Identification of soybean purple acid phosphatase genes and their expression responses to phosphorus availability and symbiosis

From genes to traits: maximizing phosphorus utilization efficiency in crop plants

Phosphorus (P) is a critical macronutrient for plant growth, but its limited availability requires efficient utilization strategies. The excessive use of P fertilizers leads to low phosphorus utilization efficiency (PUE), causing severe environmental impacts and speeding up the exhaustion of P mineral reserves. Plants respond to inorganic phosphate (Pi) deficiency through complex signaling pathways that trigger changes in gene expression, root architecture, and metabolic pathways to enhance P acquisition and utilization efficiency. By exploring the interplay between genetic regulators and microorganisms, cultivars with superior PUE traits can be developed, which will ensure agricultural resilience and productivity in the face of depleting global P reserves. We highlight the synergistic interaction between genetic regulators and microorganisms to boost PUE as well as recent advancements in unraveling molecular mechanisms governing P homeostasis in plants, emphasizing the urgency to improve plant traits for improved P utilization.

Phytic acid is an available phosphorus source for maize plants in juvenile phase belonging to two populations with different breeding backgrounds

BACKGROUND

Applying animal effluent/digestate to forage crops can improve the sustainability of intensive livestock husbandry. Organic phosphorus (P) forms, in particular phytic acid (InsP6) present in animal effluent/digestate, would benefit from an effective uptake and assimilation by crops thus representing an alternative to mineral P fertilization and controlling P losses in water system. A maize (Zea mays L.) traditional Italian population (VA572), bred before the widespread diffusion of crop chemical fertilization, and a modern commercial hybrid (P1547) were used in this study to investigate their ability of growing in soilless medium using phytic acid (Po) vs phosphate P (Pi) as P sources in a 28-day experiment. The hypothesis was that the different agronomical context in which the two varieties were selected could have brought to different abilities in exploiting P sources for plant growth.

RESULTS

Quantitative and qualitative growth parameters, root enzymatic phosphatase activities and root transcriptome by RNA-seq analysis were analyzed in this study. Both maize populations were able to grow using phytic acid as the sole P source but organic P utilization was less efficient than Pi; a significant root-released phytase activity, induced by the presence of InsP6, was detected in Po treatment. The RNA-seq analysis showed different expression patterns induced by organic P treatment (Po) in the two populations. The upregulation in Po treatment of a Purple Acid Phosphatase (PAP) gene and of genes involved in inositol transport indicate that both phosphate hydrolysis from InsP6 by root-secreted PAPs and a direct uptake of myo-inositol at various degrees of phosphorylation could be involved in maize phytic acid exploitation. Root system development and the relationship of P sources with other macro and micro nutrient uptake (N, K, metal ions) were also implied in the response to Po treatment.

CONCLUSIONS

This study indicates that phytic acid is a bioavailable P source for maize seedling growth. A wider mobilization of genes/pathways was induced by Po treatment in VA572 with respect to P1547 hybrid. The physiological responses to Po treatment were similar in both populations but the patterns of genes involved often differed being specific to each one.

Identification and Expression Analysis of Acid Phosphatase Gene (PAP) in Brassica napus: Effects of cis-Acting Elements on Two BnaPAP10 Genes in Response to Phosphorus Stress

Purple acid phosphatases (PAPs) play a key role in phosphorus (P) assimilation and redistribution in plants, catalyzing the hydrolysis of phosphate esters to produce inorganic phosphate (Pi). In this study, a total of 77 PAP genes were identified in B. napus. The candidate genes were divided into three groups and ten subgroups based on the phylogenetic analyses and exon-intron organization. Among these 77 BnaPAP proteins, 35 exhibit typical metal-ligating residues characteristic of known PAPs, whereas certain unaltered amino acid residues were absent or displaced in other BnaPAPs. A computational prediction was conducted, revealing that the majority of PAPs contain signal peptide motifs and display a range of N-glycosylation levels, as well as transmembrane helix motifs. An analysis of previously obtained RNA-seq data revealed that 55.84% (43 of 77) of the BnaPAPs responded to Pi deficiency. Moreover, we conducted a preliminary examination of the expression profiles of BnaPAP genes in response to salt stress, and discovered that 42.86% (33 of 77) of these genes were induced under salt stress, either in the shoots or in the roots. Further qRT-PCR and GUS analyses revealed that BnaC9.PAP10 and BnaA7.PAP10, two paralogs of BnaPAP10s, were induced by Pi deficiency. Notably, BnaC9.PAP10 exhibits robust induction, compared to the relatively mild induction observed in BnaA7.PAP10. Our research shows that BnaA7.PAP10 uniquely responds to Pi stress via the W-box, while BnaA7.PAP10 predominantly responds via the P1BS element, and the differences in cis-regulatory elements (CREs) within their promoter regions specifically contribute to their distinct expression levels under Pi stress. Our findings provide valuable insights and establish a foundation for future functional studies of BnaPAPs.

Genome-Wide Analysis, Identification, and Transcriptional Profile of the Response to Abiotic Stress of the Purple Acid Phosphatases (PAP) Gene Family in Apple

Purple acid phosphatases (PAPs) play a significant role in plant phosphorus nutrition and can not only release phosphorus from the soil but also regulate the distribution of phosphorus in plants throughout their entire growth and development process. Moreover, members of the PAP protein family exert a more extensive influence on plant mineral homeostasis, developmental processes, and stress responses. Three clusters of purple acid phosphatases, including 31 putative genes, were identified in apples (Malus domestica) by searching the Genome Database for Rosaceae. The structure, chromosomal distribution and location, phylogeny, motifs, and cis-acting elements in the gene promoter regions of the MdPAP gene family are reviewed. These genes exhibit different expression patterns in different tissues. For example, almost all MdPAP genes are strongly expressed in the roots, except for MdPAP10, MdPAP12, and MdPAP27. Similarily, all MdPAPs were expressed in the leaves while the transcript levels of MdPAP7, MdPAP10, MdPAP15, MdPAP21, MdPAP24, MdPAP26, MdPAP29, and MdPAP30 were highest in apple flowers. Overall, the expression of the 31 genes significantly changed in either the roots or leaves following the application of phosphorus and/or drought stress. These results indicate that MdPAP family members play a role in plant adaptation to adverse environments. This work explores the adaptative responses to phosphorus and/or drought conditions in apple and establishes a foundation for an enhanced comprehension of the evolution of PAP families and the exploration of the genes of interest.

Analysis and profiling of the purple acid phosphatase gene family in wheat (Triticum aestivum L.)

Purple acid phosphatases (PAPs) play a vital role in plant phosphorus nutrition, serving as a crucial family of metallo-phosphoesterase enzymes. This research aimed to identify the PAP genes from the A/B/D genomes of Triticum aestivum to elucidate evolutionary mechanisms of the gene family in plants and provide genomic information for subsequent research on phosphorous-use efficiency in wheat crops. In total, 105 PAP genes (TaPAPs) were identified from the A/B/D genomes by using the Arabidopsis thaliana and Oryza sativa PAP protein sequences as queries for BLASTP against the wheat protein database. The TaPAPs were grouped into six subfamilies, Ia (17), Ib (26), IIa (11), IIb (30), IIIa (12), and IIIb (9), based on their similarities in the structure of genes and the presence of conserved protein motifs. A majority of TaPAPs were derived from tandemly (20) or segmentally (87) duplicated, with the homoeologous chromosomes 5A/B/D harboring the most duplicated PAP genes. Further analysis indicated that TaPAPs were responsible for the modulation of seed, root, and leaf development and hormone synthesis and signaling, as well as plant responses to abiotic stresses, including low temperatures, drought, and anaerobic conditions. Nine TaPAPs (TaPAP9-4A/4B/4D, TaPAP24-6A/6B/6D, and TaPAP28-7A/7B/7D) were constitutively expressed in diverse tissues such as root, shoot, leaf, spike, and seed, while the remaining genes exhibited tissue-specific expression patterns. Concerning the response to phosphate (Pi) deprivation, 57 TaPAPs were highly expressed in roots under Pi stress, including TaPAP31-4A, 4B, and 4D homeologs from the subfamily IIIb. A TaPAP31-4A transgene in A. thaliana promoted plant growth and development while increasing plant resistance to Pi-deficiency stress by enhancing the secretion of phosphatase. These discoveries provide a scientific foundation for comprehending the role of TaPAPs, offering valuable insights for identifying additional candidate genes and fostering the development of new wheat varieties with enhanced tolerance to low phosphorus conditions.

