OsHAD1, a Haloacid Dehalogenase-Like APase, Enhances Phosphate Accumulation

OsPHR2-mediated recruitment of Pseudomonadaceae enhances rice phosphorus uptake

Plants can shape their root microbiome to promote growth and nutrient uptake. PHOSPHATE STARVATION RESPONSE 2 (OsPHR2) is a central regulator of phosphate signaling in rice, but whether OsPHR2 can shape the root microbiome to promote phosphorus uptake is unclear. Here, we investigate the role of OsPHR2 in recruiting microbiota for phosphorus uptake using high-throughput sequencing and metabolite analysis. OsPHR2-overexpressing (OsPHR2 OE) rice showed 69.8% greater shoot P uptake in natural soil compared with sterilized soil under high-phosphorus (HP) conditions, but there was only a 54.8% increase in the wild-type (WT). The abundance of the family Pseudomonadaceae was significantly enriched in OsPHR2 OE roots relative to those of WT rice. Compared with the WT, OsPHR2 OE rice had a relatively higher abundance of succinic acid and methylmalonic acid, which could stimulate the growth of Pseudomonas sp. (P6). After inoculation with P6, phosphorus uptake in WT and OsPHR2 OE rice was higher than that in uninoculated rice under low-phosphorus (LP) conditions. Taken together, our results suggest that OsPHR2 can increase phosphorus use in rice through root exudate-mediated recruitment of Pseudomonas. This finding reveals a cooperative contribution of the OsPHR2-modulated root microbiome, which is important for improving phosphorus use in agriculture.

Hypoxia in the Blue Mussel Mytilus chilensis Induces a Transcriptome Shift Associated with Endoplasmic Reticulum Stress, Metabolism, and Immune Response

The increase in hypoxia events, a result of climate change in coastal and fjord ecosystems, impacts the health and survival of mussels. These organisms deploy physiological and molecular responses as an adaptive mechanism to maintain cellular homeostasis under environmental stress. However, the specific effects of hypoxia on mussels of socioeconomic interest, such as Mytilus chilensis, are unknown. Using RNA-seq, we investigated the transcriptomic profiles of the gills, digestive gland, and adductor muscle of M. chilensis under hypoxia (10 days at 2 mg L-1) and reoxygenation (10 days at 6 mg L-1). There were 15,056 differentially expressed transcripts identified in gills, 11,864 in the digestive gland, and 9862 in the adductor muscle. The response varied among tissues, showing chromosomal changes in Chr1, Chr9, and Chr10 during hypoxia. Hypoxia regulated signaling genes in the Toll-like, mTOR, citrate cycle, and apoptosis pathways in gills, indicating metabolic and immunological alterations. These changes suggest that hypoxia induced a metabolic shift in mussels, reducing reliance on aerobic respiration and increasing reliance on anaerobic metabolism. Furthermore, hypoxia appeared to suppress the immune response, potentially increasing disease susceptibility, with negative implications for the mussel culture industry and natural bed populations. This study provides pivotal insights into metabolic and immunological adaptations to hypoxia in M. chilensis, offering candidate genes for adaptive traits.

The Impact of Various Organic Phosphorus Carriers on the Uptake and Use Efficiency in Barley

Organic phosphorus (OP) is an essential component of the soil P cycle, which contributes to barley nutrition after its mineralization into inorganic phosphorus (Pi). However, the dynamics of OP utilization in the barley rhizosphere remain unclear. In this study, phytin was screened out from six OP carriers, which could reflect the difference in OP utilization between a P-inefficient genotype Baudin and a P-efficient genotype CN4027. The phosphorus utilization efficiency (PUE), root morphological traits, and expression of genes associated with P utilization were assessed under P deficiency or phytin treatments. P deficiency resulted in a greater root surface area and thicker roots. In barley fed with phytin as a P carrier, the APase activities of CN4027 were 2-3-fold lower than those of Baudin, while the phytase activities of CN4027 were 2-3-fold higher than those of Baudin. The PUE in CN4027 was mainly enhanced by activating phytase to improve the root absorption and utilization of Pi resulting from OP mineralization, while the PUE in Baudin was mainly enhanced by activating APase to improve the shoot reuse capacity. A phosphate transporter gene HvPHT1;8 regulated P transport from the roots to the shoots, while a purple acid phosphatase (PAP) family gene HvPAPhy_b contributed to the reuse of P in barley.

Overexpression of OsHAD3, a Member of HAD Superfamily, Decreases Drought Tolerance of Rice

Haloacid dehalogenase-like hydrolase (HAD) superfamily have been shown to get involved in plant growth and abiotic stress response. Although the various functions and regulatory mechanism of HAD superfamily have been well demonstrated, we know little about the function of this family in conferring abiotic stress tolerance to rice. Here, we report OsHAD3, a HAD superfamily member, could affect drought tolerance of rice. Under drought stress, overexpression of OsHAD3 increases the accumulation of reactive oxygen species and malondialdehyde than wild type. OsHAD3-overexpression lines decreased but antisense-expression lines increased the roots length under drought stress and the transcription levels of many well-known stress-related genes were also changed in plants with different genotypes. Furthermore, overexpression of OsHAD3 also decreases the oxidative tolerance. Our results suggest that overexpression of OsHAD3 could decrease the drought tolerance of rice and provide a new strategy for improving drought tolerance in rice.

Root-Expressed Rice PAP3b Enhances Secreted APase Activity and Helps Utilize Organic Phosphate

Phosphate (Pi) deficiency leads to the induction of purple acid phosphatases (PAPs) in plants, which dephosphorylate organic phosphorus (P) complexes in the rhizosphere and intracellular compartments to release Pi. In this study, we demonstrate that OsPAP3b belongs to group III low-molecular weight PAP and is low Pi-responsive, preferentially in roots. The expression of OsPAP3b is negatively regulated with Pi resupply. Interestingly, OsPAP3b was found to be dual localized to the nucleus and secretome. Furthermore, OsPAP3b is transcriptionally regulated by OsPHR2 as substantiated by DNA-protein binding assay. Through in vitro biochemical assays, we further demonstrate that OsPAP3b is a functional acid phosphatase (APase) with broad substrate specificity. The overexpression (OE) of OsPAP3b in rice led to increased secreted APase activity and improved mineralization of organic P sources, which resulted in better growth of transgenics compared to the wild type when grown on organic P as an exogenous P substrate. Under Pi deprivation, OsPAP3b knock-down and knock-out lines showed no significant changes in total P content and dry biomass. However, the expression of other phosphate starvation-induced genes and the levels of metabolites were found to be altered in the OE and knock-down lines. In addition, in vitro pull-down assay revealed multiple putative interacting proteins of OsPAP3b. Our data collectively suggest that OsPAP3b can aid in organic P utilization in rice. The APase isoform behavior and nuclear localization indicate its additional role, possibly in stress signaling. Considering its important roles, OsPAP3b could be a potential target for improving low Pi adaptation in rice.

Food waste digestate composting enhancement by sodium polyacrylate addition: Effects on nitrogen transformation processes and bacterial community dynamics

The influences of sodium polyacrylate (PAAS) at the ratios of 0% (CK), 0.5% (F1), 1.0% (F2), 1.5% (F3), 2.0% (F4) and 2.5% (F5) on nitrogen transformation and bacterial community composition were investigated in the composting of food waste digestate (FWD) and corn straw (CS). PAAS addition increased the thermophilic temperature but had no significant effect on pH values. PAAS exerted significantly effects on the concentration of total nitrogen (TN), ammonia nitrogen (NH₄⁺-N), nitrite-nitrogen (NO₂^--N) and nitrate-nitrogen (NO₃^--N). The compost product in 1.0% PAAS treatment was more active in absorbing nutrients. Firmicutes (9.40-83.54%), Actinobacteriota (9.98-51.50%), Proteobacteria (0.20-27.87%) and Bacteroidota (0.11-34.69%) were the dominant phyla in FWD composting. Moreover, relative to CK, PAAS promoted the propagation of dominant bacterial phyla Firmicutes with increment of 30.05-102.06% in the thermophilic phase. Kroppenstedtia, Thermobifida and Saccharomonospora were observed to be dominant at the maturing phase and correlated with NH₄⁺-N, NO₂^--N, TN and NO₃^--N. Therefore, they might be regarded as probable biomarkers symbolic for the maturing phase during FWD composting. The compost product had the highest maturity degree in 1.0% PAAS treatment. These results indicated that PAAS addition improved the maturity and nutrient contents of the compost product as well as altered compost bacterial community dynamics.

