Phosphate concentration and arbuscular mycorrhizal colonisation influence the growth, yield and expression of twelve PHT1 family phosphate transporters in foxtail millet (Setaria italica)

Biodegradation pathway and mechanism of tri (2-chloropropyl) phosphate by Providencia rettgeri

Tri (2-chloropropyl) phosphate (TCPP) was an emerging contaminant of global concern because of its frequent occurrence, potential toxic effects, and persistence in the environment. Microbial degradation might be an efficient and safe removal method, but limited information was available. In this study, Providencia rettgeri was isolated from contaminated sediment and showed it could use TCPP as unique phosphorus source to promote growth, and decompose 34.7% of TCPP (1 mg/L) within 5 days. The microbial inoculation and the initial concentration of TCPP could affect the biodegradation efficient. Further study results indicated that TCPP decomposition by Providencia rettgeri was mainly via phosphoester bond hydrolysis, evidenced by the production of bis (2-chloropropyl) phosphate (C6H13Cl2PO4) and mono-chloropropyl phosphate (C3H8ClPO4). Both intracellular and extracellular enzymes could degrade TCPP, but intracellular degradation was dominant in the later reaction stage, and the presence of Cu2+ ions had a promoting effect. These findings developed novel insights into the potential mechanism of TCPP microbial degradation.

Protein research in millets: current status and way forward

MAIN CONCLUSION

Millets' protein studies are lagging behind those of major cereals. Current status and future insights into the investigation of millet proteins are discussed. Millets are important small-seeded cereals majorly grown and consumed by people in Asia and Africa and are considered crops of future food security. Although millets possess excellent climate resilience and nutrient supplementation properties, their research advancements have been lagging behind major cereals. Although considerable genomic resources have been developed in recent years, research on millet proteins and proteomes is currently limited, highlighting a need for further investigation in this area. This review provides the current status of protein research in millets and provides insights to understand protein responses for climate resilience and nutrient supplementation in millets. The reference proteome data is available for sorghum, foxtail millet, and proso millet to date; other millets, such as pearl millet, finger millet, barnyard millet, kodo millet, tef, and browntop millet, do not have any reference proteome data. Many studies were reported on stress-responsive protein identification in foxtail millet, with most studies on the identification of proteins under drought-stress conditions. Pearl millet has a few reports on protein identification under drought and saline stress. Finger millet is the only other millet to have a report on stress-responsive (drought) protein identification in the leaf. For protein localization studies, foxtail millet has a few reports. Sorghum has the highest number of 40 experimentally proven crystal structures, and other millets have fewer or no experimentally proven structures. Further proteomics studies will help dissect the specific proteins involved in climate resilience and nutrient supplementation and aid in breeding better crops to conserve food security.

Brown-top millet: an overview of breeding, genetic, and genomic resources development for crop improvement

MAIN CONCLUSION

Brown-top millet is a lesser-known millet with a high grain nutrient value, early maturation, and drought tolerance that needs basic research to understand and conserve food security. Brown-top millet [Urochloa ramosa (L.)] is currently cultivated in some developing countries (especially in India) for food and fodder, although it is less known among the small millets. Like other millets, it contains macro- and micronutrients, vitamins, minerals, proteins, and fiber, all of which have rich health benefits. The nutritional importance and health benefits of brown-top millet are still unknown to many people due to a lack of awareness, wide cultivation, and research. Hence, this millet is currently overshadowed by other major cereals. This review article aims to present the nutritional, breeding, genetic, and genomic resources of brown-top millet to inform millet and other plant researchers. It is important to note that genetic and genomic resources have not yet been created for this millet. To date, there are no genomic and transcriptomic resources for brown-top millet to develop single nucleotide polymorphisms (SNP) and insertion/Deletions (InDels) for breeding studies. Furthermore, studies regarding nutritional significance and health benefits are required to investigate the exact nutritional contents and health benefits of the brown-top millet. The present review delves into the nutritional value and health advantages of brown-top millet, as supported by the available literature. The limitations of producing brown-top millet have been enumerated. We also cover the status of marker-assisted breeding and functional genomics research on closely related species. Lastly, we draw insights for further research such as developing omics resources and applying genome editing to study and improve brown-top millet. This review will help to start breeding and other molecular studies to increase the growth and development of this cereal.

Molecular and Systems Biology Approaches for Harnessing the Symbiotic Interaction in Mycorrhizal Symbiosis for Grain and Oil Crop Cultivation

Mycorrhizal symbiosis, the mutually beneficial association between plants and fungi, has gained significant attention in recent years due to its widespread significance in agricultural productivity. Specifically, arbuscular mycorrhizal fungi (AMF) provide a range of benefits to grain and oil crops, including improved nutrient uptake, growth, and resistance to (a)biotic stressors. Harnessing this symbiotic interaction using molecular and systems biology approaches presents promising opportunities for sustainable and economically-viable agricultural practices. Research in this area aims to identify and manipulate specific genes and pathways involved in the symbiotic interaction, leading to improved cereal and oilseed crop yields and nutrient acquisition. This review provides an overview of the research frontier on utilizing molecular and systems biology approaches for harnessing the symbiotic interaction in mycorrhizal symbiosis for grain and oil crop cultivation. Moreover, we address the mechanistic insights and molecular determinants underpinning this exchange. We conclude with an overview of current efforts to harness mycorrhizal diversity to improve cereal and oilseed health through systems biology.

Isolation and Characterization of Erianthus arundinaceus Phosphate Transporter 1 (PHT1) Gene Promoter and 5' Deletion Analysis of Transcriptional Regulation Regions under Phosphate Stress in Transgenic Tobacco

Phosphorus deficiency highly interferes with plant growth and development. Plants respond to persistent P deficiency by coordinating the expression of genes involved in the alleviation of stress. Promoters of phosphate transporter genes are a great choice for the development of genetically modified plants with enhanced phosphate uptake abilities, which improve crop yields in phosphate-deficient soils. In our previous study, the sugarcane phosphate transporter PHT1;2 gene showed a significantly high expression under salinity stress. In this study, the Erianthus arundinaceus EaPHT1;2 gene was isolated and characterized using various in silico tools. The deduced 542 amino acid residues have 10 transmembrane domains, with a molecular weight and isoelectric point of 58.9 kDa and 9.80, respectively. They displayed 71-96% similarity with Arabidopsis thaliana, Zea mays, and the Saccharum hybrid. To elucidate the function of the 5' regulatory region, the 1.1 kb promoter was isolated and validated in tobacco transgenics under Pi stress. The EaPHT1;2 promoter activity was detected using a β-glucuronidase (GUS) assay. The EaPHT1;2 promoter showed 3- to 4.2-fold higher expression than the most widely used CaMV35S promoter. The 5' deletion analysis with and without 5' UTRs revealed a small-sized 374 bp fragment with the highest promoter activity among 5' truncated fragments, which was 2.7 and 4.2 times higher than the well-used CaMV35S promoter under normal and Pi deprivation conditions, respectively. The strong and short promoter of EaPHT1;2 with 374 bp showed significant expression in low-Pi-stress conditions and it could be a valuable source for the development of stress-tolerant transgenic crops.