Genome-wide association study identified BnaPAP17 genes involved in exogenous ATP utilization and regulating phosphorous content in Brassica napus

KEY MESSAGE

BnaPAP17s associated with root-secreted APases activity were identified by genome-wide association study, and those were induced by Pi-deficiency. BnaPAP17s were involved in improving exogenous organophosphorus utilization as secreted APases. Deficiency of available phosphorus (P) in soil has become an important limiting factor for yield and quality in oilseed rape (Brassica napus). In many soils, organic P (Po) is the main component of the soil P pool. Po must be hydrolyzed to inorganic P (Pi) through acid Phosphatase (APases), and then taken up by plants. However, root-secreted APases (SAP) activity, as a quantitative trait, plays an important role in soil Po utilization; those genetic loci are not clear in B. napus. In this study, we performed a genome-wide association study for SAP activity under Pi-deficiency using a panel of 350 accessions of B. napus and more than 4.5 million polymorphic single nucleotide polymorphisms (SNPs). Thirty-five significant SNPs associated with SAP activity were identified. BnaA01.PAP17 (BnaA01g27810D) was a candidate gene underlying lead SNP (ChrA01_19576615). We experimentally verified that both BnaA01.PAP17 and its three homologous genes had similar expression pattern in response to Pi-deficiency. The dynamic changes in BnaPAP17s expression level were opposite to those of Pi concentration in both roots and leaves, suggesting their potential utility as Pi marker genes in B. napus. Transient expression of BnaPAP17s in tobacco leaves proved that BnaPAP17s were located in the apoplast as secreted APases. The overexpression of BnaPAP17s enhanced SAP activity in response to Pi-deficiency and resulting in increased P content in plants when ATP was supplied as the sole P resource. Taken together, these results suggest that BnaPAP17s contributed to SAP activity, thus having a function in extracellular Po utilization in B. napus.

GmIRT1.1 from soybean (Glycine max L.) is involved in transporting Fe, Mn and Cd

Soybean is one of the most important crops for producing high quality oil and protein. Mineral nutrient deficiencies are frequently observed in soybeans. However, there are few studies to understand the absorption process of mineral nutrients in soybeans. Here, we investigated the functions of soybean (Glycine max L.) IRT1.1 (IRON-REGULATED TRANSPORTER 1.1) in the transportation of mineral elements. Heterologous expression of GmIRT1.1 in yeast mutants revealed that GmIRT1.1 compensated for the growth defects of Δfet3fet4 and Δsmf1 mutants under iron (Fe) and manganese (Mn) deficiency conditions, respectively, and enhanced the sensitivity of the Δycf1 mutant to cadmium (Cd) toxicity. Expression analysis revealed that GmIRT1.1 was only significantly induced by Fe deficiency and was primarily expressed in roots. Furthermore, the GmIRT1.1 overexpression lines enhanced Arabidopsis tolerance to Fe deficiency, leading to increased accumulation of Fe in the roots and shoots. Additionally, the transgenic lines increased the sensitivity to Mn and Cd toxicity. Subcellular localization analysis revealed that GmIRT1.1 was localized on the plasma membrane. Moreover, the results obtained from the soybean hairy roots system indicated that the localization of GmIRT1.1 was dependent on the regulation of Fe homeostasis in plant. Consequently, these results suggested that GmIRT1.1 was responsible for the transportation of Fe, Mn and Cd.

Novel phosphatase PvPAP1 from the As-hyperaccumulator Pteris vittata promotes organic P utilization and plant growth: Extracellular exudation and phytate hydrolysis

Organic phosphorus (Po) is a large component of soil P, but it is often unavailable for plant uptake. Purple acid phosphatases (PAP) can hydrolyze a wide range of Po, playing an important role in Po utilization by plants. In this study, we investigated a novel secretary PvPAP1 from the As-hyperaccumulator Pteris vittata, which can effectively utilize exogenous Po, including adenosine triphosphate (ATP) and phytate. Unlike other PAP, PvPAP1 was abundantly-expressed in P. vittata roots, which was upregulated 3.5-folds under P-deprivation than P-sufficient conditions. When expressed in tobacco, its activity in the roots of PvPAP1-Ex lines was ∼8 folds greater than that in wild-type (WT) plants. Besides, PvPAP1 exhibited its secretory ability as evidenced by the sapphire-blue color on the root surface after treating with 5-bromo-4-chloro-3-indolyl phosphate. In a long-term experiment using sand media, PvPAP1-expressing tobacco plants showed 25-30 % greater root biomass than WT plants when using ATP as the sole P source. This is because PvPAP1-expression enhanced its phosphatase activity by 6.5-9.2 folds in transgenic tobacco, thereby increasing the P contents by 39-41 % in its roots under ATP treatment and 9.4-30 % under phytate treatment. The results highlight PvPAP1 as a novel secreted phosphatase crucial for external Po utilization in P. vittata, suggesting that PvPAP1 has the potential to serve as a valuable gene resource for enhancing Po utilization by crop plants.

Exploring the dynamic adaptive responses of Epimedium pubescens to phosphorus deficiency by Integrated transcriptome and miRNA analysis

Phosphorus, a crucial macronutrient essential for plant growth and development. Due to widespread phosphorus deficiency in soils, phosphorus deficiency stress has become one of the major abiotic stresses that plants encounter. Despite the evolution of adaptive mechanisms in plants to address phosphorus deficiency, the specific strategies employed by species such as Epimedium pubescens remain elusive. Therefore, this study observed the changes in the growth, physiological reponses, and active components accumulation in E. pubescensunder phosphorus deficiency treatment, and integrated transcriptome and miRNA analysis, so as to offer comprehensive insights into the adaptive mechanisms employed by E. pubescens in response to phosphorus deficiency across various stages of phosphorus treatment. Remarkably, our findings indicate that phosphorus deficiency induces root growth stimulation in E. pubescens, while concurrently inhibiting the growth of leaves, which are of medicinal value. Surprisingly, this stressful condition results in an augmented accumulation of active components in the leaves. During the early stages (30 days), leaves respond by upregulating genes associated with carbon metabolism, flavonoid biosynthesis, and hormone signaling. This adaptive response facilitates energy production, ROS scavenging, and morphological adjustments to cope with short-term phosphorus deficiency and sustain its growth. As time progresses (90 days), the expression of genes related to phosphorus cycling and recycling in leaves is upregulated, and transcriptional and post-transcriptional regulation (miRNA regulation and protein modification) is enhanced. Simultaneously, plant growth is further suppressed, and it gradually begins to discard and decompose leaves to resist the challenges of long-term phosphorus deficiency stress and sustain survival. In conclusion, our study deeply and comprehensively reveals adaptive strategies utilized by E. pubescens in response to phosphorus deficiency, demonstrating its resilience and thriving potential under stressful conditions. Furthermore, it provides valuable information on potential target genes for the cultivation of E. pubescens genotypes tolerant to low phosphorus.

Overexpression of GmPAP4 Enhances Symbiotic Nitrogen Fixation and Seed Yield in Soybean under Phosphorus-Deficient Condition

Legume crops establish symbiosis with nitrogen-fixing rhizobia for biological nitrogen fixation (BNF), a process that provides a prominent natural nitrogen source in agroecosystems; and efficient nodulation and nitrogen fixation processes require a large amount of phosphorus (P). Here, a role of GmPAP4, a nodule-localized purple acid phosphatase, in BNF and seed yield was functionally characterized in whole transgenic soybean (Glycine max) plants under a P-limited condition. GmPAP4 was specifically expressed in the infection zones of soybean nodules and its expression was greatly induced in low P stress. Altered expression of GmPAP4 significantly affected soybean nodulation, BNF, and yield under the P-deficient condition. Nodule number, nodule fresh weight, nodule nitrogenase, APase activities, and nodule total P content were significantly increased in GmPAP4 overexpression (OE) lines. Structural characteristics revealed by toluidine blue staining showed that overexpression of GmPAP4 resulted in a larger infection area than wild-type (WT) control. Moreover, the plant biomass and N and P content of shoot and root in GmPAP4 OE lines were also greatly improved, resulting in increased soybean yield in the P-deficient condition. Taken together, our results demonstrated that GmPAP4, a purple acid phosphatase, increased P utilization efficiency in nodules under a P-deficient condition and, subsequently, enhanced symbiotic BNF and seed yield of soybean.

Phosphate starvation response precedes abscisic acid response under progressive mild drought in plants

Drought severely damages crop production, even under conditions so mild that the leaves show no signs of wilting. However, it is unclear how field-grown plants respond to mild drought. Here, we show through six years of field trials that ridges are a useful experimental tool to mimic mild drought stress in the field. Mild drought reduces inorganic phosphate levels in the leaves to activate the phosphate starvation response (PSR) in soybean plants in the field. Using Arabidopsis thaliana and its mutant plants grown in pots under controlled environments, we demonstrate that PSR occurs before abscisic acid response under progressive mild drought and that PSR plays a crucial role in plant growth under mild drought. Our observations in the field and laboratory using model crop and experimental plants provide insight into the molecular response to mild drought in field-grown plants and the relationship between nutrition and drought stress response.