Exogenous abscisic acid alleviates Cd toxicity in Arabidopsis thaliana by inhibiting Cd uptake, translocation and accumulation, and promoting Cd chelation and efflux

Exogenous abscisic acid (ABA) has been implicated in plant response to cadmium (Cd) stress, but the underlying mechanism remains unclear. In the present study, we found that exogenous ABA application decreased Cd fixation in wild type (WT) root cell wall through reducing the hemicelluloses content, in parallel with the decreased expression of IRT1, ZIP1, ZIP4, HMA2 and HMA4, which are related to Cd uptake and translocation, and the increased expression of PDF2.6, PDR8 and AIT1, which are related to Cd chelation, efflux, and accumulation inhibition. These changes might be associated with the reduced Cd accumulation in roots and shoots and the alleviated Cd toxicity. In contrast, the mutation of ABI4, a transcription factor in ABA signaling pathway, significantly increased the expression of IRT1, ZIP1, ZIP4, HMA2 and HMA4, while decreased the expression of AIT1, PDF2.6 and PDR8, enhancing Cd accumulation in roots and shoots of abi4. The enhanced Cd-sensitivity in abi4 mutant could not be rescued by exogenous ABA addition compared with WT. In a word, we conclude that exogenous ABA mitigates Cd toxicity in Arabidopsis thaliana via inhibiting Cd uptake, translocation and accumulation, promoting Cd chelation and efflux, a pathway that might be regulated by ABI4.

Adaptive strategies of plants to conserve internal phosphorus under P deficient condition to improve P utilization efficiency

Phosphorus (P) is one of the limiting factors for plant growth and productivity due to its slow diffusion and immobilization in the soil which necessitates application of phosphatic fertilizers to meet the crop demand and obtain maximum yields. However, plants have evolved mechanisms to adapt to low P stress conditions either by increasing acquisition (alteration of belowground processes) or by internal inorganic P (Pi) utilization (cellular Pi homeostasis) or both. In this review, we have discussed the adaptive strategies that conserve the use of P and maintain cellular Pi homeostasis in the cytoplasm. These strategies involve modification in membrane lipid composition, flavanol/anthocyanin level, scavenging and reutilization of Pi adsorbed in cell wall pectin, remobilization of Pi during senescence by enzymes like RNases and purple acid phosphatases, alternative mitochondrial electron transport, and glycolytic pathways. The remobilization of Pi from senescing tissues and its internal redistribution to various cellular organelles is mediated by various Pi transporters. Although much efforts have been made to enhance P acquisition efficiency, an understanding of the physiological mechanisms conserving internal Pi and their manipulation would be useful for plants that can utilize P more efficiently to produce optimum growth per unit P uptake.

A major quantitative trait locus for wheat total root length associated with precipitation distribution

Optimizing root system architecture (RSA) allows crops to better capture water and nutrients and adapt to harsh environment. Parental reproductive environment (PRE) has been reported to significantly affect growth and development throughout the life cycle of the next generation. In this study, 10 RSA-related traits were evaluated in seedling stage from five independent hydroponic tests using seeds harvested from five different PREs. Based on the Wheat55K SNP array-based genetic map, quantitative trait loci (QTL) for these traits were detected in a recombinant inbred line population. Twenty-eight putative QTL for RSA-related traits were detected, covering thirteen chromosomal regions. A major QTL, QTrl.sicau-2SY-4D for total root length (TRL), which was likely independent of PREs, explained 15.81-38.48% of phenotypic variations and was located at 14.96-19.59 Mb on chromosome arm 4DS. Interestingly, it showed pleiotropic effects on TRL, root area, root volume, root forks, root dry weight, and shoot dry weight. The functional marker KASP-Rht-D1 for Rht-D1 was used to genotype 2SY population and remapping QTL for TRL showed that QTrl.sicau-2SY-4D was not linked to Rht-D1. The kompetitive allele-specific PCR (KASP) marker, KASP-AX-110527441 linked to this major QTL, was developed and used to successfully validate its effect in three different genetic populations. Further analysis suggested that the positive allele at QTrl.sicau-2SY-4D was mainly utilized in wheat breeding of northwest China where precipitation was significantly lower, indicating that wheat requires longer TRL to capture water and nutrients in arid or semi-arid regions due to deficient precipitation. Additionally, four genes (TraesCS4D03G0059800, TraesCS4D03G0057800, TraesCS4D03G0064000, and TraesCS4D03G0064400) possibly related to root development were predicted in physical interval of QTrl.sicau-2SY-4D. Taken together, these results enrich our understanding on the genetic basis of RSA and provide a potentially valuable TRL QTL for wheat breeding.

Monogalactosyl diacylglycerol synthase 3 affects phosphate utilization and acquisition in rice

Galactolipids are essential to compensate for the loss of phospholipids by 'membrane lipid remodelling' in plants under phosphorus (P) deficiency conditions. Monogalactosyl diacylglycerol (MGDG) synthases catalyse the synthesis of MGDG which is further converted into digalactosyl diacylglycerol (DGDG), later replacing phospholipids in the extraplastidial membranes. However, the roles of these enzymes are not well explored in rice. In this study, the rice MGDG synthase 3 gene (OsMGD3) was identified and functionally characterized. We showed that the plant phosphate (Pi) status and the transcription factor PHOSPHATE STARVATION RESPONSE 2 (OsPHR2) are involved in the transcriptional regulation of OsMGD3. CRISPR/Cas9 knockout and overexpression lines of OsMGD3 were generated to explore its potential role in rice adaptation to Pi deficiency. Compared with the wild type, OsMGD3 knockout lines displayed a reduced Pi acquisition and utilization while overexpression lines showed an enhancement of the same. Further, OsMGD3 showed a predominant role in roots, altering lateral root growth. Our comprehensive lipidomic analysis revealed a role of OsMGD3 in membrane lipid remodelling, in addition to a role in regulating diacylglycerol and phosphatidic acid contents that affected the expression of Pi transporters. Our study highlights the role of OsMGD3 in affecting both internal P utilization and P acquisition in rice.

OsJAZ11 regulates spikelet and seed development in rice

Seed size is one of the major determinants of seed weight and eventually, crop yield. As the global population is increasing beyond the capacity of current food production, enhancing seed size is a key target for crop breeders. Despite the identification of several genes and QTLs, current understanding about the molecular regulation of seed size/weight remains fragmentary. In the present study, we report novel role of a jasmonic acid (JA) signaling repressor, OsJAZ11 controlling rice seed width and weight. Transgenic rice lines overexpressing OsJAZ11 exhibited up to a 14% increase in seed width and ~30% increase in seed weight compared to wild type (WT). Constitutive expression of OsJAZ11 dramatically influenced spikelet morphogenesis leading to extra glume-like structures, open hull, and abnormal numbers of floral organs. Furthermore, overexpression lines accumulated higher JA levels in spikelets and developing seeds. Expression studies uncovered altered expression of JA biosynthesis/signaling and MADS box genes in overexpression lines compared to WT. Yeast two-hybrid and pull-down assays revealed that OsJAZ11 interacts with OsMADS29 and OsMADS68. Remarkably, expression of OsGW7, a key negative regulator of grain size, was significantly reduced in overexpression lines. We propose that OsJAZ11 participates in the regulation of seed size and spikelet development by coordinating the expression of JA-related, OsGW7 and MADS genes.