Effects of Individual or Combined Deficiency of Phosphorous and Zinc on Phenotypic, Nutrient Uptake, and Molecular Responses of Finger Millet (Eleusine coracana): A Nutri-Rich Cereal Crop

Deficiencies of either phosphorus (P) or zinc (Zn) or both are one of the major abiotic constraints influencing agricultural production. Research on the effects of individual or combined P and Zn deficiency is limited in cereals. This study reports the effects of the individual or combined deficiency of inorganic phosphate (Pi) and Zn on the phenotypic, root hair modification, nutrient uptake, and molecular responses of finger millet (Eleusine coracana), a nutri-rich cereal crop. Finger millet seedlings were grown hydroponically under control (+Pi+Zn), individual Pi deficiency (-Pi), individual Zn deficiency (-Zn), and combined Pi and Zn deficiency (-Pi-Zn) conditions for 30 days to find the phenotypic, root hair modification, nutrient uptake, and molecular responses. Compared to the individual -Zn condition, the individual -Pi condition had more of an effect in terms of biomass reduction. The combined -Pi-Zn condition increased the root hair length and density compared to the other three conditions. The individual -Zn condition increased the Pi uptake, while the individual -Pi condition favored the Zn uptake. EcZIP2 was highly upregulated in shoot tissues under the individual -Zn condition, and EcPHT1;2 was highly expressed in root tissues under the individual -Pi condition. This is the first study to report the effects of the individual or combined deficiency of Pi and Zn in finger millet and may lead to future studies to better manage P and Zn deficiency.

Function identification and characterization of Oryza sativa ZRT and IRT-like proteins computationally for nutrition and biofortification in rice

Zinc plays a very critical role and function in all organisms. Its deficiency can cause a serious issue. In Oryza sativa, the ZRT/IRT transporter-like proteins play a role in the zinc metal uptake and transport. Few OsZIPs genes have been validated and characterized for their biological functions and most of OsZIPs are not well physiologically, biochemically and phenotypically characterized. In the current study, they analyzed for their function through subcellular localization, phylogenetic analysis, homology modeling, expression analysis, protein-protein interaction (PPI) network prediction, and prediction of their binding sites. Hierarchical clustering of OsZIP genes based on different anatomical parts and developmental stages also orthologs prediction was identified. The presence of SNPs, SSRs, ESTs, FSTs, MPSS, and SAGE tags were analyzed for useful development of markers. SNPs were identified in all OsZIPs genes and each gene was further classified based on their number and position in the 3'UTR and 5'UTR regions of the gene-specific sequences. Binding clusters and their location on the protein sequences were predicted. We found Changing in residues number and position which were due to partial overlapping and sequence alignment, but they share the same mechanism of binding and transporting Zinc. A wide range of CRISPR Cas9 gRNAs was designed based on single nucleotide polymorphism (SNP) for each OsZIP transporter gene for well-function identification and characterization with genome-wide association studies. Hence this study would provide useful information, understanding, and predicting molecular insights for the future studies that will help for improvement of nutritional quality of rice varieties.Communicated by Ramaswamy H. Sarma.

Genome-Wide Analysis of the PHT Gene Family and Its Response to Mycorrhizal Symbiosis in Tomatoes under Phosphate Starvation Conditions

Phosphate is one of the essential mineral nutrients. Phosphate transporter genes (PHTs) play an important role in Pi acquisition and homeostasis in tomato plants. However, basic biological information on PHT genes and their responses of symbiosis with arbuscular mycorrhizal in the genome remains largely unknown. We analyzed the physiological changes and PHT gene expression in tomatoes (Micro-Tom) inoculated with arbuscular mycorrhizal (AM) fungi (Funneliformis mosseae) under different phosphate conditions (P1: 0 µM, P2: 25 µM, and P3: 200 µM Pi). Twenty-three PHT genes were identified in the tomato genomics database. Protein sequence alignment further divided the 23 PHT genes into three groups, with similar classifications of exons and introns. Good colonization of plants was observed under low phosphate conditions (25 µM Pi), and Pi stress and AM fungi significantly affected P and N accumulation and root morphological plasticity. Moreover, gene expression data showed that genes in the SlPHT1 (SlPT3, SlPT4, and SlPT5) gene family were upregulated by Funneliformis mosseae under all conditions, which indicated that these gene levels were significantly increased with AM fungi inoculation. None of the analyzed SlPHT genes in the SlPH2, SlPHT3, SlPHT4, and SlPHO gene families were changed at any Pi concentration. Our results indicate that inoculation with AM fungi mainly altered the expression of the PHT1 gene family. These results will lay a foundation for better understanding the molecular mechanisms of inorganic phosphate transport under AM fungi inoculation.

Variation of growth and transcriptome responses to arbuscular mycorrhizal symbiosis in different foxtail millet lines

BACKGROUND

Arbuscular mycorrhizal fungi (AMF) have been applied to promote the growth of different crop species, but knowledge about the impacts of symbiosis on foxtail millet at the physiological and molecular levels have remained limited. In this study, we compared the mycorrhization phenotypes of one cultivar and three different landraces and performed a comprehensive transcriptomic analysis to assess the effects of genetic variation on the responses to symbiosis.

RESULTS

Our results showed that colonization by AMF did not enhance biomass accumulation but significantly increased grain production only in three lines. More than 2,000 genes were affected by AMF colonization in all lines. Most AM symbiosis-conserved genes were induced, but the induction levels varied between lines. Gene Ontology (GO) analysis showed that Biological Function terms related to nitrogen transport and assimilation were only enriched in TT8. Similarly, two of phosphate starvation-induced phosphate transporters were only simultaneously downregulated in TT8. In the other two lines, the enrichment of GO terms associated with cell wall reorganization and lignification was observed, though the effects were different.

CONCLUSION

This study reveals the impacts of genetic variation of millet lines on the responses to AM symbiosis and provides information regarding AMF application for millet production.

Zinc supply influenced the growth, yield, zinc content, and expression of ZIP family transporters in sorghum

Zinc deficiency altered shoot and root growth, plant biomass, yield, and ZIP family transporter gene expression in sorghum. Zinc (Zn) deficiency affects several crop plants' growth and yield, including sorghum. We have evaluated the sorghum under various concentrations of Zn supply for phenotypic changes, Zn content, and expression of Zn-regulated, iron-regulated transporter-like proteins (ZIP) family genes. Zn deficiency reduced the shoot and root growth, plant biomass, and yield by > 50%. The length and number of lateral roots were increased by more than 50% under deficient Zn compared to sufficient Zn. Ten SbZIP family transporter genes showed dynamic expression in shoot and root tissues of sorghum under deficient and sufficient Zn. SbZIP2, 5, 6, 7, and 8 were expressed in all tissues under deficient and sufficient Zn. SbZIP2, 4, 5, 6, 7, 8, and 10 were highly induced in shoot tissues by deficient Zn. The expression level of SbZIP6, 7, 8, and 9 was higher in root tissues under deficient Zn. The phylogenetic analysis revealed that most SbZIP family proteins are closely associated with the ZmZIP family of maize. The functional residues His177 and Gly182 are fully conserved in all SbZIP family transporters, as revealed by homology modeling and multiple sequence alignment. This study may provide a foundation for improving the Zn-use efficiency of sorghum.

A Eucalyptus Pht1 Family Gene EgPT8 Is Essential for Arbuscule Elongation of Rhizophagus irregularis

The majority of vascular flowering plants can establish arbuscular mycorrhizal (AM) symbiosis with AM fungi. These associations contribute to plant health and plant growth against various environmental stresses. In the mutualistic endosymbiosis, the AM fungi deliver phosphate (Pi) to the host root through highly branched hyphae called arbuscules. The molecular mechanisms of Pi transfer from AM fungi to the plant have been determined, which are dominated by AM-specific Pi transporters belonging to the PHOSPHATE TRANSPORTER 1 (Pht1) family within the subfamily I. However, it is unknown whether Pht1 family proteins are involved in other regulations in AM symbiosis. Here, we report that the expression of EgPT8 is specifically activated by AM fungus Rhizophagus irregularis and is localized in root cortical cells containing arbuscules. Interestingly, knockdown of EgPT8 function does not affect the Eucalyptus grandis growth, total phosphorous (P) concentration, and arbuscule formation; however, the size of mature arbuscules was significantly suppressed in the RNAi-EgPT8 lines. Heterogeneous expression of EgPT4, EgPT5, and EgPT8 in the Medicago truncatula mutant mtpt4-2 indicates that EgPT4 and EgPT5 can fully complement the defects of mutant mtpt4-2 in mycorrhizal Pi uptake and arbuscule formation, while EgPT8 cannot complement the defective AM phenotype of the mtpt4-2 mutant. Based on our results, we propose that the AM fungi-specific subfamily I transporter EgPT8 has novel functions and is essential to arbuscule elongation. IMPORTANCE Arbuscular mycorrhizal (AM) formation in host root cortical cells is initiated by exchanges of diffusible molecules, among which Pi uptake is known as the important feature of AM fungi on symbiosis functioning. Over the last two decades, it has been repeatedly proven that most vascular plants harbor two or more AM-specific Pht1 proteins; however, there is no direct evidence regarding the potential link among these Pi transporters at the symbiotic interface. This work revealed a novel function of a structurally conserved protein involved in lateral arbuscule development. In total, we confirmed that three AM-specific Pht1 family proteins are nonredundant in Eucalyptus grandis and that EgPT8 is responsible for fungal arbuscule elongation of Rhizophagus irregularis.