Allelic Variation in GmPAP14 Alters Gene Expression to Affect Acid Phosphatase Activity in Soybean

Improvement in acid phosphatase (APase) activity is considered as an important approach to enhance phosphorus (P) utilization in crops. Here, GmPAP14 was significantly induced by low P (LP), and its transcription level in ZH15 (P efficient soybean) was higher than in NMH (P inefficient soybean) under LP conditions. Further analyses demonstrated that there were several variations in gDNA (G-GmPAP14Z and G-GmPAP14N) and the promoters (P-GmPAP14Z and P-GmPAP14N) of GmPAP14, which might bring about differential transcriptional levels of GmPAP14 in ZH15 and NMH. Histochemical staining measurements revealed that a stronger GUS signal was present in transgenic Arabidopsis with P-GmPAP14Z under LP and normal P (NP) conditions compared with the P-GmPAP14N plant. Functional research demonstrated that transgenic Arabidopsis with G-GmPAP14Z had a higher level of GmPAP14 expression than the G-GmPAP14N plant. Meanwhile, higher APase activity was also observed in the G-GmPAP14Z plant, which led to increases in shoot weight and P content. Additionally, validation of variation in 68 soybean accessions showed that varieties with Del36 displayed higher APase activities than the del36 plant. Thus, these results uncovered that allelic variation in GmPAP14 predominantly altered gene expression to influence APase activity, which provided a possible direction for research of this gene in plants.

Understandings and future challenges in soybean functional genomics and molecular breeding

Soybean (Glycine max) is a major source of plant protein and oil. Soybean breeding has benefited from advances in functional genomics. In particular, the release of soybean reference genomes has advanced our understanding of soybean adaptation to soil nutrient deficiencies, the molecular mechanism of symbiotic nitrogen (N) fixation, biotic and abiotic stress tolerance, and the roles of flowering time in regional adaptation, plant architecture, and seed yield and quality. Nevertheless, many challenges remain for soybean functional genomics and molecular breeding, mainly related to improving grain yield through high-density planting, maize-soybean intercropping, taking advantage of wild resources, utilization of heterosis, genomic prediction and selection breeding, and precise breeding through genome editing. This review summarizes the current progress in soybean functional genomics and directs future challenges for molecular breeding of soybean.

Cooperative interactions between nitrogen fixation and phosphorus nutrition in legumes

Legumes such as soybean are considered important crops as they provide proteins and oils for humans and livestock around the world. Different from other crops, leguminous crops accumulate nitrogen (N) for plant growth through symbiotic nitrogen fixation (SNF) in coordination with rhizobia. A number of studies have shown that efficient SNF requires the cooperation of other nutrients, especially phosphorus (P), a nutrient deficient in most soils. During the last decades, great progress has been made in understanding the molecular mechanisms underlying the interactions between SNF and P nutrition, specifically through the identification of transporters involved in P transport to nodules and bacteroids, signal transduction, and regulation of P homeostasis in nodules. These studies revealed a distinct N-P interaction in leguminous crops, which is characterized by specific signaling cross talk between P and SNF. This review aimed to present an updated picture of the cross talk between N fixation and P nutrition in legumes, focusing on soybean as a model crop, and Medicago truncatula and Lotus japonicus as model plants. We also discuss the possibilities for enhancing SNF through improving P nutrition, which are important for high and sustainable production of leguminous crops.

Integration of the transcriptome and metabolome reveals the mechanism of resistance to low phosphorus in wild soybean seedling leaves

Plant growth, development, yield and quality are limited by barren soil. Soil phosphorus deficiency is one of the common factors causing soil barrenness. Plants have evolved morphological, physiological and molecular adaptations to resist to phosphorus deficiency. Wild soybean, a wild relative of cultivated soybean, has an obvious genetic relationship with cultivated soybean and has many beneficial characteristics such as strong low phosphorus resistance. Therefore, in this study, the integration analysis of transcriptome and metabolome of wild and cultivated soybean seedlings leaves were applied under phosphorus deficiency to reveal the mechanism of resistance to low phosphorus stress in wild soybean leaves, especially the key role of membrane phospholipid reuse and protection. Under phosphorus deficiency, wild soybean resisted low phosphorus stress by enhancing phosphorus reuse and strengthening membrane protection mechanisms, that is, by enhancing phospholipid metabolism, degrading membrane phospholipids, releasing phosphorus, increasing phosphorus reuse, and enhancing galactolipid biosynthesis. This, in turn, produced digalactosyl diacylglycerol to replace missing phospholipids for membrane maintenance and enhanced glutathione metabolism to protect the membrane system from damage. At the same time, phosphorus deficiency increased the levels of the intermediate metabolites glycine and ornithine, while significantly regulating the expression of transcription factors WRKY75 and MYB86. The enhancement of these metabolic pathways and the significant regulation of gene expression play an important role in improving the low phosphorus tolerance of wild soybean. This study will provide a useful theoretical basis for breeding soybean with low phosphorus tolerance.

Integrated multi-omics reveals the molecular mechanisms underlying efficient phosphorus use under phosphate deficiency in elephant grass (Pennisetum purpureum)

Phosphorus (P) is an essential macronutrient element for plant growth, and deficiency of inorganic phosphate (Pi) limits plant growth and yield. Elephant grass (Pennisetum purpureum) is an important fodder crop cultivated widely in tropical and subtropical areas throughout the world. However, the mechanisms underlying efficient P use in elephant grass under Pi deficiency remain poorly understood. In this study, the physiological and molecular responses of elephant grass leaves and roots to Pi deficiency were investigated. The results showed that dry weight, total P concentration, and P content decreased in Pi-deprived plants, but that acid phosphatase activity and P utilization efficiency (PUE) were higher than in Pi-sufficient plants. Regarding Pi starvation-responsive (PSR) genes, transcriptomics showed that 59 unigenes involved in Pi acquisition and transport (especially 18 purple acid phosphatase and 27 phosphate transporter 1 unigenes) and 51 phospholipase unigenes involved in phospholipids degradation or Pi-free lipids biosynthesis, as well as 47 core unigenes involved in the synthesis of phenylpropanoids and flavonoids, were significantly up-regulated by Pi deprivation in leaves or roots. Furthermore, 43 unigenes related to Pi-independent- or inorganic pyrophosphate (PPi)-dependent bypass reactions were markedly up-regulated in Pi-deficient leaves, especially five UDP-glucose pyrophosphorylase and 15 phosphoenolpyruvate carboxylase unigenes. Consistent with PSR unigene expression changes, metabolomics revealed that Pi deficiency significantly increased metabolites of Pi-free lipids, phenylpropanoids, and flavonoids in leaves and roots, but decreased phospholipid metabolites. This study reveals the mechanisms underlying the responses to Pi starvation in elephant grass leaves and roots, which provides candidate unigenes involved in efficient P use and theoretical references for the development of P-efficient elephant grass varieties.

Genome wide association studies for acid phosphatase activity at varying phosphorous levels in Brassica juncea L

Acid phosphatases (Apases) are an important group of enzymes that hydrolyze soil and plant phosphoesters and anhydrides to release Pi (inorganic phosphate) for plant acquisition. Their activity is strongly correlated to the phosphorus use efficiency (PUE) of plants. Indian mustard (Brassica juncea L. Czern & Coss) is a major oilseed crop that also provides protein for the animal feed industry. It exhibits low PUE. Understanding the genetics of PUE and its component traits, especially Apase activity, will help to reduce Pi fertilizer application in the crop. In the present study, we evaluated 280 genotypes of the diversity fixed foundation set of Indian mustard for Apase activity in the root (RApase) and leaf (LApase) tissues at three- low (5µM), normal (250µM) and high (1mM) Pi levels in a hydroponic system. Substantial effects of genotype and Pi level were observed for Apase activity in both tissues of the evaluated lines. Low Pi stress induced higher mean RApase and LApase activities. However, mean LApase activity was relatively more than mean RApase at all three Pi levels. JM06016, IM70 and Kranti were identified as promising genotypes with higher LApase activity and increased R/S at low Pi. Genome-wide association study revealed 10 and 4 genomic regions associated with RApase and LApase, respectively. Annotation of genomic regions in the vicinity of peak associated SNPs allowed prediction of 15 candidates, including genes encoding different family members of the acid phosphatase such as PAP10 (purple acid phosphatase 10), PAP16, PNP (polynucleotide phosphorylase) and AT5G51260 (HAD superfamily gene, subfamily IIIB acid phosphatase) genes. Our studies provide an understanding of molecular mechanism of the Apase response of B. juncea at varying Pi levels. The identified SNPs and candidate genes will support marker-assisted breeding program for improving PUE in Indian mustard. This will redeem the crop with enhanced productivity under restricted Pi reserves and degrading agro-environments.