The MADS transcription factor GhFYF is involved in abiotic stress responses in upland cotton (Gossypium hirsutum L.)

Cotton is an important textile industry raw material crops, which plays a critical role in the development of society. MADS transcription factors (TFs) play a key role about the flowering time, flower development, and abiotic stress responses in plants, but little is known about their functions on abiotic stress in cotton. In this study, a MIKC^C subfamily gene from cotton, GhFYF (FOREVER YOUNG FLOWER), was isolated and characterized. Our data showed that GhFYF localized to the nucleus. A β-glucuronidase (GUS) activity assay revealed that the promoter of GhFYF was mainly expressed in the flower and seed of ProGhFYF::GUS transgenic A. thaliana plants. The GUS staining of flowers and seeds was deepened after drought, salt treatment, and the expression level of the GUS gene and corresponding stress genes AtERD10, AtAnnexin1 are up-regulated in the inflorescence. Overexpression GhFYF in A. thaliana could promote the seed germination and growth under different salt concentrations, and determin the proline content. Yeast two-hybrid (Y2H) assays showed that GhFYF interacted with the HAD-like protein GhGPP2, which has responds to abiotic stress. Our findings indicate that GhFYF is involved in abiotic stress responses, especially for salt stress. This work establishes a solid foundation for further functional analysis of the GhFYF gene in cotton.

Mining of Potential Gene Resources for Breeding Nutritionally Improved Maize

Maize is one of the leading food crops and its kernel is rich in starch, lipids, protein and other energy substances. In addition, maize kernels also contain many trace elements that are potentially beneficial to human health, such as vitamins, minerals and other secondary metabolites. However, gene resources that could be applied for nutrient improvement are limited in maize. In this review, we summarized 107 genes that are associated with nutrient content from different plant species and identified 246 orthologs from the maize genome. In addition, we constructed physical maps and performed a detailed expression pattern analysis for the 246 maize potential gene resources. Combining expression profiles and their potential roles in maize nutrient improvement, genetic engineering by editing or ectopic expression of these genes in maize are expected to improve resistant starch, oil, essential amino acids, vitamins, iron, zinc and anthocyanin levels of maize grains. Thus, this review provides valuable gene resources for maize nutrient improvement.

AtHAD1, A haloacid dehalogenase-like phosphatase, is involved in repressing the ABA response

Abscisic acid (ABA) plays an important role in seed germination, stomatal closure, and seedling growth inhibition in plants. Among downstream genes whose expression levels are regulated by AFA1 (Arabidopsis F-box Protein Hypersensitive to ABA 1), one gene, AtHAD1 upregulated by ABA was selected from Arabidopsis. AtHAD1 was induced by drought and salt stresses as well as by ABA and was found in dry seeds. Its loss-of-function mutants exhibited increased ABA-sensitivity in germination, seedling growth, and stomatal closure. In addition, the mutants displayed a lower water loss rate and higher survival rate under drought stress than the wild-type plants, indicating that a loss of AtHAD1 leads to enhanced drought tolerance. These results show that AtHAD1 has an inhibitory role in the ABA response and ABA-mediated drought tolerance. The expression levels of several ABA-responsive genes in athad1 were higher than those in the wild-type under the ABA treatment, suggesting that AtHAD1, as a negative regulator in the ABA response, could be associated with the downregulation of the ABA-responsive genes. The phosphatase assay showed that AtHAD1 exhibits phosphatase activity. Monitoring of the subcellular localization of GFP-fused AtHAD1 proteins indicated that AtHAD1 exists in the nucleus and cytoplasm. Overall, this study shows that Arabidopsis HAD1 as an intracellular phosphatase negatively functions in the ABA-mediated cellular responses. This research could serve as a research basis to understand the functional link between ABA signaling and the regulation process of the cellular phosphate level.

Rice ACID PHOSPHATASE 1 regulates Pi stress adaptation by maintaining intracellular Pi homeostasis

The concentration and homeostasis of intracellular phosphate (Pi) are crucial for sustaining cell metabolism and growth. During short-term Pi starvation, intracellular Pi is maintained relatively constant at the expense of vacuolar Pi. After the vacuolar stored Pi is exhausted, the plant cells induce the synthesis of intracellular acid phosphatase (APase) to recycle Pi from expendable organic phosphate (Po). In this study, the expression, enzymatic activity and subcellular localization of ACID PHOSPHATASE 1 (OsACP1) were determined. OsACP1 expression is specifically induced in almost all cell types of leaves and roots under Pi stress conditions. OsACP1 encodes an acid phosphatase with broad Po substrates and localizes in the endoplasmic reticulum (ER) and Golgi apparatus (GA). The phylogenic analysis demonstrates that OsACP1 has a similar structure with human acid phosphatase PHOSPHO1. Overexpression or mutation of OsACP1 affected Po degradation and utilization, which further influenced plant growth and productivity under both Pi-sufficient and Pi-deficient conditions. Moreover, overexpression of OsACP1 significantly affected intracellular Pi homeostasis and Pi starvation signalling. We concluded that OsACP1 is an active acid phosphatase that regulates rice growth under Pi stress conditions by recycling Pi from Po in the ER and GA.

Toward identification of a putative candidate gene for nutrient mineral accumulation in wheat grains for human nutrition purposes

A multilocus genome-wide association study of a panel of 369 diverse wheat (Triticum aestivum) genotypes was carried out in order to examine the genetic basis of variations in nutrient mineral concentrations in the grains. The panel was grown under field conditions for three consecutive years and the concentrations of Ca, K, Mg, Mn, P, and S were determined. Wide ranges of natural variation were detected among the genotypes. Strong positive correlations were found among the minerals except for K, which showed negative correlation trends with the other minerals. Genetic association analysis detected 86 significant marker-trait associations (MTAs) underlying the natural variations in mineral concentrations in grains. The major MTA was detected on the long arm of chromosome 5A and showed a pleiotropic effect on Ca, K, Mg, Mn, and S. Further significant MTAs were distributed among the whole genome except for chromosomes 3D and 6D. We identified putative candidate genes that are potentially involved in metal uptake, transport, and assimilation, including TraesCS5A02G542600 on chromosome 5A, which was annotated as a Major Facilitator Superfamily transporter and acted on all the minerals except K. TraesCS5A02G542600 was highly expressed in seed coat, and to a lesser extent in the peduncle, awns, and lemma. Our results provide important insights into the genetic basis of enhancement of nutrient mineral concentrations that can help to inform future breeding studies in order to improve human nutrition.

OsJAZ11 regulates phosphate starvation responses in rice

OsJAZ11 regulates phosphate homeostasis by suppressing jasmonic acid signaling and biosynthesis in rice roots. Jasmonic Acid (JA) is a key plant signaling molecule which negatively regulates growth processes including root elongation. JAZ (JASMONATE ZIM-DOMAIN) proteins function as transcriptional repressors of JA signaling. Therefore, targeting JA signaling by deploying JAZ repressors may enhance root length in crops. In this study, we overexpressed JAZ repressor OsJAZ11 in rice to alleviate the root growth inhibitory action of JA. OsJAZ11 is a low phosphate (Pi) responsive gene which is transcriptionally regulated by OsPHR2. We report that OsJAZ11 overexpression promoted primary and seminal root elongation which enhanced Pi foraging. Expression studies revealed that overexpression of OsJAZ11 also reduced Pi starvation response (PSR) under Pi limiting conditions. Moreover, OsJAZ11 overexpression also suppressed JA signaling and biosynthesis as compared to wild type (WT). We further demonstrated that the C-terminal region of OsJAZ11 was crucial for stimulating root elongation in overexpression lines. Rice transgenics overexpressing truncated OsJAZ11ΔC transgene (i.e., missing C-terminal region) exhibited reduced root length and Pi uptake. Interestingly, OsJAZ11 also regulates Pi homeostasis via physical interaction with a key Pi sensing protein, OsSPX1. Our study highlights the functional connections between JA and Pi signaling and reveals JAZ repressors as a promising candidate for improving low Pi tolerance of elite rice genotypes.

