eliminate reactive oxygen species (ROS) than 31778. In addition, 16 miRNAs in roots and 12 miRNAs in shoots, including miRNA399s, were identified as DEGs between CCM454 and 31778.

CONCLUSIONS

The results indicate that the tolerance to low P of CCM454 is mainly due to the rapid responsiveness to P stress and efficient elimination of ROS. Our findings increase the understanding of the molecular events involved in the diversity of responses to P stress among maize accessions.

Identification and expression analysis of OsLPR family revealed the potential roles of OsLPR3 and 5 in maintaining phosphate homeostasis in rice

BACKGROUND

Phosphorus (P), an essential macronutrient, is often limiting in soils and affects plant growth and development. In Arabidopsis thaliana, Low Phosphate Root1 (LPR1) and its close paralog LPR2 encode multicopper oxidases (MCOs). They regulate meristem responses of root system to phosphate (Pi) deficiency. However, the roles of LPR gene family in rice (Oryza sativa) in maintaining Pi homeostasis have not been elucidated as yet.

RESULTS

Here, the identification and expression analysis for the homologs of LPR1/2 in rice were carried out. Five homologs, hereafter referred to as OsLPR1-5, were identified in rice, which are distributed on chromosome1 over a range of 65 kb. Phylogenetic analysis grouped OsLPR1/3/4/5 and OsLPR2 into two distinct sub-clades with OsLPR3 and 5 showing close proximity. Quantitative real-time RT-PCR (qRT-PCR) analysis revealed higher expression levels of OsLPR3-5 and OsLPR2 in root and shoot, respectively. Deficiencies of different nutrients ie, P, nitrogen (N), potassium (K), magnesium (Mg) and iron (Fe) exerted differential and partially overlapping effects on the relative expression levels of the members of OsLPR family. Pi deficiency (-P) triggered significant increases in the relative expression levels of OsLPR3 and 5. Strong induction in the relative expression levels of OsLPR3 and 5 in osphr2 suggested their negative transcriptional regulation by OsPHR2. Further, the expression levels of OsLPR3 and 5 were either attenuated in ossiz1 and ospho2 or augmented in rice overexpressing OsSPX1.

CONCLUSIONS

The results from this study provided insights into the evolutionary expansion and a likely functional divergence of OsLPR family with potential roles of OsLPR3 and 5 in the maintenance of Pi homeostasis in rice.

Systematic characterization of novel lncRNAs responding to phosphate starvation in Arabidopsis thaliana

BACKGROUND

Previously, several long non-coding RNAs (lncRNAs) were characterized as regulators in phosphate (Pi) starvation responses. However, systematic studies of novel lncRNAs involved in the Pi starvation signaling pathways have not been reported.

RESULTS

Here, we used a genome-wide sequencing and bioinformatics approach to identify both poly(A) + and poly(A)- lncRNAs that responded to Pi starvation in Arabidopsis thaliana. We sequenced shoot and root transcriptomes of the Arabidopsis seedlings grown under Pi-sufficient and Pi-deficient conditions, and predicted 1212 novel lncRNAs, of which 78 were poly(A)- lncRNAs. By employing strand-specific RNA libraries, we discovered many novel antisense lncRNAs for the first time. We further defined 309 lncRNAs that were differentially expressed between P+ and P- conditions in either shoots or roots. Through Gene Ontology enrichment of the associated protein-coding genes (co-expressed or close on the genome), we found that many lncRNAs were adjacent or co-expressed with the genes involved in several Pi starvation related processes, including cell wall organization and photosynthesis. In total, we identified 104 potential lncRNA targets of PHR1, a key regulator for transcriptional response to Pi starvation. Moreover, we identified 16 candidate lncRNAs as potential targets of miR399, another key regulator of plant Pi homeostasis.

CONCLUSIONS

Altogether, our data provide a rich resource of candidate lncRNAs involved in the Pi starvation regulatory network.