Purple acid phosphatases in coffee-genome-wide identification and the transcriptional profile of selected members in roots upon Pi starvation

Phosphorus (P) availability is determinant for crop productivity and, despite the sufficient amount of this nutrient in arable land, most of it remains insoluble, leading to the need of high fertilizer input. To cope with P scarcity forecasts and also for cropping costs alleviation, genotypes better adapted to promote P solubilization and absorption are required, especially for perennial crops. Coffee is one of these important perennial crops cultivated in soils with low P availability, and thus we aimed to study adaptive strategies to coffee genotypes in acquire phosphorus. In this study, we focused on rhizosphere phosphatase activity, a major characteristic related to P solubilization from organic pools. To explore the genetic basis of this characteristic, we firstly identified 29 Purple Acid Phosphatases (PAP) genes in C. canephora genome and selected five candidates with higher potential to encode secreted PAPs. We found that C. arabica genotypes have diverse profiles of rhizosphere phosphatase activity, as well as microbial biomass carbon, which we measured to explore the impact of the plant on microbiota and also to discriminate the phosphatase activity origin (plant or microorganism-derived). We selected two C. arabica cultivars with contrasting phosphatase activity and found that one PAP gene has a correlated gene expression profile with this characteristic. This work explores coffee adaptative responses to P starvation conditions, and the information provided can further contribute to breeding programs aiming better adapted genotypes for sustainable agriculture in face of current challenges.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-022-03399-6.

Integrating transcriptomic and metabolomic analysis in roots of wild soybean seedlings in response to low-phosphorus stress

INTRODUCTION

Plants undergo divergent adaptations to form different ecotypes when exposed to different habitats. Ecotypes with ecological adaptation advantages are excellent germplasm resources for crop improvement.

METHODS

his study comprehensively compared the differences in morphology and physiological mechanisms in the roots of two different ecotypes of wild soybean (Glycine soja) seedlings under artificially simulated low-phosphorus (LP) stress.

RESULT

The seedlings of barren-tolerant wild soybean (GS2) suffered less damage than common wild soybean (GS1). GS2 absorbed more phosphorus (P) by increasing root length. In-depth integrated analyses of transcriptomics and metabolomics revealed the formation process of the ecological adaptability of the two different ecotypes wild soybean from the perspective of gene expression and metabolic changes. This study revealed the adaptation process of GS2 from the perspective of the adaptation of structural and molecular metabolism, mainly including: (1) Enhancing the metabolism of phenolic compounds, lignin, and organic acid metabolism could activate unavailable soil P; (2) Up-regulating genes encoding pectinesterase and phospholipase C (PLC) specifically could promote the reuse of structural P; (3) Some factors could reduce the oxidative damage to the membranes caused by LP stress, such as accumulating the metabolites putrescine and ascorbate significantly, up-regulating the genes encoding SQD2 (the key enzyme of sulfolipid substitution of phospholipids) substantially and enhancing the synthesis of secondary antioxidant metabolite anthocyanins and the AsA-GSH cycle; (4) enhancing the uptake of soil P by upregulating inorganic phosphate transporter, acid phosphatase ACP1, and purple acid phosphatase genes; (5) HSFA6b and MYB61 are the key TFs to resist LP stress.

DISCUSSION

In general, GS2 could resist LP stress by activating unavailable soil P, reusing plant structural P, rebuilding membrane lipids, and enhancing the antioxidant membrane protection system. Our study provides a new perspective for the study of divergent adaptation of plants.

Prospects of genetics and breeding for low-phosphate tolerance: an integrated approach from soil to cell

Improving phosphorus (P) crop nutrition has emerged as a key factor toward achieving a more resilient and sustainable agriculture. P is an essential nutrient for plant development and reproduction, and phosphate (Pi)-based fertilizers represent one of the pillars that sustain food production systems. To meet the global food demand, the challenge for modern agriculture is to increase food production and improve food quality in a sustainable way by significantly optimizing Pi fertilizer use efficiency. The development of genetically improved crops with higher Pi uptake and Pi-use efficiency and higher adaptability to environments with low-Pi availability will play a crucial role toward this end. In this review, we summarize the current understanding of Pi nutrition and the regulation of Pi-starvation responses in plants, and provide new perspectives on how to harness the ample repertoire of genetic mechanisms behind these adaptive responses for crop improvement. We discuss on the potential of implementing more integrative, versatile, and effective strategies by incorporating systems biology approaches and tools such as genome editing and synthetic biology. These strategies will be invaluable for producing high-yielding crops that require reduced Pi fertilizer inputs and to develop a more sustainable global agriculture.

Multi-omics analysis of the regulatory effects of low-phosphorus stress on phosphorus transport in soybean roots

The regulatory effects of uneven phosphorus supplies on phosphorus transport in soybean roots are still unclear. To further analyze the regulatory effects of low-phosphorus stress on phosphorus transport in soybean roots and the effects of uneven phosphorus application on the physiological mechanism of phosphorus transport in soybean roots, dual-root soybean plants were prepared via grafting, and a sand culture experiment was performed. From the unfolded cotyledon stage to the initial flowering stage, one side of each dual-root soybean system was irrigated with a low-phosphorus-concentration solution (phosphorus-application [P+] side), and the other side was irrigated with a phosphorus-free nutrient solution (phosphorus-free [P-] side); this setup allowed the study of the effects of different phosphorus supply levels on the expression of genes and proteins and the accumulation of metabolites in soybean roots on the P- side to clarify the method through which phosphorus transport is regulated in soybean roots and to provide a theoretical basis for improving the use rate of phosphorus fertilizer. The results revealed that the unilateral supply of low-concentration phosphorus promoted the uptake of phosphorus by soybean roots and the transport of phosphorus from the P+ side to the P- side. Compared with the normal concentration of phosphorus supply and the phosphorus-free supply, the low concentration phosphorus supply affected the regulation of the metabolic pathways involved in starch and sucrose metabolism, glycolysis, fructose, and mannose metabolism, etc., thereby affecting soybean root phosphorus transport. The low-phosphorus stress inhibited fructose synthesis and sucrose synthase synthesis in the soybean roots and the synthesis of hexokinase (HK) and fructose kinase, which catalyzes the conversion of fructose to fructose-6-phosphate. Low-phosphorus stress promoted the synthesis of sucrose invertase and the conversion of sucrose into maltose by the activity of starch synthase (StS) and stimulated the synthesis of UDPG pyrophosphorylase (UGP) and phosphoglucose isomerase (GP1), which is involved in the conversion of UDP-glucose to glucose-6-phosphate. The phosphorus transport pathway of soybean roots was then affected, which promoted phosphorus allocation to UTP and glucose-6-phosphate. Additionally, low-phosphorus stress hastened glycolysis in the soybean roots and inhibited the synthesis of malic acid, thereby promoting the transport of phosphorus in the roots. In addition, low-phosphorus stress inhibited the synthesis of fructose, mannose, and mannose-1-phosphate and the synthesis of other enzymes involved in phosphorus transport as well as invertase, thereby inhibiting the transport and synthesis of several organic phosphorus-containing compounds.

The purple acid phosphatase GmPAP17 predominantly enhances phosphorus use efficiency in soybean

Purple acid phosphatase (PAP) is an important plant acid phosphatase, which can secrete to the rhizosphere to decompose organophosphorus, promote phosphorus use efficiency, plant growth and development. However, little is known about the functions of intracellular PAP in plants, especially for soybean. Our previous study integrating QTL mapping and transcriptome analysis identified an promising low phosphorus (LP)-induced gene GmPAP17. Here, we determined that GmPAP17 was mainly expressed in roots and had a strong response to LP stress. Furthermore, and the relative expression in the root of LP tolerant genotypes NN94-156 was significantly greater than that of LP sensitive genotype Bogao after LP stress treatment. The overexpression of GmPAP17 significantly enhanced both acid phosphatase activity and growth performance of hairy roots under LP stress condition, it was vice versa for RNAi interference of GmPAP17, indicating that GmPAP17 plays an important role in P use efficiency. Moreover, yeast two-hybrid and bimolecular fluorescence complementation analysis showed that GmRAP2.2 was involved in the regulation network of GmPAP17. Taken together, our results suggest that GmPAP17 is a novel plant PAP that functions in the adaptation of soybean to LP stress, possibly through its involvement in P recycling in plants.

Narrowing down molecular targets for improving phosphorus-use efficiency in maize (Zea mays L.)