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.

Application of CRISPR/Cas system in cereal improvement for biotic and abiotic stress tolerance

Application of the recently developed CRISPR/Cas tools might help enhance cereals' growth and yield under biotic and abiotic stresses. Cereals are the most important food crops for human life and an essential source of nutrients for people in developed and developing countries. The growth and yield of all major cereals are affected by both biotic and abiotic stresses. To date, molecular breeding and functional genomic studies have contributed to the understanding and improving cereals' growth and yield under biotic and abiotic stresses. Clustered, regularly inter-spaced, short palindromic repeats (CRISPR)/CRISPR-associated protein (Cas) system has been predicted to play a major role in precision plant breeding and developing non-transgenic cereals that can tolerate adverse effects of climate change. Variants of next-generation CRISPR/Cas tools, such as prime editor, base editor, CRISPR activator and repressor, chromatin imager, Cas12a, and Cas12b, are currently used in various fields, including plant science. However, few studies have been reported on applying the CRISPR/Cas system to understand the mechanism of biotic and abiotic stress tolerance in cereals. Rice is the only plant used frequently for such studies. Genes responsible for biotic and abiotic stress tolerance have not yet been studied by CRISPR/Cas system in other major cereals (sorghum, barley, maize and small millets). Examining the role of genes that respond to biotic and abiotic stresses using the CRISPR/Cas system may help enhance cereals' growth and yield under biotic and abiotic stresses. It will help to develop new and improved cultivars with biotic- and abiotic-tolerant traits for better yields to strengthen food security. This review provides information for cereal researchers on the current status of the CRISPR/Cas system for improving biotic and abiotic stress tolerance in cereals.

Selenium uptake and accumulation in winter wheat as affected by level of phosphate application and arbuscular mycorrhizal fungi

Selenium (Se) is an advantageous element to crops. However, the influence of arbuscular mycorrhizal fungi (AMF), phosphate (P) and selenite in soil on Se uptake by winter wheat remain elusive. Pot trials were carried out including seven levels of P (0, 12.5, 25, 50, 100, 200 or 400 mg kg^-1) and non-mycorrhizal inoculation (NM), inoculation of Funneliformis mosseae (F.m) or Glomus versiforme (G.v). The present results found that grain phosphorus concentration increased with increase of P level from 0 to 100 mg kg^-1 and then tended to plateau, while grain Se concentration decreased with the level of P from 0 to 400 mg kg^-1. Based on mathematical modeling, inoculation of F.m or G.v dramatically improved grain Se concentration by 16.90% or 12.53% under the lower level of P (48.76 mg kg^-1). Furthermore, partial least squares path modeling (PLS-PM) identified that both up-regulated of the expression of AMF-inducible phosphate transporter and improved Se bioavailability in rhizosphere soil contributed to enhancing plant Se concentration under P levels ≤ 100 mg kg^-1. The present study demonstrated that AMF combined with 48.76 mg kg^-1 P applied in soil can not only achieve high grain yield, but also fully exploit the biological potential of Se uptake in wheat.

Insights to improve the plant nutrient transport by CRISPR/Cas system

We need to improve food production to feed the ever growing world population especially in a changing climate. Nutrient deficiency in soils is one of the primary bottlenecks affecting the crop production both in developed and developing countries. Farmers are forced to apply synthetic fertilizers to improve the crop production to meet the demand. Understanding the mechanism of nutrient transport is helpful to improve the nutrient-use efficiency of crops and promote the sustainable agriculture. Many transporters involved in the acquisition, export and redistribution of nutrients in plants are characterized. In these studies, heterologous systems like yeast and Xenopus were most frequently used to study the transport function of plant nutrient transporters. CRIPSR/Cas system introduced recently has taken central stage for efficient genome editing in diverse organisms including plants. In this review, we discuss the key nutrient transporters involved in the acquisition and redistribution of nutrients from soil. We draw insights on the possible application CRISPR/Cas system for improving the nutrient transport in plants by engineering key residues of nutrient transporters, transcriptional regulation of nutrient transport signals, engineering motifs in promoters and transcription factors. CRISPR-based engineering of plant nutrient transport not only helps to study the process in native plants with conserved regulatory system but also aid to develop non-transgenic crops with better nutrient use-efficiency. This will reduce the application of synthetic fertilizers and promote the sustainable agriculture strengthening the food and nutrient security.

Understanding the Adaptive Mechanisms of Plants to Enhance Phosphorus Use Efficiency on Podzolic Soils in Boreal Agroecosystems

Being a macronutrient, phosphorus (P) is the backbone to complete the growth cycle of plants. However, because of low mobility and high fixation, P becomes the least available nutrient in podzolic soils; hence, enhancing phosphorus use efficiency (PUE) can play an important role in different cropping systems/crop production practices to meet ever-increasing demands in food, fiber, and fuel. Additionally, the rapidly decreasing mineral phosphate rocks/stocks forced to explore alternative resources and methods to enhance PUE either through improved seed P reserves and their remobilization, P acquisition efficiency (PAE), or plant's internal P utilization efficiency (IPUE) or both for sustainable P management strategies. The objective of this review article is to explore and document important domains to enhance PUE in crop plants grown on Podzol in a boreal agroecosystem. We have discussed P availabilities in podzolic soils, root architecture and morphology, root exudates, phosphate transporters and their role in P uptake, different contributors to enhance PAE and IPUE, and strategies to improve plant PUE in crops grown on podzolic soils deficient in P and acidic in nature.

Spectroscopic analysis reveals that soil phosphorus availability and plant allocation strategies impact feedstock quality of nutrient-limited switchgrass

The perennial native switchgrass adapts better than other plant species do to marginal soils with low plant-available nutrients, including those with low phosphorus (P) content. Switchgrass roots and their associated microorganisms can alter the pools of available P throughout the whole soil profile making predictions of P availability in situ challenging. Plant P homeostasis makes monitoring of P limitation via measurements of plant P content alone difficult to interpret. To address these challenges, we developed a machine-learning model trained with high accuracy using the leaf tissue chemical profile, rather than P content. By applying this learned model in field trials across two sites with contrasting extractable soil P, we observed that actual plant available P in soil was more similar than expected, suggesting that adaptations occurred to alleviate the apparent P constraint. These adaptations come at a metabolic cost to the plant that have consequences for feedstock chemical components and quality. We observed that other biochemical signatures of P limitation, such as decreased cellulose-to-lignin ratios, were apparent, indicating re-allocation of carbon resources may have contributed to increased P acquisition. Plant P allocation strategies also differed across sites, and these differences were correlated with the subsequent year’s biomass yields.

Hao et al. develop a machine learning approach to spectroscopy data of the tissue biochemistry of the switchgrass Panicum virgatum L. Using field and lab data with phosphorus-limited conditions, the authors show how soil phosphorus availability and nutrient allocations strategies may impact feedstock chemical components and quality.