Characterization of the AtSPX3 Promoter Elucidates its Complex Regulation in Response to Phosphorus Deficiency

AtSPX3, responding to phosphate (Pi) deficiency by its expression, is an important gene involved in Pi homeostasis in Arabidopsis. To understand its transcriptional regulation, we characterized the AtSPX3 promoter by distal truncation, internal deletion and mutation of the predicted cis-elements, and identified multiple cis-elements responsive to Pi status. The P1BS (AtPHR-binding site) and AtMyb4 (putative MYB4-binding site) elements were two main cis-elements in the AtSPX3 promoter. P1BS is essential and has a dosage effect for activating expression of the gene under Pi deficiency, while the element AtMyb4 possesses a dual function: one is to enhance AtSPX3 expression in roots under Pi deficiency, and the other one is to repress AtSPX3 expression in shoots under both Pi deficiency and sufficiency. Moreover, we confirmed that AtPHR1, a key transcription factor in Pi homeostasis of plants, was required for the negative regulation function of the AtMyb4 element in shoots. Additionally, we also found that the AtSPX3 promoter had a length limitation for activating gene expression. Generally, our findings in this work are useful for understanding the molecular regulation mechanism of genes involved in Pi uptake and homeostasis.

Regulation of phosphorus uptake and utilization: transitioning from current knowledge to practical strategies

Phosphorus is a poorly bioavailable macronutrient that is essential for crop growth and yield. Overuse of phosphorus fertilizers results in low phosphorus use efficiency (PUE), has serious environmental consequences and accelerates the depletion of phosphorus mineral reserves. It has become extremely challenging to improve PUE while preserving global food supplies and maintaining environmental sustainability. Molecular and genetic analyses have revealed the primary mechanisms of phosphorus uptake and utilization and their relationships to phosphorus transporters, regulators, root architecture, metabolic adaptations, quantitative trait loci, hormonal signaling and microRNA. The ability to improve PUE requires a transition from this knowledge of molecular mechanisms and plant architecture to practical strategies. These could include: i) the use of arbuscular mycorrhizal fungal symbioses for efficient phosphorus mining and uptake; ii) intercropping with suitable crop species to achieve phosphorus activation and mobilization in the soil; and iii) tissue-specific overexpression of homologous genes with advantageous agronomic properties for higher PUE along with breeding for phosphorus-efficient varieties and introgression of key quantitative trait loci. More effort is required to further dissect the mechanisms controlling phosphorus uptake and utilization within plants and provide new insight into the means to efficiently improve PUE.

Strigolactones are required for nitric oxide to induce root elongation in response to nitrogen and phosphate deficiencies in rice

The response of the root system architecture to nutrient deficiencies is critical for sustainable agriculture. Nitric oxide (NO) is considered a key regulator of root growth, although the mechanisms remain unknown. Phenotypic, cellular and genetic analyses were undertaken in rice to explore the role of NO in regulating root growth and strigolactone (SL) signalling under nitrogen-deficient and phosphate-deficient conditions (LN and LP). LN-induced and LP-induced seminal root elongation paralleled NO production in root tips. NO played an important role in a shared pathway of LN-induced and LP-induced root elongation via increased meristem activity. Interestingly, no responses of root elongation were observed in SL d mutants compared with wild-type plants, although similar NO accumulation was induced by sodium nitroprusside (SNP) application. Application of abamine (the SL inhibitor) reduced seminal root length and pCYCB1;1::GUS expression induced by SNP application in wild type; furthermore, comparison with wild type showed lower SL-signalling genes in nia2 mutants under control and LN treatments and similar under SNP application. Western blot analysis revealed that NO, similar to SL, triggered proteasome-mediated degradation of D53 protein levels. Therefore, we presented a novel signalling pathway in which NO-activated seminal root elongation under LN and LP conditions, with the involvement of SLs.