Conventional agricultural practices rely heavily on chemical fertilizers to boost production. Among the fertilizers, phosphatic fertilizers are copiously used to ameliorate low-phosphate availability in the soil. However, phosphorus-use efficiency (PUE) for major cereals, including maize, is less than 30%; resulting in more than half of the applied phosphate being lost to the environment. Rock phosphate reserves are finite and predicted to exhaust in near future with the current rate of consumption. Thus, the dependence of modern agriculture on phosphatic fertilizers poses major food security and sustainability challenges. Strategies to optimize and improve PUE, like genetic interventions to develop high PUE cultivars, could have a major impact in this area. Here, we present the current understanding and recent advances in the biological phenomenon of phosphate uptake, translocation, and adaptive responses of plants under phosphate deficiency, with special reference to maize. Maize is one of the most important cereal crops that is cultivated globally under diverse agro-climatic conditions. It is an industrial, feed and food crop with multifarious uses and a fast-rising global demand and consumption. The interesting aspects of diversity in the root system architecture traits, the interplay between signaling pathways contributing to PUE, and an in-depth discussion on promising candidate genes for improving PUE in maize are elaborated.

Overexpression of purple acid phosphatase GmPAP2.1 confers resistance to Soybean mosaic virus in a susceptible soybean cultivar

A purple acid phosphatase, GmPAP2.1, from the soybean (Glycine max) cultivar L29 may function as a resistance factor acting against specific strains of Soybean mosaic virus (SMV). In this study, we found that overexpression of GmPAP2.1 from L29 conferred SMV resistance to a susceptible cultivar, Lee 74. We determined that GmPAP2.1 interacted with the SMV protein P1 in the chloroplasts, resulting in the up-regulation of the ICS1 gene, which in turn promoted the pathogen-induced salicylic acid (SA) pathway. SA accumulation was elevated in response to the co-expression of GmPAP2.1 and SMV, while transient knockdown of endogenous SA-related genes resulted in systemic infection by SMV strain G5H, suggesting that GmPAP2.1-derived resistance depended on the SA-pathway for the activation of a defense response. Our findings thus suggest that GmPAP2.1 purple acid phosphatase of soybean cultivar L29 functions as an SA-pathway-dependent resistance factor acting against SMV.

The PAP Gene Family in Tomato: Comprehensive Comparative Analysis, Phylogenetic Relationships and Expression Profiles

Purple acid phosphatase (PAP) plays a vital role in plant phosphate acquisition and utilization, as well as cell wall synthesis and redox reactions. In this study, comprehensive comparative analyses of PAP genes were carried out using the integration of phylogeny, chromosomal localization, intron/exon structural characteristics, and expression profiling. It was shown that the number of introns of the PAP genes, which were distributed unevenly on 12 chromosomes, ranged from 1 to 12. These findings pointed to the existence of complex structures. Phylogenetic analyses revealed that PAPs from tomato, rice, and Arabidopsis could be divided into three groups (Groups I, II, and III). It was assumed that the diversity of these PAP genes occurred before the monocot–dicot split. RNA-seq analysis revealed that most of the genes were expressed in all of the tissues analyzed, with the exception of SlPAP02, SlPAP11, and SlPAP14, which were not detected. It was also found that expression levels of most of the SlPAP gene family of members were changed under phosphorus stress conditions, suggesting potential functional diversification. The findings of this work will help us to achieve a better insight into the function of SlPAP genes in the future, as well as enhance our understanding of their evolutionary relationships in plants.

Mechanisms for improving phosphorus utilization efficiency in plants

BACKGROUND

Limitation of plant productivity by phosphorus (P) supply is widespread and will probably increase in the future. Relatively large amounts of P fertilizer are applied to sustain crop growth and development and to achieve high yields. However, with increasing P application, plant P efficiency generally declines, which results in greater losses of P to the environment with detrimental consequences for ecosystems.

SCOPE

A strategy for reducing P input and environmental losses while maintaining or increasing plant performance is the development of crops that take up P effectively from the soil (P acquisition efficiency) or promote productivity per unit of P taken up (P utilization efficiency). In this review, we describe current research on P metabolism and transport and its relevance for improving P utilization efficiency.

CONCLUSIONS

Enhanced P utilization efficiency can be achieved by optimal partitioning of cellular P and distributing P effectively between tissues, allowing maximum growth and biomass of harvestable plant parts. Knowledge of the mechanisms involved could help design and breed crops with greater P utilization efficiency.

Purple acid phosphatases: roles in phosphate utilization and new emerging functions

Plants strive for phosphorus (P), which is an essential mineral for their life. Since P availability is limiting in most of the world's soils, plants have evolved with a complex network of genes and their regulatory mechanisms to cope with soil P deficiency. Among them, purple acid phosphatases (PAPs) are predominantly associated with P remobilization within the plant and acquisition from the soil by hydrolyzing organic P compounds. P in such compounds remains otherwise unavailable to plants for assimilation. PAPs are ubiquitous in plants, and similar enzymes exist in bacteria, fungi, mammals, and unicellular eukaryotes, but having some differences in their catalytic center. In the recent past, PAPs' roles have been extended to multiple plant processes like flowering, seed development, senescence, carbon metabolism, response to biotic and abiotic stresses, signaling, and root development. While new functions have been assigned to PAPs, the underlying mechanisms remained understood poorly. Here, we review the known functions of PAPs, the regulatory mechanisms, and their relevance in crop improvement for P-use-efficiency. We then discuss the mechanisms behind their functions and propose areas worthy of future research. Finally, we argue that PAPs could be a potential target for improving P utilization in crops. In turn, this is essential for sustainable agriculture.

Physiological responses and transcriptomic changes reveal the mechanisms underlying adaptation of Stylosanthes guianensis to phosphorus deficiency

BACKGROUND

Phosphorus (P) is an essential macronutrient for plant growth that participates in a series of biological processes. Thus, P deficiency limits crop growth and yield. Although Stylosanthes guianensis (stylo) is an important tropical legume that displays adaptation to low phosphate (Pi) availability, its adaptive mechanisms remain largely unknown.

RESULTS

In this study, differences in low-P stress tolerance were investigated using two stylo cultivars ('RY2' and 'RY5') that were grown in hydroponics. Results showed that cultivar RY2 was better adapted to Pi starvation than RY5, as reflected by lower values of relative decrease rates of growth parameters than RY5 at low-P stress, especially for the reduction of shoot and root dry weight. Furthermore, RY2 exhibited higher P acquisition efficiency than RY5 under the same P treatment, although P utilization efficiency was similar between the two cultivars. In addition, better root growth performance and higher leaf and root APase activities were observed with RY2 compared to RY5. Subsequent RNA-seq analysis revealed 8,348 genes that were differentially expressed under P deficient and sufficient conditions in RY2 roots, with many Pi starvation regulated genes associated with P metabolic process, protein modification process, transport and other metabolic processes. A group of differentially expressed genes (DEGs) involved in Pi uptake and Pi homeostasis were identified, such as genes encoding Pi transporter (PT), purple acid phosphatase (PAP), and multidrug and toxin extrusion (MATE). Furthermore, a variety of genes related to transcription factors and regulators involved in Pi signaling, including genes belonging to the PHOSPHATE STARVATION RESPONSE 1-like (PHR1), WRKY and the SYG1/PHO81/XPR1 (SPX) domain, were also regulated by P deficiency in stylo roots.

CONCLUSIONS

This study reveals the possible mechanisms underlying the adaptation of stylo to P deficiency. The low-P tolerance in stylo is probably manifested through regulation of root growth, Pi acquisition and cellular Pi homeostasis as well as Pi signaling pathway. The identified genes involved in low-P tolerance can be potentially used to design the breeding strategy for developing P-efficient stylo cultivars to grow on acid soils in the tropics.

Role of Cell Wall Polyphosphates in Phosphorus Transfer at the Arbuscular Interface in Mycorrhizas

Arbuscular mycorrhizal fungi provide plants with soil mineral nutrients, particularly phosphorus. In this symbiotic association, the arbuscular interface is the main site for nutrient exchange. To understand phosphorus transfer at the interface, we analyzed the subcellular localization of polyphosphate (polyP) in mature arbuscules of Rhizophagus irregularis colonizing roots of Lotus japonicus wild-type (WT) and H⁺-ATPase ha1-1 mutant, which is defective in phosphorus acquisition through the mycorrhizal pathway. In both, the WT and the ha1-1 mutant, polyP accumulated in the cell walls of trunk hyphae and inside fine branch modules close to the trunk hyphae. However, many fine branches lacked polyP. In the mutant, most fine branch modules showed polyP signals compared to the WT. Notably, polyP was also observed in the cell walls of some fine branches formed in the ha1-1 mutant, indicating phosphorus release from fungal cells to the apoplastic regions. Intense acid phosphatase (ACP) activity was detected in the periarbuscular spaces around the fine branches. Furthermore, double staining of ACP activity and polyP revealed that these had contrasting distribution patterns in arbuscules. These observations suggest that polyP in fungal cell walls and apoplastic phosphatases may play an important role in phosphorus transfer at the symbiotic interface in arbuscules.

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.