Improvement of millets in the post-genomic era

Millets are food and nutrient security crops in the semi-arid tropics of developing countries. Crop improvement using modern tools is one of the priority areas of research in millets. The whole-genome sequence (WGS) of millets provides new insight into understanding and studying the genes, genome organization and genomic-assisted improvement of millets. The WGS of millets helps to carry out genome-wide comparison and co-linearity studies among millets and other cereal crops. This approach might lead to the identification of genes underlying biotic and abiotic stress tolerance in millets. The available genome sequence of millets can be used for SNP identification, allele discovery, association and linkage mapping, identification of valuable candidate genes, and marker-assisted breeding (MAB) programs. Next generation sequencing (NGS) technology provides opportunities for genome-assisted breeding (GAB) through genomic selection (GS) and genome-wide association studies (GAWS) for crop improvement. Clustered, regularly interspaced, short palindromic repeats (CRISPR)-CRISPR-associated protein 9 (Cas9) genome editing (GE) system provides new opportunities for millet improvement. In this review, we discuss the details on the WGS available for millets and highlight the importance of utilizing such resources in the post-genomic era for millet improvement. We also draw inroads on the utilization of various approaches such as GS, GWAS, functional genomics, gene validation and GE for millet improvement. This review might be helpful for understanding the developments in the post-genomic era of millet improvement.

Genome-editing in millets: current knowledge and future perspectives

Millets are small seeded cereal crops predominantly cultivated and consumed by resource-poor farmers in the semi-arid tropics of Asia and Africa. Millets possess rich nutrients and a climate resilience property when compared to the other cereals such as rice and wheat. Millet improvement using modern genetic and genomic tools is falling behind other cereal crops due to their cultivation being restricted to less developed countries. Genome editing tools have been successfully applied to major cereal crops and, as a result, many key traits have been introduced into rice, wheat and maize. However, genome editing tools have not yet been used for most millets although they possess rich nutrients. The foxtail millet is the only millet utilised up to now for genome editing works. Limited genomic resources and lack of efficient transformation systems may slow down genome editing in millets. As millets possess many important traits of agricultural importance, high resolution studies with genome editing tools will help to understand the specific mechanism and transfer such traits to major cereals in the future. This review covers the current status of genome editing studies in millets and discusses the future prospects of genome editing in millets to understand key traits of nutrient fortification and develop climate resilient crops in the future.

Management of phosphorus nutrient amid climate change for sustainable agriculture

Nutrients are essential for plant growth and development and influence overall agricultural production. Phosphorus (P) is a major nutrient required for many physiological and biochemical functions of a plant. Phosphate rock is the major source of phosphate fertilizer but is becoming increasingly limited in both developing and developed countries. The resources of phosphate rock need to be conserved, and import dependency on phosphate fertilizer needs to be minimized; this will help increase the availability of phosphate fertilizer over the next 300 yr. Climate change creates new challenges in the management of nutrients including P, affecting the overall production of crops. The availability, acquisition, and translocation of P are influenced by the fluctuation of temperatures, pH, drought, and elevated CO₂ . Both lower and higher soil temperatures reduce uptake and translocation of P. High soil pH affects P concentration and decreases the rate of plant P uptake. Low soil pH decreases the activity of soil microorganisms, the rate of transpiration, and P uptake and utilization. Elevated CO₂ decreases P uptake from soil by the plants. Future research is needed on chemical, molecular, microbiological, and physiological aspects to improve the understanding on how temperature, pH, drought, and elevated CO₂ affect the availability, acquisition, and transport of P by plants. Better P management strategies are required to secure the P supply to ensure long-term protection of soil fertility and to avoid environmental impacts such as eutrophication and water pollution, ensuring sustainable food production.

Improving abiotic stress tolerance in sorghum: focus on the nutrient transporters and marker-assisted breeding

Identification of molecular markers and characterization of nutrient transporters could help to improve the tolerance under abiotic and low nutrient stresses in sorghum ensuring higher yield to conserve food security Sorghum is an important cereal crop delivering food and energy security in the semi-arid tropics of the world. Adverse climatic conditions induced by global warming and low input agriculture system in developing countries demand for the improvement of sorghum to tolerate various abiotic stresses. In this review, we discuss the application of marker-assisted breeding and nutrient transporter characterization studies targeted towards improving the tolerance of sorghum under drought, salinity, cold, low phosphate and nitrogen stresses. Family members of some nutrient transporters such as nitrate transporter (NRT), phosphate transporter (PHT) and sulphate transporter (SULTR) were identified and characterized for improving the low nutrient stress tolerance in sorghum. Several quantitative trait loci (QTL) were identified for drought, salinity and cold stresses with an intention to enhance the tolerance of sorghum under these stresses. A very few QTL and nutrient transporters have been identified and validated under low nitrogen and phosphorus stresses compared to those under drought, salinity and cold stresses. Marker-assisted breeding and nutrient transporter characterization have not yet been attempted in sorghum under other macro- and micro-nutrient stresses. We hope this review will raise awareness among plant breeders, scientists and biotechnologists about the importance of sorghum and need to conduct the studies on marker-assisted breeding and nutrient transporter under low nutrient stresses to improve the sorghum production.

Expression of PHT1 family transporter genes contributes for low phosphate stress tolerance in foxtail millet (Setaria italica) genotypes

This is a first comprehensive study to analyze the 12 PHT1 family phosphate transporter genes in 20 foxtail millet genotypes for the improvement of millets and other crops for phosphate use efficiency. Phosphorus (P), absorbed from soil solutions as inorganic phosphate (Pi), is a limiting nutrient for plant growth and yield. Twenty genotypes of foxtail millet (Setaria italica) with contrasting degree of growth and Pi uptake responses under low Pi (LP) and high Pi (HP) supply were chosen based on a previous study. To gain molecular insights, expression dynamics of 12 PHosphate Transporter 1 (PHT1) family (SiPHT1;1 to 1;12) genes were analyzed in these 20 genotypes and compared with their Pi and total P (TP) contents. SiPHT1;1, 1;2, 1;3 and 1;8 genes were expressed in shoot tissues of three (ISe 1209, ISe 1305 and Co-6) of the LP best performing genotypes (LPBG); however, they were expressed in only one of the LP worst performing genotype (LPWG) (ISe 748). More importantly, this is correlating with higher shoot Pi and TP contents of the LPBG compared to LPWG. Apart from this condition, expression of SiPHT1 genes and their Pi and TP contents do not correlate directly for many genotypes in other conditions; genotypes with low Pi and TP contents induced more SiPHT1 genes and vice versa. Promoter analysis revealed that genotype ISe 1888 with a high level of SiPHT1;8 expression possesses two additional root box motifs compared to other genotypes. The PHT1 family genes seem to play a key role for LP stress tolerance in foxtail millet and further studies will help to improve the P-use efficiency in foxtail millet and other cereals.

Genome-Wide Analysis of the Five Phosphate Transporter Families in Camelina sativa and Their Expressions in Response to Low-P

Phosphate transporters (PHTs) play pivotal roles in phosphate (Pi) acquisition from the soil and distribution throughout a plant. However, there is no comprehensive genomic analysis of the PHT families in Camelina sativa, an emerging oilseed crop. In this study, we identified 73 CsPHT members belonging to the five major PHT families. A whole-genome triplication event was the major driving force for CsPHT expansion, with three homoeologs for each Arabidopsis ortholog. In addition, tandem gene duplications on chromosome 11, 18 and 20 further enlarged the CsPHT1 family beyond the ploidy norm. Phylogenetic analysis showed clustering of the CsPHT1 and CsPHT4 family members into four distinct groups, while CsPHT3s and CsPHT5s were clustered into two distinct groups. Promoter analysis revealed widespread cis-elements for low-P response (P1BS) specifically in CsPHT1s, consistent with their function in Pi acquisition and translocation. In silico RNA-seq analysis revealed more ubiquitous expression of several CsPHT1 genes in various tissues, whereas CsPHT2s and CsPHT4s displayed preferential expression in leaves. While several CsPHT3s were expressed in germinating seeds, most CsPHT5s were expressed in floral and seed organs. Suneson, a popular Camelina variety, displayed better tolerance to low-P than another variety, CS-CROO, which could be attributed to the higher expression of several CsPHT1/3/4/5 family genes in shoots and roots. This study represents the first effort in characterizing CsPHT transporters in Camelina, a promising polyploid oilseed crop that is highly tolerant to abiotic stress and low-nutrient status, and may populate marginal soils for biofuel production.