Organic acids: versatile stress-response roles in plants

Organic acids (OAs) are central to cellular metabolism. Many plant stress responses involve the exudation of OAs at the root-soil interface, which can improve soil mineral acquisition and toxic metal tolerance. Because of their simple structure, the low-molecular-weight OAs are widely studied. We discuss the conventional roles of OAs, and some newly emerging roles in plant stress tolerance. OAs are more versatile in their role in plant stress tolerance and are more efficient chelating agents than other acids, such as amino acids. Root OA exudation is important in soil carbon sequestration. These functions are key processes in combating climate change and helping with more sustainable food production. We briefly review the mechanisms behind enhanced biosynthesis, secretion, and regulation of these activities under different stresses, and provide an outline of the transgenic approaches targeted towards the enhanced production and secretion of OAs. A recurring theme of OAs in plant biology is their role as 'acids' modifying pH, as 'chelators' binding metals, or as 'carbon sources' for microbes. We argue that these multiple functions are key factors for understanding these molecules' important roles in plant stress biology. Finally, we discuss how the functions of OAs in plant stress responses could be used, and identify the important unanswered questions.

Genome-wide association study reveals the genetic basis of yield- and quality-related traits in wheat

BACKGROUND

Identifying the loci and dissecting the genetic architecture underlying wheat yield- and quality-related traits are essential for wheat breeding. A genome-wide association study was conducted using a high-density 90 K SNP array to analyze the yield- and quality-related traits of 543 bread wheat varieties.

RESULTS

A total of 11,140 polymorphic SNPs were distributed on 21 chromosomes, including 270 significant SNPs associated with 25 yield- and quality-related traits. Additionally, 638 putative candidate genes were detected near the significant SNPs based on BLUP data, including three (TraesCS7A01G482000, TraesCS4B01G343700, and TraesCS6B01G295400) related to spikelet number per spike, diameter of the first internode, and grain volume. The three candidate genes were further analyzed using stage- and tissue- specific gene expression data derived from an RNA-seq analysis. These genes are promising candidates for enhancing yield- and quality-related traits in wheat.

CONCLUSIONS

The results of this study provide a new insight to understand the genetic basis of wheat yield and quality. Furthermore, the markers detected in this study may be applicable for marker-assisted selection in wheat breeding programs.

Pi-starvation induced transcriptional changes in barley revealed by a comprehensive RNA-Seq and degradome analyses

BACKGROUND

Small RNAs (sRNAs) are 20-30 nt regulatory elements which are responsible for plant development regulation and participate in many plant stress responses. Insufficient inorganic phosphate (Pi) concentration triggers plant responses to balance the internal Pi level.

RESULTS

In this study, we describe Pi-starvation-responsive small RNAs and transcriptome changes in barley (Hordeum vulgare L.) using Next-Generation Sequencing (NGS) RNA-Seq data derived from three different types of NGS libraries: (i) small RNAs, (ii) degraded RNAs, and (iii) functional mRNAs. We find that differentially and significantly expressed miRNAs (DEMs, Bonferroni adjusted p-value < 0.05) are represented by 15 molecules in shoot and 13 in root; mainly various miR399 and miR827 isomiRs. The remaining small RNAs (i.e., those without perfect match to reference sequences deposited in miRBase) are considered as differentially expressed other sRNAs (DESs, p-value Bonferroni correction < 0.05). In roots, a more abundant and diverse set of other sRNAs (DESs, 1796 unique sequences, 0.13% from the average of the unique small RNA expressed under low-Pi) contributes more to the compensation of low-Pi stress than that in shoots (DESs, 199 unique sequences, 0.01%). More than 80% of differentially expressed other sRNAs are up-regulated in both organs. Additionally, in barley shoots, up-regulation of small RNAs is accompanied by strong induction of two nucleases (S1/P1 endonuclease and 3'-5' exonuclease). This suggests that most small RNAs may be generated upon nucleolytic cleavage to increase the internal Pi pool. Transcriptomic profiling of Pi-starved barley shoots identifies 98 differentially expressed genes (DEGs). A majority of the DEGs possess characteristic Pi-responsive cis-regulatory elements (P1BS and/or PHO element), located mostly in the proximal promoter regions. GO analysis shows that the discovered DEGs primarily alter plant defense, plant stress response, nutrient mobilization, or pathways involved in the gathering and recycling of phosphorus from organic pools.

CONCLUSIONS

Our results provide comprehensive data to demonstrate complex responses at the RNA level in barley to maintain Pi homeostasis and indicate that barley adapts to Pi-starvation through elicitation of RNA degradation. Novel P-responsive genes were selected as putative candidates to overcome low-Pi stress in barley plants.

Genome-wide analysis of haloacid dehalogenase genes reveals their function in phosphate starvation responses in rice

The HAD superfamily is named after the halogenated acid dehalogenase found in bacteria, which hydrolyses a diverse range of organic phosphate substrates. Although certain studies have shown the involvement of HAD genes in Pi starvation responses, systematic classification and bioinformatics analysis of the HAD superfamily in plants is lacking. In this study, 41 and 40 HAD genes were identified by genomic searching in rice and Arabidopsis, respectively. According to sequence similarity, these proteins are divided into three major groups and seven subgroups. Conserved motif analysis indicates that the majority of the identified HAD proteins contain phosphatase domains. A further structural analysis showed that HAD proteins have four conserved motifs and specified cap domains. Fewer HAD genes show collinearity relationships in both rice and Arabidopsis, which is consistent with the large variations in the HAD genes. Among the 41 HAD genes of rice, the promoters of 28 genes contain Pi-responsive cis-elements. Mining of transcriptome data and qRT-PCR results showed that at least the expression of 17 HAD genes was induced by Pi starvation in shoots or roots. These HAD proteins are predicted to be involved in intracellular or extracellular Po recycling under Pi stress conditions in plants.

OsJAZ9 overexpression modulates jasmonic acid biosynthesis and potassium deficiency responses in rice

Enhanced bioactive JA (JA-Ile) accumulation in OsJAZ9 overexpressing rice helps plants tolerate K deficiency. Potassium (K) represents up to 10% of the plant's total dry biomass, and its deficiency makes plants highly susceptible to both abiotic and biotic stresses. K shortage results in the inhibition of root and shoots growth, but the underlying mechanism of this response is unclear. Our RNA-Seq and qPCR analysis suggested leading roles for JA pathway genes under K deficiency in rice. Notably, K deficiency and JA application produced similar phenotypic and transcriptional responses. Here, we integrated molecular, physiological and morphological studies to analyze the role of OsJAZ9 in JA homeostasis and K deficiency responses. We raised OsJAZ9 over-expression, knockdown, transcriptional reporter, translational reporter and C-terminal deleted translational reporter lines in rice to establish the role of JA signaling in K ion homeostasis. JA profiling revealed significantly increased JA-Ile levels in OsJAZ9 OE lines under K deficiency. Furthermore, we established that OsJAZ9 overexpression and knockdown result in K deficiency tolerance and sensitivity, respectively, by modulating various K transporters and root system architecture. Our data provide evidence on the crucial roles of OsJAZ9 for improving K deficiency tolerance in rice by altering JA levels and JA responses.