The soybean β-expansin gene GmINS1 contributes to nodule development in response to phosphate starvation

Legume biological nitrogen fixation (BNF) is the most important N source in agricultural ecosystems. Nodule organogenesis from the primordia to the development of mature nodules with the ability to fix N2 largely determines BNF capacity. However, nodule growth is often limited by low phosphorus (P) availability, while the mechanisms underlying nodule development responses to P deficiency remain largely unknown. In this study, we found that nodule enlargement is severely inhibited by P deficiency, as reflected by the smaller individual nodule size from a soybean core collection in the field. Wide-ranging natural diversity in nodule size was further identified in soybeans reared in low P soils, with the FC-1 genotype outperforming FC-2 in assessments of nodulation under low P conditions. Among β-expansin members, GmINS1 expression is most abundantly enhanced by P deficiency in FC-1 nodules, and its transcript level is further displayed to be tightly associated with nodule enlargement. Four single nucleotide polymorphisms discovered in the GmINS1 promoter distinguished the FC-1 and FC-2 genotypes and accounted for the differential expression levels of GmINS1 responses to P deficiency. GmINS1 overexpression led to increases in nodule size, infected cell abundance, and N2 fixation capacity and subsequently promoted increases in N and P content, soybean biomass, and yield. Our findings provide a candidate gene for optimizing BNF capacity responses to low P stress in soybean molecular breeding programs.

GmPTF1 modifies root architecture responses to phosphate starvation primarily through regulating GmEXPB2 expression in soybean

Though root architecture modifications may be critically important for improving phosphorus (P) efficiency in crops, the regulatory mechanisms triggering these changes remain unclear. In this study, we demonstrate that genotypic variation in GmEXPB2 expression is strongly correlated with root elongation and P acquisition efficiency, and enhancing its transcription significantly improves soybean yield in the field. Promoter deletion analysis was performed using 5' truncation fragments (P1-P6) of GmEXPB2 fused with the GUS gene in soybean transgenic hairy roots, which revealed that the P1 segment containing three E-box elements significantly enhances induction of gene expression in response to phosphate (Pi) starvation. Further experimentation demonstrated that GmPTF1, a basic-helix-loop-helix transcription factor, is the regulatory factor responsible for the induction of GmEXPB2 expression in response to Pi starvation. In short, Pi starvation induced expression of GmPTF1, with the GmPTF1 product directly binding to the E-box motif in the P1 region of the GmEXPB2 promoter. Plus, both GmPTF1 and GmEXPB2 highly expressed in lateral roots, and were significantly enhanced by P deficiency. Further work with soybean stable transgenic plants through RNA sequencing analysis showed that altering GmPTF1 expression significantly impacted the transcription of a series of cell wall genes, including GmEXPB2, and thereby affected root growth, biomass and P uptake. Taken together, this work identifies a novel regulatory factor, GmPTF1, involved in changing soybean root architecture partially through regulation of the expression of GmEXPB2 by binding the E-box motif in its promoter region.

Phylogeny, tissue-specific expression, and activities of root-secreted purple acid phosphatases for P uptake from ATP in P starved poplar

Plants secrete purple acid phosphatases (PAPs) under phosphorus (P) shortage but the contribution of plant PAPs to P acquisition is not well understood. The goals of this study were to investigate comprehensively the transcription patterns of PAPs under P shortage in poplar (Populus × canescens), to identify secreted PAPs and to characterize their contribution to mobilize organic P. Phylogenetic analyses of the PAP family revealed 33 putative members. In this study, distinct, tissue-specific P responsive expression patterns could be shown for 23 PAPs in roots and leaves. Root-associated PAP activities were localized on the root surface by in-vivo staining. The activities of root-surface PAPs increased significantly under low P availability, but were suppressed by a PAP inhibitor and corresponded to elevated P uptake from ATP as an organic P source. By proteomic analyses of the root apoplast, we identified three newly secreted proteins under P shortage: PtPAP1 (Potri.005G233400) and two proteins with unknown functions (Potri.013G100800 and Potri.001G209300). Our results, based on the combination of transcriptome and proteome analyses with phosphatase activity assays, support that PtPAP1 plays a central role in enhanced P acquisition from organic sources, when the phosphate concentrations in soil are limited.

Quantitative Proteomics Reveals that GmENO2 Proteins Are Involved in Response to Phosphate Starvation in the Leaves of Glycine max L

Soybean (Glycine max L.) is a major crop providing important source for protein and oil for human life. Low phosphate (LP) availability is a critical limiting factor affecting soybean production. Soybean plants develop a series of strategies to adapt to phosphate (Pi) limitation condition. However, the underlying molecular mechanisms responsible for LP stress response remain largely unknown. Here, we performed a label-free quantification (LFQ) analysis of soybean leaves grown under low and high phosphate conditions. We identified 267 induced and 440 reduced differential proteins from phosphate-starved leaves. Almost a quarter of the LP decreased proteins are involved in translation processes, while the LP increased proteins are accumulated in chlorophyll biosynthetic and carbon metabolic processes. Among these induced proteins, an enolase protein, GmENO2a was found to be mostly induced protein. On the transcriptional level, GmENO2a and GmENO2b, but not GmENO2c or GmENO2d, were dramatically induced by phosphate starvation. Among 14 enolase genes, only GmENO2a and GmENO2b genes contain the P1BS motif in their promoter regions. Furthermore, GmENO2b was specifically induced in the GmPHR31 overexpressing soybean plants. Our findings provide molecular insights into how soybean plants tune basic carbon metabolic pathway to adapt to Pi deprivation through the ENO2 enzymes.

Identification, structure analysis, and transcript profiling of purple acid phosphatases under Pi deficiency in tomato (Solanum lycopersicum L.) and its wild relatives

Purple acid phosphatases (PAPs), a family of metallo-phosphoesterase enzymes, are involved in phosphorus nutrition in plants. In this study, we report that the tomato genome encodes 25 PAP members. Physio-biochemical analyses revealed relatively lower total root-associated acid phosphatase activity in the seedlings of Solanum pimpinellifolium than their cultivated tomato seedlings under Pi deficiency. Scrutiny of their transcript abundance shows that most of PAPs are activated, although to varying levels, under Pi deficiency in tomato. Further investigation demonstrates that the magnitude of induction of phosphate starvation inducible root-associated PAP homologs remains lower in the Pi-starved S. pimpinellifolium seedlings, hence, accounting for the lower acid phosphatase activity in this wild relative. Examination of their amino acid sequences revealed significant variation in their substrate-specificity defining residues. Among all members, only SlPAP15 possesses the critical lysine residue (R337) and atypical REKA motif in its C-terminal region. Homology modeling and docking studies revealed that ADP and ATP are preferred substrates of SlPAP15. We also identified other amino acid residues present in the vicinity of the active site, possibly facilitating such physical interactions. Altogether, the results presented here will help in the functional characterization of these genes in the tomato in the future.

Identification of loci and candidate gene GmSPX-RING1 responsible for phosphorus efficiency in soybean via genome-wide association analysis

BACKGROUND

Phosphorus (P) is an essential element in maintaining high biomass and yield in crops. Soybean [Glycine max (L.) Merr.] requires a large amount of P during growth and development. Improvement of P efficiency and identification of P efficiency genes are important strategies for increasing soybean yield.

RESULTS

Genome-wide association analysis (GWAS) with NJAU 355 K SoySNP array was performed to identify single nucleotide polymorphisms (SNPs) significantly associated with three shoot P efficiency-related traits of a natural population of 211 cultivated soybeans and relative values of these traits under normal P (+P) condition and P deficiency (-P) condition. A total of 155 SNPs were identified significantly associated with P efficiency-related traits. SNPs that were significantly associated with shoot dry weight formed a SNP cluster on chromosome 11, while SNPs that were significantly associated with shoot P concentration formed a SNP cluster on chromosome 10. Thirteen haplotypes were identified based on 12 SNPs, and Hap9 was considered as the optimal haplotype. Four SNPs (AX-93636685, AX-93636692, AX-93932863, and AX-93932874) located on chromosome 10 were identified to be significantly associated with shoot P concentration under +P condition in two hydroponic experiments. Among these four SNPs, two of them (AX-93636685 and AX-93932874) were also significantly associated with the relative values of shoot P concentration under two P conditions. One SNP AX-93932874 was detected within 5'-untranslated region of Glyma.10 g018800, which contained SPX and RING domains and was named as GmSPX-RING1. Furthermore, the function research of GmSPX-RING1 was carried out in soybean hairy root transformation. Compared with their respective controls, P concentration in GmSPX-RING1 overexpressing transgenic hairy roots was significantly reduced by 32.75% under +P condition; In contrast, P concentration in RNA interference of GmSPX-RING1 transgenic hairy roots was increased by 38.90 and 14.51% under +P and -P conditions, respectively.

CONCLUSIONS

This study shows that the candidate gene GmSPX-RING1 affects soybean phosphorus efficiency by negatively regulating soybean phosphorus concentration in soybean hairy roots. The SNPs and candidate genes identified should be potential for improvement of P efficiency in future soybean 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.