Overexpression of a Eutrema salsugineum phosphate transporter gene EsPHT1;4 enhances tolerance to low phosphorus stress in soybean

OBJECTIVE

To enhance Pi absorption and utilization efficiency of soybean, a member of PHT1 gene family was isolated and characterized from E. salsugineum, which was a homologous gene of AtPHT1;4 and consequently designated as EsPHT1;4.

RESULTS

Quantitative real-time PCR (qRT-PCR) analysis showed that the transcript level of EsPHT1;4 significantly increased both in roots and leaves of E. salsugineum under Pi deficient conditions. Furthermore, EsPHT1;4 was transferred to soybean cultivar "YD22" using an Agrobacterium-mediated cotyledonary-node transformation method. Overexpression of EsPHT1;4 in soybean not only promoted the increase of plant biomass and yield of transgenic plants upon low P stress, but also increased the accumulation and transportation of Pi from roots to leaves in the transgenic soybean lines.

CONCLUSION

EsPHT1;4 was critical for controlling the accumulation and translocation of Pi in plants, and can be subsequently used as an effective foreign gene for the improvement of P use efficiency of crops by genetic manipulation.

Effect of Root Colonization by Arbuscular Mycorrhizal Fungi on Growth, Productivity and Blast Resistance in Rice

BACKGROUND

Arbuscular mycorrhizal (AM) fungi form symbiotic associations with roots in most land plants. AM symbiosis provides benefits to host plants by improving nutrition and fitness. AM symbiosis has also been associated with increased resistance to pathogen infection in several plant species. In rice, the effects of AM symbiosis is less studied, probably because rice is mostly cultivated in wetland areas, and plants in such ecosystems have traditionally been considered as non-mycorrhizal. In this study, we investigated the effect of AM inoculation on performance of elite rice cultivars (Oryza sativa, japonica subspecies) under greenhouse and field conditions, focusing on growth, resistance to the rice blast fungus Magnaporthe oryzae and productivity.

RESULTS

The response to inoculation with either Funneliformis mosseae or Rhizophagus irregularis was evaluated in a panel of 12 rice cultivars. Root colonization was confirmed in all rice varieties. Under controlled greenhouse conditions, R. irregularis showed higher levels of root colonization than F. mosseae. Compared to non-inoculated plants, the AM-inoculated plants had higher Pi content in leaves. Varietal differences were observed in the growth response of rice cultivars to inoculation with an AM fungus, which were also dependent on the identity of the fungus. Thus, positive, negligible, and negative responses to AM inoculation were observed among rice varieties. Inoculation with F. mosseae or R. irregularis also conferred protection to the rice blast fungus, but the level of mycorrhiza-induced blast resistance varied among host genotypes. Rice seedlings (Loto and Gines varieties) were pre-inoculated with R. irregularis, transplanted into flooded fields, and grown until maturity. A significant increase in grain yield was observed in mycorrhizal plants compared with non-mycorrhizal plants, which was related to an increase in the number of panicles.

CONCLUSION

Results here presented support that rice plants benefit from the AM symbiosis while illustrating the potential of using AM fungi to improve productivity and blast resistance in cultivated rice. Differences observed in the mycorrhizal responsiveness among the different rice cultivars in terms of growth promotion and blast resistance indicate that evaluation of benefits received by the AM symbiosis needs to be carefully evaluated on a case-by-case basis for efficient exploitation of AM fungi in rice cultivation.

Phenotypic responses of foxtail millet (Setaria italica) genotypes to phosphate supply under greenhouse and natural field conditions

Food insecurity is a looming threat for the burgeoning world population. Phosphorus (P), which is absorbed from soil as inorganic phosphate (Pi), is an essential macronutrient for the growth of all agricultural crops. This study reports phenotype analysis for P responses in natural field and greenhouse conditions, using 54 genotypes of foxtail millet (Setaria italica) representing wide geographic origins. The genotype responses were assessed in natural field conditions in two different seasons (monsoon and summer) under Pi-fertilized (P+) and unfertilized (P-) soil for eight above-ground traits. Enormous variations were seen among the genotypes in phenotypic responses for all the measured parameters under low P stress conditions. Variations were significant for plant height, leaf number and length, tillering ability and seed yield traits. Genotypes ISe 1234 and ISe 1541 were P+ responders, and the genotypes ISe 1181, ISe 1655, ISe 783 and ISe 1892 showed tolerance to low P for total seed yield. Genotypes that performed well under P- conditions were almost as productive as genotypes that performed well under P+ conditions suggesting some genotypes are well adapted to nutrient-poor soils. In the greenhouse, most of the genotypes produced changes in root architecture that are characteristic of P- stress, but to differing degrees. Significant variation was seen in root hair density and root hair number and in fresh and dry weight of shoot and root under P- stress. However, there was not much difference in the shoot and root total P and Pi levels of five selected high and low responding genotypes. We noticed contrasting responses in the greenhouse and natural field experiments for most of these genotypes. The leads from the study form the basis for breeding and improvement of foxtail millet for better Pi-use efficiency.

Structure, Function, Regulation and Phylogenetic Relationship of ZIP Family Transporters of Plants

Zinc (Zn) is an essential micronutrient for plants and humans. Nearly 50% of the agriculture soils of world are Zn-deficient. The low availability of Zn reduces the yield and quality of the crops. The zinc-regulated, iron-regulated transporter-like proteins (ZIP) family and iron-regulated transporters (IRTs) are involved in cellular uptake of Zn, its intracellular trafficking and detoxification in plants. In addition to Zn, ZIP family transporters also transport other divalent metal cations (such as Cd2+, Fe2+, and Cu2+). ZIP transporters play a crucial role in biofortification of grains with Zn. Only a very limited information is available on structural features and mechanism of Zn transport of plant ZIP family transporters. In this article, we present a detailed account on structure, function, regulations and phylogenetic relationships of plant ZIP transporters. We give an insight to structure of plant ZIPs through homology modeling and multiple sequence alignment with Bordetella bronchiseptica ZIP (BbZIP) protein whose crystal structure has been solved recently. We also provide details on ZIP transporter genes identified and characterized in rice and other plants till date. Functional characterization of plant ZIP transporters will help for the better crop yield and human health in future.

Adaptation of Foxtail Millet (Setaria italica L.) to Abiotic Stresses: A Special Perspective of Responses to Nitrogen and Phosphate Limitations

Amongst various environmental constraints, abiotic stresses are increasing the risk of food insecurity worldwide by limiting crop production and disturbing the geographical distribution of food crops. Millets are known to possess unique features of resilience to adverse environments, especially infertile soil conditions, although the underlying mechanisms are yet to be determined. The small diploid genome, short stature, excellent seed production, C₄ photosynthesis, and short life cycle of foxtail millet make it a very promising model crop for studying nutrient stress responses. Known to be a drought-tolerant crop, it responds to low nitrogen and low phosphate by respective reduction and enhancement of its root system. This special response is quite different from that shown by maize and some other cereals. In contrast to having a smaller root system under low nitrogen, foxtail millet enhances biomass accumulation, facilitating root thickening, presumably for nutrient translocation. The low phosphate response of foxtail millet links to the internal nitrogen status, which tends to act as a signal regulating the expression of nitrogen transporters and hence indicates its inherent connection with nitrogen nutrition. Altogether, the low nitrogen and low phosphate responses of foxtail millet can act as a basis to further determine the underlying molecular mechanisms. Here, we will highlight the abiotic stress responses of foxtail millet with a key note on its low nitrogen and low phosphate adaptive responses in comparison to other crops.