Fine mapping of qKRN8, a QTL for maize kernel row number, and prediction of the candidate gene

KEY MESSAGE: qKRN8, a major QTL for kernel row number in maize, was fine mapped to an interval of ~ 520 kb on chromosome 8 and the key candidate gene was identified via expression analysis. Kernel row number (KRN) is one of the most important yield-influencing traits and is closely associated with female inflorescence development in maize (Zea mays L.). In this study, an F2:3 population derived from a cross between V54 (low KRN line) and Lian87 (high KRN line) was used to map quantitative trait loci (QTLs) conferring KRN in maize. We identified 12 QTLs for KRN in four environments, each explaining 1.40-14.95% of phenotypic variance. Among these, one novel major QTL (named qKRN8) was mapped to bin 8.03 in all four environments, explaining 8.79-14.95% of phenotypic variation. By combining map-based cloning with progeny testing of recombinants, we ultimately mapped qKRN8 to an ~ 520 kb genomic interval, harboring six putative candidate genes. Among them, one candidate gene showed contrasted expression level in immature ears of the near-isogenic lines qKRN8Lian87 and qKRN8V54. These findings should facilitate molecular breeding for KRN and the further identification of the polymorphism underlying this QTL.

Heavy Metal Transporters-Associated Proteins in S. tuberosum: Genome-Wide Identification, Comprehensive Gene Feature, Evolution and Expression Analysis

Plants have evolved a number of defense and adaptation responses to protect themselves against challenging environmental stresses. Genes containing a heavy metal associated (HMA) domain are required for the spatiotemporal transportation of metal ions that bind with various enzymes and co-factors within the cell. To uncover the underlying mechanisms mediated by StHMA genes, we identified 36 gene members in the StHMA family and divided them into six subfamilies by phylogenetic analysis. The StHMAs had high collinearity and were segmentally duplicated. Structurally, most StHMAs had one HMA domain, StHIPPc and StRNA1 subfamilies had two, and 13 StHMAs may be genetically variable. The StHMA gene structures and motifs varied considerably among the various classifications, this suggests the StHMA family is diverse in genetic functions. The promoter analysis showed that the StHMAs had six main cis-acting elements with abiotic stress. An expression pattern analysis revealed that the StHMAs were expressed tissue specifically, and a variety of abiotic stresses may induce the expression of StHMA family genes. The HMA transporter family may be regulated and expressed by a series of complex signal networks under abiotic stress. The results of this study may help to establish a theoretical foundation for further research investigating the functions of HMA genes in Solanum tuberosum to elucidate their regulatory role in the mechanism governing the response of plants to abiotic stress.

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.

Genome-wide association study for phosphate deficiency responsive root hair elongation in chickpea

Root hairs (RHs) are single-celled elongated epidermal cells and play a vital role in nutrient absorption, particularly for immobile minerals like phosphorus (P). As an adaptive response to P deficiency, an increase in RH length enhances root-soil contact and absorptive area for P absorption. Genetic variations have been reported for RH length and its response to P deficiency in plants. However, only a few association studies have been conducted to identify genes and genetic loci associated with RH length. Here, we screened desi chickpea accessions for RH length and its plasticity under P deficiency. Further, the genome-wide association study (GWAS) was conducted to identify the genetic loci associated with RH length in P deficient and sufficient conditions. Although high variability was observed in terms of RH length in diverse genotypes, majority of the accessions showed typical response of increase in RH length in low P. Genome-wide association mapping identified many SNPs with significant associations with RH length in P-sufficient and P-deficient conditions. A few candidate genes for RH length in P deficient (SIZ1-like and HAD superfamily protein) and sufficient (RSL2-like and SMAP1-like) conditions were identified which have known roles in RH development and P deficiency response or both. Highly associated loci and candidate genes identified in this study would be useful for genomic-assisted breeding to develop P-efficient chickpea.

A rice glutaredoxin regulate the expression of aquaporin genes and modulate root responses to provide arsenic tolerance

Rice is the most consumed food crop and essential determinant in global food security program. Currently, arsenic (As) accumulation in rice is a critical concern in terms of both crop productivity and grain quality; therefore, it is an urgent need to reduce As accumulation. Here, we selected a glutaredoxin (OsGrx_C7) gene that plays an essential role in AsIII tolerance in rice. To explore the mechanism, we raised OsGrx_C7 overexpression (OE) rice lines, which showed improved plant AsIII tolerance and lowered its accumulation in grains. Arsenic accumulation in husk, unpolished, and polished rice reduced by ca. 65%, 67%, and 85%, respectively, in OE lines, compared to wild-type (WT) plants. To know the rationale, expression of AsIII transporters (aquaporins) in root and shoot tissues were examined, and revealed that OsGrx_C7 regulates the expression of these genes, which ultimately reduces root to shoot AsIII translocation. Additionally, OsGrx_C7 improves root growth by regulating the expression of oxidative stress-induced root expansion related genes, promote root growth and plant health. Overall, current study suggested that AsIII induced OsGrx_C7 markedly enhanced tolerance to AsIII with reduced accumulation in grains by regulating root expansion and controlling root to shoot As transport by altered expression of AsIII aquaporins.

Biochemical and Molecular Characterization of PvNTD2, a Nucleotidase Highly Expressed in Nodules from Phaseolus vulgaris

Nucleotides are molecules of great importance in plant physiology. In addition to being elementary units of the genetic material, nucleotides are involved in bio-energetic processes, play a role as cofactors, and are also components of secondary metabolites and the hormone cytokinin. The common bean (Phaseolus vulgaris) is a legume that transports the nitrogen fixed in nodules as ureides, compounds synthetized from purine nucleotides. The first step in this pathway is the removal of the 5’-phosphate group by a phosphatase. In this study, a gene that codes for a putative nucleotidase (PvNTD2) has been identified in P. vulgaris. The predicted peptide contains the conserved domains for haloacid dehalogenase-like hydrolase superfamily. The protein has been overexpressed in Escherichia coli, and the purified protein showed molybdate-resistant phosphatase activity with nucleoside monophosphates as substrates, confirming that the identified gene codes for a nucleotidase. The optimum pH for the activity was 7–7.5. The recombinant enzyme did not show special affinity for any particular nucleotide, although the behaviour with AMP was different from that with the other nucleotides. The activity was inhibited by adenosine, and a regulatory role for this nucleoside was proposed. The expression pattern of PvNTD2 shows that it is ubiquitously expressed in all the tissues analysed, with higher expression in nodules of adult plants. The expression was maintained during leaf ontogeny, and it was induced during seedling development. Unlike PvNTD1, another NTD previously described in common bean, the high expression of PvNTD2 was maintained during nodule development, and its possible role in this organ is discussed.

Sustained substrate cycles between hexose phosphates and free sugars in phosphate-deficient potato (Solanum tuberosum) cell cultures

Futile cycling between free sugars and hexose phosphates occurring under phosphate deficiency could be involved in the maintenance of a threshold level of free cellular phosphate to preserve respiratory metabolism. We studied the metabolic response of potato cell cultures growing in Pi sufficient (2.5 mM, +Pi) or deficient (125 µM, -Pi) conditions. Under Pi deficiency, cellular growth was severely affected, however -Pi cells were able to maintain a low but steady level of free Pi. We surveyed the activities of 33 primary metabolic enzymes during the course of a 12 days Pi deficiency period. Our results show that many of these enzymes had higher specific activity in -Pi cells. Among these, we found typical markers of Pi deficiency such as phosphoenolpyruvate phosphatase and phosphoenolpyruvate carboxylase as well as enzymes involved in the biosynthesis of organic acids. Intriguingly, several ATP-consuming enzymes such as hexokinase (HK) and phosphofructokinase also displayed increased activity in -Pi condition. For HK, this was associated with an increase in the steady state of a specific HK polypeptide. Quantification of glycolytic intermediates showed a pronounced decrease in phosphate esters under Pi deficiency. Adenylate levels also decreased in -Pi cells, but the Adenylate Energy Charge was not affected by the treatment. To investigate the significance of HK induction under low Pi, [U-¹⁴C]-glucose tracer studies were conducted. We found in vivo evidence of futile cycling between pools of hexose phosphates and free sugars under Pi deficiency. Our study suggests that the futile cycling between hexose phosphates and free sugars which is active under +Pi conditions is sustained under Pi deficiency. The possibility that this process represents a metabolic adaptation to Pi deficiency is discussed with respect to Pi homeostasis in Pi-deficient conditions.