TabHLH1, a bHLH-type transcription factor gene in wheat, improves plant tolerance to Pi and N deprivation via regulation of nutrient transporter gene transcription and ROS homeostasis

Basic helix-loop-helix (bHLH) transcription factors (TFs) comprise a large TF family and act as crucial regulators in various biological processes in plants. Here, we report the functional characterization of TabHLH1, a bHLH TF member in wheat (Triticum aestivum). TabHLH1 shares conserved bHLH domain and targets to nucleus with transactivation activity. Upon Pi and N deprivation, the expression of TabHLH1 was up-regulated in roots and leaves, showing a pattern to be gradually increased within 23-h treatment regimes. The lines with overexpression of TabHLH1 exhibited drastically improved tolerance to Pi and N deprivation, showing larger plant phenotype, more biomass, higher concentration and more accumulation of P and N than wild type (WT) upon the Pi- and N-starvation stresses. NtPT1 and NtNRT2.2, the genes encoding phosphate transporter (PT) and nitrate transporter (NRT) in tobacco, respectively, showed up-regulated expression in TabHLH1-overexpressing plants; knockdown expression of them led to deteriorated growth feature, lowered biomass, and decreased nutrient accumulation of plants under Pi- and N-deficient conditions. Compared with WT, the TabHLH1-overexpressing plants also showed lowered reactive oxygen species (ROS) accumulation and improved antioxidant enzyme (AE) activities, such as those of superoxide dismutase (SOD), catalase (CAT), and peroxidase (POD). NtSOD1, NtCAT1, and NtPOD1;6 that encode SOD, CAT, and POD, respectively, were up-regulated in TabHLH1-overexpressing plants. Further knockdown of these AE gene expression caused reduced antioxidant enzymatic activities, indicative of their crucial roles in mediating cellular ROS homeostasis in Pi- and N-starvation conditions. Together, TabHLH1 plays an important role in mediating adaptation to the Pi- and N-starvation stresses through transcriptional regulation of a set of genes encoding PT, NRT and AEs that mediate the taken up of Pi and N and the cellular homeostasis of ROS initiated by the nutrient stresses.

Ecological speciation in sympatric palms: 1. Gene expression, selection and pleiotropy

Ecological speciation requires divergent selection, reproductive isolation and a genetic mechanism to link the two. We examined the role of gene expression and coding sequence evolution in this process using two species of Howea palms that have diverged sympatrically on Lord Howe Island, Australia. These palms are associated with distinct soil types and have displaced flowering times, representing an ideal candidate for ecological speciation. We generated large amounts of RNA‐Seq data from multiple individuals and tissue types collected on the island from each of the two species. We found that differentially expressed loci as well as those with divergent coding sequences between Howea species were associated with known ecological and phenotypic differences, including response to salinity, drought, pH and flowering time. From these loci, we identified potential ‘ecological speciation genes’ and further validate their effect on flowering time by knocking out orthologous loci in a model plant species. Finally, we put forward six plausible ecological speciation loci, providing support for the hypothesis that pleiotropy could help to overcome the antagonism between selection and recombination during speciation with gene flow.

Phytohormone regulation of root growth triggered by P deficiency or Al toxicity

Phosphorus (P) deficiency and aluminum (Al) toxicity often coexist and limit plant growth on acid soils. It has been well documented that both P deficiency and Al toxicity alter root growth, including inhibition of primary roots and promotion of lateral roots. This suggests that plants adapt to both stresses through a common regulation pathway. Although an expanding set of results shows that phytohormones play vital roles in controlling root responses to Pi starvation and Al toxicity, it remains largely unknown whether P and Al coordinately regulate root growth through interacting phytohormone biosynthesis and signal transduction pathways. This review provides a summary of recent results concerning the influences of P deficiency and Al toxicity on root growth through the action of phytohormones, most notably auxin and ethylene. The objective is to facilitate increasing insights into complex responses of plants to adverse factors common on acid soils, which can spur development of 'smart' cultivars with better root growth and higher yield on these globally distributed marginal soils.

The regulation and plasticity of root hair patterning and morphogenesis

Root hairs are highly specialized cells found in the epidermis of plant roots that play a key role in providing the plant with water and mineral nutrients. Root hairs have been used as a model system for understanding both cell fate determination and the morphogenetic plasticity of cell differentiation. Indeed, many studies have shown that the fate of root epidermal cells, which differentiate into either root hair or non-hair cells, is determined by a complex interplay of intrinsic and extrinsic cues that results in a predictable but highly plastic pattern of epidermal cells that can vary in shape, size and function. Here, we review these studies and discuss recent evidence suggesting that environmental information can be integrated at multiple points in the root hair morphogenetic pathway and affects multifaceted processes at the chromatin, transcriptional and post-transcriptional levels.