Expression analysis and functional characterization of two PHT1 family phosphate transporters in ryegrass

The phosphate transporters LpPHT1;1 and LpPHT1;4 have different roles in phosphate uptake and translocation in ryegrass under P stress condition. The phosphate transporter 1 (PHT1) family are integral membrane proteins that operate in phosphate uptake, distribution and remobilization within plants. In this study, we report on the functional characterization and expression of two PHT1 family members from ryegrass plants (Lolium perenne L.) and determine their roles in the specificity of Pi transport. The expression level of LpPHT1;4 was strongly influenced by phosphorus (P) status, being higher under P-starvation condition. In contrast, the expression level of LpPHT1;1 was not correlated with P supply. Yeast mutant complementation assays showed that LpPHT1;4 can complement the growth defect of the yeast mutant Δpho84 under Pi-deficient conditions, whereas the yeast mutant expressing LpPHT1;1 was not able to restore growth. Phylogenetic and molecular analyses indicated high sequence similarity to previously identified PHT1s from other species in the Poaceae. These results suggest that LpPHT1;1 may function as a low-affinity Pi transporter, whereas LpPHT1;4 could acts as a high-affinity Pi transporter to maintain Pi homeostasis under stress conditions in ryegrass plants. This study will form the basis for the long-term goal of improving the phosphate use efficiency of ryegrass plants.

Phosphate supply influenced the growth, yield and expression of PHT1 family phosphate transporters in seven millets

Phosphate starvation altered the root morphology and phosphate uptake with the induction of PHT1 family transporter genes in root and shoot tissues of seven millets. Millets are nutrient-rich cereals majorly cultivated in Asia and Africa. Foxtail millet (FoxM), pearl millet (PeaM), finger millet (FinM), kodo millet (KodM), little millet (LitM), proso millet (ProM), and barnyard millet (BarM) were examined for the influence of external phosphorous (P) supply on phenotypic traits, P uptake, yield, and PHosphate Transporter1 (PHT1) family gene expression. Millet seedlings grown under low Pi condition (LPC) produced significantly lower mean values for all traits except for lateral root length (LRL) and lateral root number (LRN) which were increased under LPC. Under LPC, seed weight (SW) also reduced by > 75% and had significantly lower levels of total P (TP) and Pi contents in leaf and root tissues. Expression dynamics of 12 PHT1 family (PHT1;1-1;12) transporters genes were analyzed in 7 millets. PHT1;2 has been found to be a constitutive transporter gene in all millets. Under LPC, root tissues showed the overexpression of PHT1;2, 1;3, 1;4 and 1;9 in FoxM, PHT1;1, 1;2, 1;3, 1;4, 1;8 and 1;10 in PeaM, PHT1;2 and 1;3 in FinM and ProM and PHT1;3, 1;6 and 1;11 in BarM. In leaf, LPC induced the expression of PHT1;3, 1;4 and 1;6 in FoxM, PHT1;2, 1;3, 1;4 and 1;8 in PeaM, PHT1;2, 1;3 and 1;4 in FinM and KodM, PHT1;2 in LitM and PHT1;4 in ProM and BarnM. This comprehensive study on the influence of P in phenotype, physiology, and molecular responses may help to improve the P uptake and its use efficiency of millets in future.

Role of activated charcoal and amino acids in developing an efficient regeneration system for foxtail millet (Setaria italica (L.) Beauv.) using leaf base segments

An efficacious, reproducible direct in vitro regeneration system has been developed from leaf base segments (LBs) of six high yielding genotypes of foxtail millet (Setaria italica (L.) Beauv.). LBs excised from 4-day-old seedling were inoculated on Murashige and Skoog (MS) medium supplemented with different types and concentrations of cytokinins. The shoots induced per explant significantly increased with the supplementation of BAP to auxin containing medium. The results showed that a maximum shoot induction, 58.8% was obtained on MS medium incorporated with 8.9 µM BAP and 2.7 µM NAA in 'CO5' genotype. Further, the highest frequency of multiple shoots was produced on MS(I) medium containing 8.9 µM BAP, 2.7 µM NAA, 700 mg L^-1 proline, 0.5 mg L^-1 cysteine, 2.0 mg L^-1 glycine and 150 mg L^-1 arginine. MS(I) medium additionally fortified with 5.0 g L^-1 activated charcoal (AC) was found to achieve the best precocious plant regeneration. Elongated shoots were rooted on half-strength MS medium amended with 2.9 µM IAA and achieved maximum root number (8.7) within 10 days. Rooted plantlets were acclimated in soil with 92% survival rate. Molecular marker analysis of in vitro regenerated and field grown plants revealed no somaclonal variations. Briefly, amino acids and activated charcoal could significantly enhance the foxtail millet direct multiple shoot proliferation and plant regeneration. Here we report, a short-term, genotype independent, direct plant regeneration protocol for future genetic transformation studies in foxtail millet genotypes.

Genome-wide Identification and in silico Analysis of PHT1 Family Genes and Proteins in Setaria viridis: The Best Model to Study Nutrient Transport in Millets

Millets are small-seeded cereals predominantly cultivated and consumed by millions of poor people living in developing countries in Asia and Africa. Limited availability of genomic resources hinders studies of nutrient transport in millets. Two species, foxtail millet [ (L.) P. Beauv.] and its wild relative green foxtail [ (L.) P. Beauv.], are considered to be suitable models to study the genomics of other millets. Understanding the nutrient mobilization of millets is essential for improving nutrient use efficiency and biofortification in millets and other cereal crops. Millets are adapted for low-input agriculture, so understanding and improving the phosphate use efficiency of these plants is important because (i) subsistence farmers cannot afford to buy expensive phosphate fertilizers and (ii) the phosphate rock used for phosphate fertilizer production is depleting quickly. In this minireview, I discuss various studies on nutrient transport in millets and highlight phosphate transport studies. I report the identification and phylogenetic and multiple sequence analyses of 12 PHosphate Transporter1 (PHT1) family genes and proteins of green foxtail for the first time. With the exception of PHT1;5, all other green foxtail PHT1 transporters are closely clustered with foxtail millet PHT1 transporters. The multiple sequence analysis of SvPHT1s revealed that the key residues involved in phosphate and H-binding and transport are well conserved, as in other PHT1 transporters. Efforts need to be undertaken to understand and improve phosphate uptake and utilization in millets to strengthen food security in the developing world.

The impact of domestication and crop improvement on arbuscular mycorrhizal symbiosis in cereals: insights from genetics and genomics

Contents Summary 1135 I. Introduction 1135 II. Recruitment of plant metabolites and hormones as signals in AM symbiosis 1136 III. Phytohormones are regulators of AM symbiosis and targets of plant breeding 1137 IV. Variation in host response to AM symbiosis 1137 V. Outlook 1137 Acknowledgements 1139 References 1139 SUMMARY: Cereals (rice, maize, wheat, sorghum and the millets) provide over 50% of the world's caloric intake, a value that rises to > 80% in developing countries. Since domestication, cereals have been under artificial selection, largely directed towards higher yield. Throughout this process, cereals have maintained their capacity to interact with arbuscular mycorrhizal (AM) fungi, beneficial symbionts that associate with the roots of most terrestrial plants. It has been hypothesized that the shift from the wild to cultivation, and above all the last c. 50 years of intensive breeding for high-input farming systems, has reduced the capacity of the major cereal crops to gain full benefit from AM interactions. Recent studies have shed further light on the molecular basis of establishment and functioning of AM symbiosis in cereals, providing insight into where the breeding process might have had an impact. Classic phytohormones, targets of artificial selection during the generation of Green Revolution semi-dwarf varieties, have emerged as important regulators of AM symbiosis. Although there is still much to be learnt about the mechanistic basis of variation in symbiotic outcome, these advances are providing an insight into the role of arbuscular mycorrhiza in agronomic systems.