A novel glycerophosphodiester phosphodiesterase improves phosphate deficiency tolerance in rice

Soil phosphate (Pi) deficiency is major constraint for rice cultivation worldwide. Cellular membranes account for one third of cellular organic phosphorus (P) in the form of phospholipids. Therefore, remobilization of Pi from membrane phospholipids under Pi deficiency can be an important strategy to improve phosphorus use efficiency. Glycerophosphodiester phosphodiesterases (GDPDs) hydrolyse intermediate product of phospholipid catabolism, glycerophosphodiesters to glycerol-3-phosphate, a precursor for P and non P-lipid biosynthesis. Here, we show that OsGDPD2 is a Pi deficiency responsive gene, which is transcriptionally regulated by OsPHR2. In silico analysis of active site residues and enzymatic assays confirmed phosphodiesterase activity of OsGDPD2. All overexpression lines showed higher GDPD activity, Pi content, root growth, and biomass accumulation as compared with wild type. Conversely, silencing of OsGDPD2 led to decreased GDPD activity and Pi content. Notably, most of the P-containing metabolites and fatty acids were elevated in transgenic lines. Further, quantitative analysis of polar lipids revealed higher accumulation of several classes of phospholipids and galactolipids in overexpression lines indicating a potential role of OsGDPD2 in de novo glycerolipid biosynthesis. Thus, present study provides insights into novel physiological roles of OsGDPD2 in low Pi acclimation in rice.

ZmAPRG, an uncharacterized gene, enhances acid phosphatase activity and Pi concentration in maize leaf during phosphate starvation

An uncharacterized gene, ZmAPRG, isolated by map-based cloning, enhances acid phosphatase activity and phosphate concentration in maize leaf during phosphate starvation. Acid phosphatase (APase) plays important roles in the absorption and utilization of phosphate (Pi) during maize growth. The information on genes regulating the acid phosphatase activity (APA) in maize leaves remains obscured. In a previous study, we delimited the quantitative trait locus, QTL-AP9 for APA to a region of about 546 kb. Here, we demonstrate that the GRMZM2G041022 located in the 546 kb region is a novel acid phosphatase-regulating gene (ZmAPRG). Its overexpression significantly increased the APA and Pi concentration in maize and rice leaves. Subcellular localization of ZmAPRG showed that it was anchored on the plasma and nuclear membrane. The transcriptome analysis of maize ZmAPRG overexpressing lines (ZmAPRG OE) revealed 1287 up-regulated and 392 down-regulated genes. Among these, we found APase, protein phosphatase, and phosphate transporter genes, which are known to be implicated in the metabolism and utilization of Pi. We inferred the ZmAPRG functions as an upstream regulation node, directly or indirectly regulating APases, protein phosphatases, and phosphate transporter genes involved in Pi metabolism and utilization in maize. These findings will pave the way for elucidating the mechanism of APase regulation, absorption and utilization of Pi, and would facilitate maize breeding for efficient use of fertilizers.

An Integrative Systems Perspective on Plant Phosphate Research

The case for improving crop phosphorus-use-efficiency is widely recognized. Although much is known about the molecular and regulatory mechanisms, improvements have been hampered by the extreme complexity of phosphorus (P) dynamics, which involves soil chemistry; plant-soil interactions; uptake, transport, utilization and remobilization within plants; and agricultural practices. The urgency and direction of phosphate research is also dependent upon the finite sources of P, availability of stocks to farmers and reducing environmental hazards. This work introduces integrative systems approaches as a way to represent and understand this complexity, so that meaningful links can be established between genotype, environment, crop traits and yield. It aims to provide a large set of pointers to potential genes and research practice, with a view to encouraging members of the plant-phosphate research community to adopt such approaches so that, together, we can aid efforts in global food security.

Genetic Engineering of the Biosynthesis of Glycine Betaine Modulates Phosphate Homeostasis by Regulating Phosphate Acquisition in Tomato

Glycine betaine (GB), as a putative compatible substance, protects plants against the damaging effects of abiotic stresses. Phosphorus deficiency is one type of abiotic stress that is detrimental to plant growth. Maintenance of phosphate (Pi) homeostasis is crucial. This study demonstrates GB-regulated phosphate homeostasis in the tomato (Solanum lycopersicum cv. 'Moneymaker') transformed with the choline oxidase gene codA from Arthrobacter globiformis. The codA-transgenic lines displayed more resistance to low-phosphate stress. The data revealed that the wild-type plants were stunted and consistently retained less Pi than transgenic lines, especially when grown under low-phosphate conditions. This difference in Pi retention was attributable to the enhanced Pi uptake ability in the transgenic lines. The transgenic plants translocated more Pi into the plant cell due to the enhanced enzymatic activity of plasma membrane H+-ATPase and increased Pi/H+ co-transport, which improved Pi uptake. The differential expression of 'PHO regulon' genes further maintained intracellular Pi homeostasis. Furthermore, GB maintained a higher photosynthesis rate, thus increasing the production and translocation of sucrose via phloem loading to enhance plant response to low-phosphate stress. We conclude that GB mediates Pi uptake and translocation by regulating physiological and biochemical processes that promote adaptation to environmental changes in Pi availability. These processes eventually lead to better growth and development of the codA-transgenic lines. This finding will help to further elucidate the signaling mechanism of how GB perceives and transmits low-phosphate signals to alleviate Pi nutritional stress.

Increased Catalase Activity and Maintenance of Photosystem II Distinguishes High-Yield Mutants From Low-Yield Mutants of Rice var. Nagina22 Under Low-Phosphorus Stress

An upland rice variety, Nagina22 (N22) and its 137 ethyl methanesulfonate (EMS)-induced mutants, along with a sensitive variety, Jaya, was screened both in low phosphorus (P) field (Olsen P 1.8) and in normal field (Olsen P 24) during dry season. Based on the grain yield (YLD) of plants in normal field and plants in low P field, 27 gain of function (high-YLD represented as hy) and 9 loss of function (low-YLD represented as ly) mutants were selected and compared with N22 for physiological and genotyping studies. In low P field, hy mutants showed higher P concentration in roots, leaves, grains, and in the whole plant than in ly mutants at harvest. In low P conditions, F v/F m and qN were 24% higher in hy mutants than in ly mutants. In comparison with ly mutants, the superoxide dismutase (SOD) activity in the roots and leaves of hy mutants in low P fields was 9% and 41% higher at the vegetative stage, respectively, but 51% and 14% lower in the roots and leaves at the reproductive stage, respectively. However, in comparison with ly mutants, the catalase (CAT) activity in the roots and leaves of hy mutants in low P fields was 35% higher at the vegetative stage and 15% and 17% higher at the reproductive stage, respectively. Similarly, hy mutants in low P field showed 20% and 80% higher peroxidase (POD) activity in the roots and leaves at the vegetative stage, respectively, but showed 14% and 16% lower POD activity at the reproductive stage in the roots and leaves, respectively. Marker trait association analysis using 48 simple sequence repeat (SSR) markers and 10 Pup1 gene markers showed that RM3648 and RM451 in chromosome 4 were significantly associated with grain YLD, tiller number (TN), SOD, and POD activities in both the roots and leaves in low P conditions only. Similarly, RM3334 and RM6300 in chromosome 5 were associated with CAT activity in leaves in low P conditions. Notably, grain YLD was positively and significantly correlated with CAT activity in the roots and shoots, F v/F m and qN in low P conditions, and the shoots' P concentration and qN in normal conditions. Furthermore, CAT activity in shoots was positively and significantly correlated with TN in both low P and normal conditions. Thus, chromosomal regions and physiological traits that have a role in imparting tolerance to low P in the field were identified.