Characterization of Purple Acid Phosphatase Family and Functional Analysis of GmPAP7a/7b Involved in Extracellular ATP Utilization in Soybean

Low phosphate (Pi) availability limits crop growth and yield in acid soils. Although root-associated acid phosphatases (APases) play an important role in extracellular organic phosphorus (P) utilization, they remain poorly studied in soybean (Glycine max), an important legume crop. In this study, dynamic changes in intracellular (leaf and root) and root-associated APase activities were investigated under both Pi-sufficient and Pi-deficient conditions. Moreover, genome-wide identification of members of the purple acid phosphatase (PAP) family and their expression patterns in response to Pi starvation were analyzed in soybean. The functions of both GmPAP7a and GmPAP7b, whose expression is up regulated by Pi starvation, were subsequently characterized. Phosphate starvation resulted in significant increases in intracellular APase activities in the leaves after 4 days, and in root intracellular and associated APase activities after 1 day, but constant increases were observed only for root intracellular and associated APase activities during day 5-16 of P deficiency in soybean. Moreover, a total of 38 GmPAP members were identified in the soybean genome. The transcripts of 19 GmPAP members in the leaves and 17 in the roots were upregulated at 16 days of P deficiency despite the lack of a response for any GmPAP members to Pi starvation at 2 days. Pi starvation upregulated GmPAP7a and GmPAP7b, and they were subsequently selected for further analysis. Both GmPAP7a and GmPAP7b exhibited relatively high activities against adenosine triphosphate (ATP) in vitro. Furthermore, overexpressing GmPAP7a and GmPAP7b in soybean hairy roots significantly increased root-associated APase activities and thus facilitated extracellular ATP utilization. Taken together, these results suggest that GmPAP7a and GmPAP7b might contribute to root-associated APase activities, thus having a function in extracellular ATP utilization in soybean.

GmPAP12 Is Required for Nodule Development and Nitrogen Fixation Under Phosphorus Starvation in Soybean

Nodulation process in legume plants is essential for biological nitrogen fixation during which process a large amount of phosphorus (P) is required. Under P deficiency, nodule formation is greatly affected, and induction of purple acid phosphatases (PAPs) is an adaptive strategy for nodules to acquire more P. However, regulation roles of PAPs in nodules remain largely understood. In this study, by transcriptome sequencing technology, five PAP genes were found to be differentially expressed, which led to the greatly increased acid phosphatase (APase) and phytase activities in soybean mature nodules under P starvation conditions; and among the five PAP genes, GmPAP12 had the highest transcript level, and RT-PCR indicated expression of GmPAP12 was gradually increasing during nodule development. GUS activity driven by GmPAP12 promoter was also significantly induced in low phosphorus conditions. Further functional analysis showed that under low phosphorus stress, overexpression of GmPAP12 resulted in higher nodule number, fresh weight, and nitrogenase activity as well as the APase activity than those of control plant nodules, whereas the growth performance and APase activity of nodules on hairy roots were greatly lower when GmPAP12 was suppressed, indicating that GmPAP12 may promote P utilization in soybean nodules under low P stress, which thus played an important role in nodulation and biological nitrogen fixation. Moreover, P1BS elements were found in the promoter of GmPAP12, and yeast one-hybrid experiment further proved the binding of P1BS by transcription factor GmPHR1 in the promoter of GmPAP12. At last, overexpression and suppression of GmPHR1 in nodules indeed caused highly increased and decreased expression of GmPAP12, respectively, indicating that GmPAP12 is regulated by GmPHR1 in soybean nodules. Taken together, these data suggested that GmPAP12 was a novel soybean PAP involved in the P utilization and metabolism in soybean root nodules and played an important role in the growth and development of root nodules and biological nitrogen fixation.

Generation of a multiplex mutagenesis population via pooled CRISPR-Cas9 in soya bean

The output of genetic mutant screenings in soya bean [Glycine max (L.) Merr.] has been limited by its paleopolypoid genome. CRISPR-Cas9 can generate multiplex mutants in crops with complex genomes. Nevertheless, the transformation efficiency of soya bean remains low and, hence, remains the major obstacle in the application of CRISPR-Cas9 as a mutant screening tool. Here, we report a pooled CRISPR-Cas9 platform to generate soya bean multiplex mutagenesis populations. We optimized the key steps in the screening protocol, including vector construction, sgRNA assessment, pooled transformation, sgRNA identification and gene editing verification. We constructed 70 CRISPR-Cas9 vectors to target 102 candidate genes and their paralogs which were subjected to pooled transformation in 16 batches. A population consisting of 407 T0 lines was obtained containing all sgRNAs at an average mutagenesis frequency of 59.2%, including 35.6% lines carrying multiplex mutations. The mutation frequency in the T1 progeny could be increased further despite obtaining a transgenic chimera. In this population, we characterized gmric1/gmric2 double mutants with increased nodule numbers and gmrdn1-1/1-2/1-3 triple mutant lines with decreased nodulation. Our study provides an advanced strategy for the generation of a targeted multiplex mutant population to overcome the gene redundancy problem in soya bean as well as in other major crops.

Transcriptome analysis of soybean (Glycine max) root genes differentially expressed in rhizobial, arbuscular mycorrhizal, and dual symbiosis

Soybean (Glycine max) roots establish associations with nodule-inducing rhizobia and arbuscular mycorrhizal (AM) fungi. Both rhizobia and AM fungi have been shown to affect the activity of and colonization by the other, and their interactions can be detected within host plants. Here, we report the transcription profiles of genes differentially expressed in soybean roots in the presence of rhizobial, AM, or rhizobial-AM dual symbiosis, compared with those in control (uninoculated) roots. Following inoculation, soybean plants were grown in a glasshouse for 6 weeks; thereafter their root transcriptomes were analyzed using an oligo DNA microarray. Among the four treatments, the root nodule number and host plant growth were highest in plants with dual symbiosis. We observed that the expression of 187, 441, and 548 host genes was up-regulated and 119, 1,439, and 1,298 host genes were down-regulated during rhizobial, AM, and dual symbiosis, respectively. The expression of 34 host genes was up-regulated in each of the three symbioses. These 34 genes encoded several membrane transporters, type 1 metallothionein, and transcription factors in the MYB and bHLH families. We identified 56 host genes that were specifically up-regulated during dual symbiosis. These genes encoded several nodulin proteins, phenylpropanoid metabolism-related proteins, and carbonic anhydrase. The nodulin genes up-regulated by the AM fungal colonization probably led to the observed increases in root nodule number and host plant growth. Some other nodulin genes were down-regulated specifically during AM symbiosis. Based on the results above, we suggest that the contribution of AM fungal colonization is crucial to biological N2-fixation and host growth in soybean with rhizobial-AM dual symbiosis.

Integration of metabolome and transcriptome analyses highlights soybean roots responding to phosphorus deficiency by modulating phosphorylated metabolite processes

Phosphorus (P) is a major constituent of biomolecules in plant cells, and is an essential plant macronutrient. Low phosphate (Pi) availability in soils is a major constraint on plant growth. Although a complex variety of plant responses to Pi starvation has been well documented, few studies have integrated both global transcriptome and metabolome analyses to shed light on molecular mechanisms underlying metabolic responses to P deficiency. This study is the first time to investigate global profiles of metabolites and transcripts in soybean (Glycine max) roots subjected to Pi starvation through targeted liquid chromatography electrospray ionization mass spectrometry (LC-ESI-MS/MS) and RNA-sequencing analyses. This integrated analysis allows for assessing coordinated transcriptomic and metabolic responses in terms of both pathway enzyme expression and regulatory levels. Between two Pi availability treatments, a total of 155 metabolites differentially accumulated in soybean roots, of which were phosphorylated metabolites, flavonoids and amino acids. Meanwhile, a total of 1644 differentially expressed genes (DEGs) were identified in soybean roots, including 1199 up-regulated and 445 down-regulated genes. Integration of metabolome and transcriptome analyses revealed Pi starvation responsive connection between specific metabolic processes in soybean roots, especially metabolic processes involving phosphorylated metabolites (e.g., phosphorylated lipids and nucleic acids). Taken together, this study suggests that complex molecular responses scavenging internal Pi from phosphorylated metabolites are typical adaptive strategies soybean roots employ as responses to Pi starvation. Identified DEGs will provide potential target region for future efforts to develop P-efficient soybean cultivars.