A Larger Root System Is Coupled With Contrasting Expression Patterns of Phosphate and Nitrate Transporters in Foxtail Millet [Setaria italica (L.) Beauv.] Under Phosphate Limitation

Foxtail millet [Setaria italica (L.) Beauv.], a widely cultivated food and fodder crop, develops a smaller root system while enlarges the root diameter facilitating nutrient transport under nitrogen limitation. How foxtail millet responds to phosphate limitation (LP) remains unaddressed. LP seedlings of the sequenced variety Yugu1 had significantly lower P concentrations in both shoots and roots and displayed higher levels of anthocyanin accumulation in leaves, indicating that the seedlings suffered from P limitation under hydroponic culture. One obvious and adaptive phenotype of LP plants was the larger root system mostly as the result of stimulation of lateral root proliferation in terms of the number, density, and length. Preferential biomass accumulation in the root under LP ensured carbon provision for root expansion and resulted in significant increases in the total and specific root length, which substantially extended the absorptive surface of P in the growth medium. Elevation of auxin and gibberellin concentrations might serve as an internal boost underpinning root architectural re-patterning under LP. Not just morphological adaptation, up-regulation of expression of SiPHT1;1 and SiPHT1;4 in roots and that of SiPHT1;2 in roots and shoots preconditioned adaptive enhancement of P uptake and translocation under LP. Interestingly, internal nitrogen surpluses occurred as indicated by dramatic increases in free amino acids in LP shoots and roots and higher concentrations of nitrogen in roots. Such nitrogen surplus 'signals' tended to switch down expression of nitrate transporters SiNRT2.1 and SiNAR2.1 in the root and that of SiNRT1.11 and SiNRT1.12 in the shoot to reduce nitrate mobilization toward or within the shoot. Together, our work provided new insights into adaption of a critical cereal crop to LP and its innate connection with nitrogen nutrition.

Feeding World Population Amidst Depleting Phosphate Reserves: The Role of Biotechnological Interventions

Phosphorus (P) is an important macronutrient affecting the growth and yield of all crop plants. Plants absorb P from the soil solution as inorganic phosphate (Pi). More than 70% of the arable land is deficient of Pi which demands the supply of an external source of synthetic P fertilizers to improve the yields. The P fertilizers are manufactured from non-renewable rock phosphate reserves which are expected to be exhausted within the next 100-200 years. This poses a great threat to food security since it is very difficult to meet the food production caused by increasing world population without the supply of an adequate P fertilizer. Several efforts have been made in the past decade to understand the mechanism of Pi uptake and its redistribution in plants. In this mini-review, we discuss the details on possible strategies to combat the crisis caused by loss of phosphate rock reserves and to improve the crop yield without much dependency on external P fertilizer. Approaches such as application of functional genomics studies to manipulate the expression levels of key transcription factors and genes involved in low Pi stress tolerance, molecular marker-assisted breeding to develop new varieties with improved yields under Pi-deficient soils and to recapture the Pi released in wastewaters for recycling back to the farm lands, will help improve the crop production without depending much on non-renewable P fertilizers and will also aid for the sustainable food production.

Finger Millet [Eleusine coracana (L.) Gaertn.] Improvement: Current Status and Future Interventions of Whole Genome Sequence

The whole genome sequence (WGS) of the much awaited, nutrient rich and climate resilient crop, finger millet (Eleusine coracana (L.) Gaertn.) has been released recently. While possessing superior mineral nutrients and excellent shelf life as compared to other major cereals, multiploidy nature of the genome and relatively small plantation acreage in less developed countries hampered the genome sequencing of finger millet, disposing it as one of the lastly sequenced genomes in cereals. The genomic information available for this crop is very little when compared to other major cereals like rice, maize and barley. As a result, only a limited number of genetic and genomic studies has been undertaken for the improvement of this crop. Finger millet is known especially for its superior calcium content, but the high-throughput studies are yet to be performed to understand the mechanisms behind calcium transport and grain filling. The WGS of finger millet is expected to help to understand this and other important molecular mechanisms in finger millet, which may be harnessed for the nutrient fortification of other cereals. In this review, we discuss various efforts made so far on the improvement of finger millet including genetic improvement, transcriptome analysis, mapping of quantitative trait loci (QTLs) for traits, etc. We also discuss the pitfalls of modern genetic studies and provide insights for accelerating the finger millet improvement with the interventions of WGS in near future. Advanced genetic and genomic studies aided by WGS may help to improve the finger millet, which will be helpful to strengthen the nutritional security in addition to food security in the developing countries of Asia and Africa.

Mechanisms of oat (Avena sativa L.) acclimation to phosphate deficiency

BACKGROUND

Deficiency of available forms of phosphorus is common in most soils and causes reduction of crop plants growth and yield. Recently, model plants responses to phosphate (Pi) deficiency have been intensively studied. However, acclimation mechanisms of cereals like oat (Avena sativa L.), to low Pi stress remains not fully understood. Oat plants have been usually cultured on poor soils, with a low nutrient content, but their responses to such conditions are not well known, therefore the main goal of the study was to investigate the mechanisms that enable oat plants to grow under low Pi conditions.

METHODS

Four oat cultivars (A. sativa, cv. Arab, Krezus, Rajtar and Szakal) were grown for three weeks in a nutrient media with various P sources: inorganic-KH2PO4 (control), organic-phytate (PA) and with no phosphate (-P). The effects of Pi deficiency on the level of P, oat growth parameters, intensity of photosynthesis, plant productivity, root exudation ability, localization, activity and isoforms of acid phosphatases, enzymes involved in Pi mobilization, were estimated. In addition, the effect of mycorrhization on plant growth was also observed.

RESULTS

All studied oat cultivars grown on Pi-deficient media had significantly decreased Pi content in the tissues. Pi deficiency caused inhibition of shoot growth, but generally it did not affect root elongation; root diameter was decreased, root/shoot ratios increased, whereas PA plants showed a similar growth to control. Photosynthesis rate and productivity parameters decreased under low Pi nutrition, however, sugar content generally increased. Studied oat cultivars did not respond to low Pi via increased exudation of carboxylates from the roots, as pH changes in the growth media were not observed. Pi starvation significantly increased the activity of extracellular and intracellular acid phosphatases (APases) in comparison to the control plants. Three major APase isoforms were detected in oat tissues and the isoform pattern was similar in all studied conditions, usually with a higher level of one of the isoforms under Pi starvation. Generally no significant effects of mycorrhizal colonization on growth of oat cultivars were observed.

DISCUSSION

We postulated that acid phosphatases played the most important role in oat cultivars acclimation to Pi deficiency, especially extracellular enzymes involved in Pi acquisition from soil organic P esters. These APases are mainly located in the epidermis of young roots, and may be released to the rhizosphere. On the other hand, intracellular APases could be involved in fast Pi remobilization from internal sources. Our study showed that oat, in contrast to other plants, can use phytates as the sole source of P. The studied oat cultivars demonstrated similar acclimation mechanisms to Pi deficiency, however, depending on stress level, they can use different pools of acid phosphatases.