Differential response of hexaploid and tetraploid wheat to interactive effects of elevated [CO2] and low phosphorus

Hexaploid wheat is more responsive than tetraploid to the interactive effects of elevated [CO₂] and low P in terms of carboxylate efflux, enzyme activity and gene expression (TaPT1 and TaPAP). Availability of mineral nutrients to plants under changing climate has become a serious challenge to food security and economic development. An understanding of how elevated [CO₂] influences phosphorus (P) acquisition processes at the whole-plant level would be critical in selecting cultivars as well as to maintain optimum yield in limited-P conditions. Wheat (Triticum aestivum and T. durum) grown hydroponically with sufficient and low P concentration were exposed to elevated and ambient [CO₂]. Improved dry matter partitioning towards root resulted in increased root-to-shoot ratio, root length, volume, surface area, root hair length and density at elevated [CO₂] with low P. Interaction of low P and [CO₂] induced activity of enzymes (phosphoenolpyruvate carboxylase, malate dehydrogenase and citrate synthase) in root tissue resulting in twofold increase in carboxylates and acid phosphatase exudation. Physiological absorption capacity of roots showed that plants alter their uptake kinetics by increasing affinity (low K_m) in response to elevated [CO₂] under low P supply. Increased relative expression of genes, purple acid phosphatase (TaPAP) and high-affinity Pi transporter (TaPT1) in roots induced by elevated [CO₂] and low P supported our physiological observations. Hexaploid wheat (PBW-396) being more responsive to elevated [CO₂] at low P supply as compared to tetraploid (PDW-233) necessitates the ploidy effect to be explored further which might be advantageous under changing climate.

Characterization of the loss-of-function mutant NH101 for yield under phosphate deficiency from EMS-induced mutants of rice variety Nagina22

In earlier studies at IIRR, Hyderabad, screening of ∼2000 EMS mutants of the rice variety Nagina22 (N22) resulted in the identification of 11 loss-of-function mutants with zero grain yield in Pi-deprived soil under field condition. Among these mutants, NH101 was selected for comparative analyses with N22 for various morphophysiological and/or molecular traits during growth in a hydroponic system (7 d) and in a pot soil (50% flowering) under different Pi regime. The total length of the seminal and adventitious roots, agronomic traits (panicle length and unfilled spikelet/panicle), activities of the antioxidant enzymes (SOD, POD, and APX), and the relative expression levels of the genes involved in the maintenance of Pi homeostasis (MPH) i.e., OsPHR2, SPX1/2 OsPT4, 6, and 8 showed significant increase in the Pi-deprived mutant compared with N22. Whereas, some of the traits showed significant reduction in NH101 than N22 such as number of tillers and filled spikelets/panicle, yield, contents of Pi and externally secreted APase, activity of CAT, and the relative expression levels of MPH genes i.e., OsmiR399a, OsPHO1;2, OsIPS1, OsPAP10a, OsPT2, 9, and 10. The study highlighted wide spectrum differential effects of the mutation in NH101 on various traits that play important roles governing the maintenance of Pi homeostasis. This mutant thus provides a rich repository of genetic material amenable for the identification of the genes that are pivotal for Pi use efficiency.

Aluminum-responsive genes revealed by RNA-Seq and related physiological responses in leaves of two Citrus species with contrasting aluminum-tolerance

Little is known about the physiological and molecular responses of leaves to aluminum (Al)-toxicity. Seedlings of Al-intolerant Citrus grandis and Al-tolerant Citrus sinensis were supplied daily with nutrient solution containing 0 mM (control) and 1.0 mM (Al-toxicity) AlCl₃·6H₂O for 18 weeks. We found that Al-treatment only decreased CO₂ assimilation in C. grandis leaves, and that the Al-induced alterations of gene expression profiles were less in C. sinensis leaves than those in C. grandis leaves, indicating that C. sinensis seedlings were more tolerant to Al-toxicity than C. grandis ones. Al concentration was similar between Al-treated C. sinensis and C. grandis roots, but it was higher in Al-treated C. grandis stems and leaves than that in Al-treated C. sinensis stems and leaves. Al-treated C. sinensis seedlings accumulated relatively more Al in roots and transported relatively little Al to shoots. This might be responsible for the higher Al-tolerance of C. sinensis. Further analysis showed that the following several aspects might account for the higher Al-tolerance of C. sinensis, including: (a) Al-treated C. sinensis leaves had higher capacity to maintain the homeostasis of energy and phosphate, the stability of lipid composition and the integrity of cell wall than did Al-treated C. grandis leaves; (b) Al-triggered production of reactive oxygen species (ROS) and the other cytotoxic compounds was less in Al-treated C. sinensis leaves than that in Al-treated C. grandis leaves, because Al-toxicity decreased CO₂ assimilation only in C. grandis leaves; accordingly, more upregulated genes involved in the detoxifications of ROS, aldehydes and methylglyoxal were identified in Al-treated C. grandis leaves; in addition, flavonoid concentration was increased only in Al-treated C. grandis leaves; (c) Al-treated C. sinensis leaves could keep a better balance between protein phosphorylation and dephosphorylation than did Al-treated C. grandis leaves; and (d) both the equilibrium of hormones and hormone-mediated signal transduction were greatly disrupted in Al-treated C. grandis leaves, but less altered in Al-treated C. sinensis leaves. Finally, we discussed the differences in Al-responsive genes between Citrus roots and leaves.

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.

Abscisic acid is involved in root cell wall phosphorus remobilization independent of nitric oxide and ethylene in rice (Oryza sativa)

BACKGROUND

Abscisic acid (ABA) is a well-studied phytohormone demonstrated to be involved in sub-sets of stress responses in plants, such as iron (Fe) deficiency and phosphorus (P) deficiency in Arabidopsis. However, whether ABA is involved in P deficiency in rice has not been frequently studied. The present study was undertaken to investigate the mechanism underlying ABA-aggravated P deficiency in rice (Oryza sativa).

RESULTS

P deficiency decreased ABA accumulation rapidly (within 1 h) in the roots. Exogenous ABA negatively regulated root and shoot soluble P contents by decreasing pectin content, inhibiting P deficiency-induced increases in pectin methylesterase activity and expression of the phosphate transporter gene-OsPT6, thereby decreasing the re-utilization of P from the cell wall and its translocation to the shoot. Moreover, neither the nitric oxide (NO) donor sodium nitroprusside nor ethylene precursor 1-aminocyclopropane-1-carboxylic acid had any effect on ABA accumulation, and application of ABA or the ABA inhibitor fluridone also had no effect on NO production and ethylene emission.

CONCLUSIONS

Under P deficiency, NO levels increase as quickly as ABA levels decrease, to inhibit both the ABA-induced reduction of pectin contents for the re-utilization of cell wall P and the ABA-induced down-regulation of OsPT6 for the translocation of P from roots to shoots. Overall, our results provide novel information indicating that the reduction of ABA under P deficiency is a very important pathway in the re-utilization of cell wall P in rice under P-deficient conditions, which should be a very effective mechanism for plant survival under P deficiency stress for common agronomic practice.

Salvia castanea Hairy Roots are More Tolerant to Phosphate Deficiency than Salvia miltiorrhiza Hairy Roots Based on the Secondary Metabolism and Antioxidant Defenses

Salvia miltiorrhiza is a well-known traditional Chinese herb which is used to treat heart disease. Salvia castanea is a substitute product for S. miltiorrhiza in the medicinal field. Previous study has shown that phosphate (Pi) deficiency could promote the accumulation of secondary metabolism in herbs, and it has also developed a strategy for saving Pi resources and increasing the yield of active substances in herbs. In the present study, the hairy roots of S. miltiorrhiza and S. castanea were used to identify the Pi deficiency response mechanisms of these two Salvia species. The results showed that Pi deficiency increased the accumulation of specifically secondary metabolites, such as phenolic acids and tanshinones, which were caused by promoting the expression levels of key enzyme genes. In addition, Pi deficiency promoted the antioxidant activity in these two Salvia species. The data demonstrated that Pi deficiency increased the quality of the medicinal material in the plant. The hairy roots of S. castanea were more adaptive to Pi deficiency than those of S. miltiorrhiza in terms of biomass, secondary metabolism, and antioxidant activity. The results of this study provide insights into breeding herbs that are better adapted to Pi deficiency, which could increase the yield of active ingredients in herbs and save Pi resources.