A purple acid phosphatase, GmPAP33, participates in arbuscule degeneration during arbuscular mycorrhizal symbiosis in soybean

Arbuscules are the central structures of the symbiotic association between terrestrial plants and arbuscular mycorrhizal (AM) fungi. However, arbuscules are also ephemeral structures, and following development, these structures are soon digested and ultimately disappear. Currently, little is known regarding the mechanism underlying the digestion of senescent arbuscules. Here, biochemical and functional analyses were integrated to test the hypothesis that a purple acid phosphatase, GmPAP33, controls the hydrolysis of phospholipids during arbuscule degeneration. The expression of GmPAP33 was enhanced by AM fungal inoculation independent of the P conditions in soybean roots. Promoter-β-glucuronidase (GUS) reporter assays revealed that the expression of GmPAP33 was mainly localized to arbuscule-containing cells during symbiosis. The recombinant GmPAP33 exhibited high hydrolytic activity towards phospholipids, phosphatidylcholine, and phosphatidic acid. Furthermore, soybean plants overexpressing GmPAP33 exhibited increased percentages of large arbuscules and improved yield and P content compared with wild-type plants when inoculated with AM fungi. Mycorrhizal RNAi plants had high phospholipid levels and a large percentage of small arbuscules. These results in combination with the subcellular localization of GmPAP33 at the plasma membrane indicate that GmPAP33 participates in arbuscule degeneration during AM symbiosis via involvement in phospholipid hydrolysis.

Identification of Tea Plant Purple Acid Phosphatase Genes and Their Expression Responses to Excess Iron

Purple acid phosphatase (PAP) encoding genes are a multigene family. PAPs require iron (Fe) to exert their functions that are involved in diverse biological roles including Fe homeostasis. However, the possible roles of PAPs in response to excess Fe remain unknown. In this study, we attempted to understand the regulation of PAPs by excess Fe in tea plant (Camellia sinensis). A genome-wide investigation of PAP encoding genes identified 19 CsPAP members based on the conserved motifs. The phylogenetic analysis showed that PAPs could be clustered into four groups, of which group II contained two specific cysteine-containing motifs “GGECGV” and “YERTC”. To explore the expression patterns of CsPAP genes in response to excessive Fe supply, RNA-sequencing (RNA-seq) analyses were performed to compare their transcript abundances between tea plants that are grown under normal and high iron conditions, respectively. 17 members were shown to be transcribed in both roots and leaves. When supplied with a high amount of iron, the expression levels of four genes were significantly changed. Of which, CsPAP15a, CsPAP23 and CsPAP27c were shown as downregulated, while the highly expressed CsPAP10a was upregulated. Moreover, CsPAP23 was found to be alternatively spliced, suggesting its post-transcriptional regulation. The present work implicates that some CsPAP genes could be associated with the responses of tea plants to the iron regime, which may offer a new direction towards a further understanding of iron homeostasis and provide the potential approaches for crop improvement in terms of iron biofortification.

A root-associated purple acid phosphatase, SgPAP23, mediates extracellular phytate-P utilization in Stylosanthes guianensis

As a major component of soil organic phosphorus (P), phytate-P is unavailable to plants unless hydrolysed by phytase to release inorganic phosphate. However, knowledge on natural variation in root-associated phytase activity and its underlying molecular mechanisms in plants remains fragmentary. In this study, variations in root internal and associated phytase activity were observed among 39 genotypes of Stylosanthes guianensis (Stylo), which is well adapted to acid soils. Furthermore, TPRC2001-1, the genotype with the highest root-associated phytase activity, was more capable of utilizing extracellular phytate-P than Fine-stem, the genotype with the lowest root-associated phytase activity. After protein liquid chromatography-tandem mass spectrometry analysis, a purple acid phosphatase (PAP), SgPAP23, was identified and cloned from TPRC2001-1. SgPAP23 exhibited high activity against phytate-P and was mainly localized on the plasma membrane. Furthermore, SgPAP23 overexpression resulted in significant increases of root-associated phytase activity and thus facilitated extracellular phytate-P utilization in both bean (Phaseolus vulgaris) hairy roots and Arabidopsis thaliana. The results herein support the conclusion that SgPAP23 is a primary contributor to the superior extracellular phytate-P utilization in stylo and thus is used to develop cultivars with efficient extracellular phytate-P utilization.

Genome Wide Transcriptome Analysis Reveals Complex Regulatory Mechanisms Underlying Phosphate Homeostasis in Soybean Nodules

Phosphorus (P) deficiency is a major limitation for legume crop production. Although overall adaptations of plant roots to P deficiency have been extensively studied, only fragmentary information is available in regard to root nodule responses to P deficiency. In this study, genome wide transcriptome analysis was conducted using RNA-seq analysis in soybean nodules grown under P-sufficient (500 μM KH₂PO₄) and P-deficient (25 μM KH₂PO₄) conditions to investigate molecular mechanisms underlying soybean (Glycine max) nodule adaptation to phosphate (Pi) starvation. Phosphorus deficiency significantly decreased soybean nodule growth and nitrogenase activity. Nodule Pi concentrations declined by 49% in response to P deficiency, but this was well below the 87% and 88% decreases observed in shoots and roots, respectively. Nodule transcript profiling revealed that a total of 2055 genes exhibited differential expression patterns between Pi sufficient and deficient conditions. A set of (differentially expressed genes) DEGs appeared to be involved in maintaining Pi homeostasis in soybean nodules, including eight Pi transporters (PTs), eight genes coding proteins containing the SYG1/PHO81/XPR1 domain (SPXs), and 16 purple acid phosphatases (PAPs). The results suggest that a complex transcriptional regulatory network participates in soybean nodule adaption to Pi starvation, most notable a Pi signaling pathway, are involved in maintaining Pi homeostasis in nodules.

Genome-wide analysis of purple acid phosphatase structure and expression in ten vegetable species

Background

Acquisition of external phosphorus (P) and optimisation of internal P are essential for plant growth and development, and insufficient availability of P in soils is a major challenge in agriculture. Members of the purple acid phosphatase (PAP) family of enzymes are candidates for increasing P use efficiency. Herein, we identified PAP homologs in the genomes of 10 vegetable species, along with Arabidopsis thaliana and Amborella trichopoda as references, to provide fundamental knowledge for this family.

Results

Phylogenetic analysis of protein sequences revealed nine distinct clades, indicating that functional differentiation of extant PAPs was established prior to the emergence of early angiosperms, and conserved among homologs in each clade. Analysis of transcript abundance in different tissues (root, stem, leaf, flower, and fruit) and following phosphates (Pi) starvation treatments from published RNA-seq transcriptome datasets facilitated comprehensive evaluation of expression patterns, and some groups of tissue-specific and Pi starvation-induced PAPs were characterised. Conserved motifs identified from upstream sequences of homologs that are highly expressed in particular tissues or following starvation treatment suggests that divergence in PAP gene expression is associated with cis-acting elements in promoters.

Conclusions

The genome-wide analysis of PAP enzyme structure and transcriptional expression patterns advance our understanding of PAP family in vegetables genomes. Therefore, PAP homologs with known enzyme structures and expression profiles could serve as targets for plant breeding and/or genetic engineering programs to improve P acquisition and use.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-5022-1) contains supplementary material, which is available to authorized users.

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.

Transcriptional responses of soybean roots to colonization with the root endophytic fungus Piriformospora indica reveals altered phenylpropanoid and secondary metabolism

Piriformospora indica, a root endophytic fungus, has been shown to enhance biomass production and confer tolerance to various abiotic and biotic stresses in many plant hosts. A growth chamber experiment of soybean (Glycine max) colonized by P. indica compared to uninoculated control plants showed that the fungus significantly increased shoot dry weight, nutrient content, and rhizobial biomass. RNA-Seq analyses of root tissue showed upregulation of 61 genes and downregulation of 238 genes in colonized plants. Gene Ontology (GO) enrichment analyses demonstrated that upregulated genes were most significantly enriched in GO categories related to lignin biosynthesis and regulation of iron transport and metabolism but also mapped to categories of nutrient acquisition, hormone signaling, and response to drought stress. Metabolic pathway analysis revealed upregulation of genes within the phenylpropanoid and derivative pathways such as biosynthesis of monolignol subunits, flavonoids and flavonols (luteolin and quercetin), and iron scavenging siderophores. Highly enriched downregulated GO categories included heat shock proteins involved in response to heat, high-light intensity, hydrogen peroxide, and several related to plant defense. Overall, these results suggest that soybean maintains an association with this root endosymbiotic fungus that improves plant growth and nutrient acquisition, modulates abiotic stress, and promotes synergistic interactions with rhizobia.

Functions and regulation of phosphate starvation-induced secreted acid phosphatases in higher plants

Phosphorus is essential for plant growth and development, but levels of inorganic phosphate (Pi), the major form of phosphorus that plants assimilate, are quite limiting in most soils. To cope with Pi deficiency, plants trigger a suite of adaptive responses, including the induction and secretion of acid phosphatases (APases). In this article, we describe how Pi starvation-induced (PSI) APases are analyzed, and we provide a brief historical review of their identification. We then discuss the current understanding of the functions of PSI-secreted APases and how these APases are regulated at the molecular level. Finally, we provide a perspective on the future direction of research in this field.