Functional characterization of the PHT1 family transporters of foxtail millet with development of a novel Agrobacterium-mediated transformation procedure

Phosphate is an essential nutrient for plant growth and is acquired from the environment and distributed within the plant in part through the action of phosphate transporters of the PHT1 family. Foxtail millet (Setaria italica) is an orphan crop essential to the food security of many small farmers in Asia and Africa and is a model system for other millets. A novel Agrobacterium-mediated transformation and direct plant regeneration procedure was developed from shoot apex explants and used to downregulate expression of 3 members of the PHT1 phosphate transporter family SiPHT1;2 SiPHT1;3 and SiPHT1;4. Transformants were recovered with close to 10% efficiency. The downregulation of individual transporters was confirmed by RT-PCR. Downregulation of individual transporters significantly reduced the total and inorganic P contents in shoot and root tissues and increased the number of lateral roots and root hairs showing they have non-redundant roles. Downregulation of SiPHT1;2 had the strongest effect on total and inorganic P in shoot and root tissues. Complementation experiments in S. cerevisiae provide evidence for the ability of SiPHT1;1, 1;2, 1;3, 1;7 and 1;8 to function as high affinity Pi transporters. This work will aid development of improved millet varieties for global food security.

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

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

The conservation of phosphate-binding residues among PHT1 transporters suggests that distinct transport affinities are unlikely to result from differences in the phosphate-binding site

The plant PHosphate Transporter 1 (PHT1) family of membrane proteins belongs to the major facilitator super family and plays a major role in the acquisition of inorganic phosphate (Pi) from the soil and its transport within the plant. These transporters have been well characterized for expression patterns, localization, and in some cases affinity. Furthermore, the crystal structure of a high-affinity eukaryotic phosphate transporter from the fungus Piriformospora indica (PiPT) has revealed important information on the residues involved in Pi transport. Using multiple-sequence alignments and homology modelling, the phosphate-binding site residues were shown to be well conserved between all the plant PHT1 proteins, Saccharomyces cerevisiae PHO84 and PiPT. For example, Asp 324 in PiPT is conserved in the equivalent position in all plant PHT1 and yeast transporters analyzed, and this residue in ScPHO84 was shown by mutagenesis to be important for both the binding and transport of Pi. Moreover, Asp 45 and Asp 149, which are predicted to be involved in proton import, and Lys 459, which is putatively involved in Pi-binding, are all fully conserved in PHT1 and ScPHO84 transporters. The conserved nature of the residues that play a key role in Pi-binding and transport across the PHT1 family suggests that the differing Pi affinities of these transporters do not reside in differences in the Pi-binding site. Recent studies suggest that phosphate transporters could possess dual affinity and that post-translational modifications may be important in regulating affinity for phosphate.

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

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

Roles, Regulation, and Agricultural Application of Plant Phosphate Transporters

Phosphorus (P) is an essential mineral nutrient for plant growth and development. Low availability of inorganic phosphate (orthophosphate; Pi) in soil seriously restricts the crop production, while excessive fertilization has caused environmental pollution. Pi acquisition and homeostasis depend on transport processes controlled Pi transporters, which are grouped into five families so far: PHT1, PHT2, PHT3, PHT4, and PHT5. This review summarizes the current understanding on plant PHT families, including phylogenetic analysis, function, and regulation. The potential application of Pi transporters and the related regulatory factors for developing genetically modified crops with high phosphorus use efficiency (PUE) are also discussed in this review. At last, we provide some potential strategies for developing high PUE crops under salt or drought stress conditions, which can be valuable for improving crop yields challenged by global scarcity of water resources and increasing soil salinization.

Phosphate Uptake and Allocation - A Closer Look at Arabidopsis thaliana L. and Oryza sativa L

This year marks the 20th anniversary of the discovery and characterization of the two Arabidopsis PHT1 genes encoding the phosphate transporter in Arabidopsis thaliana. So far, multiple inorganic phosphate (Pi) transporters have been described, and the molecular basis of Pi acquisition by plants has been well-characterized. These genes are involved in Pi acquisition, allocation, and/or signal transduction. This review summarizes how Pi is taken up by the roots and further distributed within two plants: A. thaliana and Oryza sativa L. by plasma membrane phosphate transporters PHT1 and PHO1 as well as by intracellular transporters: PHO1, PHT2, PHT3, PHT4, PHT5 (VPT1), SPX-MFS and phosphate translocators family. We also describe the role of the PHT1 transporters in mycorrhizal roots of rice as an adaptive strategy to cope with limited phosphate availability in soil.

Systematic Identification, Evolution and Expression Analysis of the Zea mays PHT1 Gene Family Reveals Several New Members Involved in Root Colonization by Arbuscular Mycorrhizal Fungi

The Phosphate Transporter1 (PHT1) family of genes plays pivotal roles in the uptake of inorganic phosphate from soils. However, there is no comprehensive report on the PHT1 family in Zea mays based on the whole genome. In the present study, a total of 13 putative PHT1 genes (ZmPHT1;1 to 13) were identified in the inbred line B73 genome by bioinformatics methods. Then, their function was investigated by a yeast PHO84 mutant complementary experiment and qRT-PCR. Thirteen ZmPHT1 genes distributed on six chromosomes (1, 2, 5, 7, 8 and 10) were divided into two paralogues (Class A and Class B). ZmPHT1;1/ZmPHT1;9 and ZmPHT1;9/ZmPHT1;13 are produced from recent segmental duplication events. ZmPHT1;1/ZmPHT1;13 and ZmPHT1;8/ZmPHT1;10 are produced from early segmental duplication events. All 13 putative ZmPHT1s can completely or partly complement the yeast Pi-uptake mutant, and they were obviously induced in maize under low Pi conditions, except for ZmPHT1;1 (p < 0.01), indicating that the overwhelming majority of ZmPHT1 genes can respond to a low Pi condition. ZmPHT1;2, ZmPHT1;4, ZmPHT1;6, ZmPHT1;7, ZmPHT1;9 and ZmPHT1;11 were up-regulated by arbuscular mycorrhizal fungi (AMF), implying that these genes might participate in mediating Pi absorption and/or transport. Analysis of the promoters revealed that the MYCS and P1BS element are widely distributed on the region of different AMF-inducible ZmPHT1 promoters. In light of the above results, five of 13 ZmPHT1 genes were newly-identified AMF-inducible high-affinity phosphate transporters in the maize genome. Our results will lay a foundation for better understanding the PHT1 family evolution and the molecular mechanisms of inorganic phosphate transport under AMF inoculation.

Mycorrhizas influence functional traits of two tallgrass prairie species

Over the past decade, functional traits that influence plant performance and thus, population, community, and ecosystem biology have garnered increasing attention. Generally lacking, however, has been consideration of how ubiquitous arbuscular mycorrhizas influence plant allometric and stoichiometric functional traits. We assessed how plant dependence on and responsiveness to mycorrhizas influence plant functional traits of a warm-season, C4 grass, Andropogon gerardii Vitman, and the contrasting, cool-season, C3 grass, Elymus canadensis L. We grew both host species with and without inoculation with mycorrhizal fungi, across a broad gradient of soil phosphorus availabilities. Both host species were facultatively mycotrophic, able to grow without mycorrhizas at high soil phosphorus availability. A. gerardii was most dependent upon mycorrhizas and E. canadensis was weakly dependent, but highly responsive to mycorrhizas. The high dependence of A. gerardii on mycorrhizas resulted in higher tissue P and N concentrations of inoculated than noninoculated plants. When not inoculated, E. canadensis was able to take up both P and N in similar amounts to inoculated plants because of its weak dependence on mycorrhizas for nutrient uptake and its pronounced ability to change root-to-shoot ratios. Unlike other highly dependent species, A. gerardii had a high root-to-shoot ratio and was able to suppress colonization by mycorrhizal fungi at high soil fertilities. E. canadensis, however, was unable to suppress colonization and had a lower root-to shoot ratio than A. gerardii. The mycorrhiza-related functional traits of both host species likely influence their performance in nature: both species attained the maximum responsiveness from mycorrhizas at soil phosphorus availabilities similar to those of tallgrass prairies. Dependence upon mycorrhizas affects performance in the absence of mycorrhizas. Responsiveness to mycorrhizal fungi is also a function of the environment and can be influenced by both mycorrhizal fungus species and soil fertility.