Regulatory feedback response mechanisms to phosphate starvation in rice

Phosphorus is a growth-limiting nutrient for plants. The growing scarcity of phosphate stocks threatens global food security. Phosphate-uptake regulation is so complex and incompletely known that attempts to improve phosphorus use efficiency have had extremely limited success. This study improves our understanding of the molecular mechanisms underlying phosphate uptake by investigating the transcriptional dynamics of two regulators: the Ubiquitin ligase PHO2 and the long non-coding RNA IPS1. Temporal measurements of RNA levels have been integrated into mechanistic mathematical models using advanced statistical techniques. Models based solely on current knowledge could not adequately explain the temporal expression profiles. Further modeling and bioinformatics analysis have led to the prediction of three regulatory features: the PHO2 protein mediates the degradation of its own transcriptional activator to maintain constant PHO2 mRNA levels; the binding affinity of the transcriptional activator of PHO2 is impaired by a phosphate-sensitive transcriptional repressor/inhibitor; and the extremely high levels of IPS1 and its rapid disappearance upon Pi re-supply are best explained by Pi-sensitive RNA protection. This work offers both new opportunities for plant phosphate research that will be essential for informing the development of phosphate efficient crop varieties, and a foundation for the development of models integrating phosphate with other stress responses.

Food security is a global priority. One aspect of this is the ability to grow crops in poorer soils with less fertilizer input, of which phosphate is both essential and resource limited. This study provides a quantitative understanding of the genetic regulation of phosphate uptake in rice upon its deficiency. The mathematical models developed in this article lead to three hypotheses for the gaps identified in current knowledge. One of these hypotheses has previously only been reported in animals while the other prompted laboratory experiments, revealing an extra level of regulation at short timescales. These models provide the basis for crop systems biologists to study other aspects of phosphate regulation, including its internal utilisation, external availability and foraging, and, more crucially, in response to other stresses.

A Genome-Wide Association Study of Wheat Spike Related Traits in China

Rapid detection of allelic variation and identification of advantage haplotypes responsible for spike related traits play a crucial role in wheat yield improvement. The released genome sequence of hexaploid wheat (Chinese Spring) provides an extraordinary opportunity for rapid detection of natural variation and promotes breeding application. Here, selection signals detection and genome-wide association study (GWAS) were conducted for spike related traits. Based on the genotyping results by 90K SNP chip, 192 common wheat samples from southwest China were analyzed. One hundred and forty-six selective windows and one hundred and eighty-four significant SNPs (51 for spike length, 28 for kernels per spike, 39 for spikelet number, 30 for thousand kernel weight, and 36 for spike number per plant) were detected. Furthermore, tightly linkage and environmental stability window clusters and SNP clusters were also obtained. As a result, four SNP clusters associated with spike length were detected on chromosome 2A, 2B, 2D, and 6A. Two SNP clusters correlated to kernels per spike were detected on 2A and 2B. One pleiotropy SNP cluster correlated to spikelet number and kernels per spike was detected on 7B. According to the genome sequence, these SNP clusters and their overlapped/flanking QTLs which have been reported previously were integrated to a physical map. The candidate genes responsible for spike length, kernels per spike and spikelet number were predicted. Based on the genotypes of cultivars in south China, two advantage haplotypes associated with spike length and one advantage haplotype associated with kernels per spike/spikelet number were detected which have not been effectively transited into cultivars. According to these haplotypes, KASP markers were developed and diagnosed across landraces and cultivars which were selected from south and north China. Consequently, KASP assay, consistent with the GWAS results, provides reliable haplotypes for MAS in wheat yield improvement.

Phosphite: a novel P fertilizer for weed management and pathogen control

The availability of orthophosphate (Pi) is a key determinant of crop productivity because its accessibility to plants is poor due to its conversion to unavailable forms. Weed's competition for this essential macronutrient further reduces its bio-availability. To compensate for the low Pi use efficiency and address the weed hazard, excess Pi fertilizers and herbicides are routinely applied, resulting in increased production costs, soil degradation and eutrophication. These outcomes necessitate the identification of a suitable alternate technology that can address the problems associated with the overuse of Pi-based fertilizers and herbicides in agriculture. The present review focuses on phosphite (Phi) as a novel molecule for its utility as a fertilizer, herbicide, biostimulant and biocide in modern agriculture. The use of Phi-based fertilization will help to reduce the consumption of Pi fertilizers and facilitate weed and pathogen control using the same molecule, thereby providing significant advantages over current orthophosphate-based fertilization.

Identification of Purple Acid Phosphatases in Chickpea and Potential Roles of CaPAP7 in Seed Phytate Accumulation

Purple acid phosphatases (PAPs) play important roles in phosphate (Pi) acquisition and utilization. These PAPs hydrolyze organic Phosphorus (P) containing compounds in rhizosphere as well as inside the plant cell. However, roles of PAPs in one of the most widely cultivated legumes, chickpea (Cicer arietnum L.), have not been unraveled so far. In the present study, we identified 25 putative PAPs in chickpea (CaPAPs) which possess functional PAP motifs and domains. Differential regulation of CaPAPs under different nutrient deficiencies revealed their roles under multiple nutrient stresses including Pi deficiency. Interestingly, most of the CaPAPs were prominently expressed in flowers and young pods indicating their roles in flower and seed development. Association mapping of SNPs underlying CaPAPs with seed traits revealed significant association of low Pi inducible CaPAP7 with seed weight and phytate content. Biochemical characterization of recombinant CaPAP7 established it to be a functional acid phosphatase with highest activity on most abundant organic-P substrate, phytate. Exogenous application of recombinant CaPAP7 enhanced biomass and Pi content of Arabidopsis seedlings supplemented with phytate as sole P source. Taken together, our results uncover the PAPs in chickpea and potential roles of CaPAP7 in seed phytate accumulation.

OsPT4 Contributes to Arsenate Uptake and Transport in Rice

Arsenic (As) is toxic to organisms, and elevated As accumulation in rice (Oryza sativa) grain may pose a significant health risk to humans. The predominant form of As in soil under aerobic conditions is As(V), which has a chemical structure similar to that of PO₄^3-. Rice roots take up As(V) by phosphate (Pi) transporters, such as OsPT1 and OsPT8. In the present study, we investigated the contribution of OsPT4, belonging to the Pht1 family, on rice As(V) uptake and transport. We determined the mRNA amounts of OsPTs in rice seedlings, and expressions of OsPT1, OsPT4, and OsPT8 were up-regulated under As(V) conditions. OsPT4-overexpressing plants were obtained to examine the As (V) transport activity of OsPT4 in rice. When transgenic rice grew in hydroponic culture with 25 and 50 μM As(V), the plants showed sensitivity to As(V) stress with aboveground parts showing delayed growth and the roots stunted. The OsPT4 CRISPR lines showed the opposite phenotype. When plants were grown in 5 μM As(V) solution for 7 days, the As accumulation of OsPT4-overexpressing plants increased up to twice in roots and shoots. Furthermore, the arsenate uptake rates of OsPT4-overexpressing lines were higher compared with wild type. The V_max of As(V) uptake in OsPT4-overexpressing plants increased 23-45% compared with Nipponbare. In the flooded soil, the As accumulation of OsPT4-overexpressing plants increased 40-66% and 22-30% in straw and grain, respectively. While in OsPT4-cr plants As accumulation in roots decreased 17-30% compared with Nipponbare. Therefore, the present study indicates that OsPT4 is involved in As(V) uptake and transport and could be a good candidate gene to generate low As-accumulating rice.