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The negative effects of phosphate (Pi) and/or nitrate (NO3−) fertilizers on the environment have raised an urgent need to develop crop varieties with higher Pi and/or nitrogen use efficiencies for cultivation in low‐fertility soils. Achieving this goal depends upon research that focuses on the identification of genes involved in plant responses to Pi and/or NO3− starvation. Although plant responses to individual deficiency in either Pi (–Pi/+NO3−) or NO3− (+Pi/–NO3−) have been separately studied, our understanding of plant responses to combined Pi and NO3− deficiency (–Pi/–NO3−) is still very limited. Using RNA‐sequencing approach, transcriptome changes in the roots and leaves of chickpea cultivated under –Pi/+NO3−, +Pi/–NO3− or –Pi/–NO3− conditions were investigated in a comparative manner. –Pi/–NO3− treatment displayed lesser effect on expression changes of genes related to Pi or NO3− transport, signalling networks, lipid remodelling, nitrogen and Pi scavenging/remobilization/recycling, carbon metabolism and hormone metabolism than –Pi/+NO3− or +Pi/–NO3− treatments. Therefore, the plant response to –Pi/–NO3− is not simply an additive result of plant responses to –Pi/+NO3− and +Pi/–NO3− treatments. Our results indicate that nutrient imbalance is a stronger stimulus for molecular reprogramming than an overall deficiency. [ABSTRACT FROM AUTHOR]

SUMMARY: Rhizoctonia solani is a soil‐borne necrotrophic fungus that causes sheath blight in grasses. The basal resistance of compatible interactions between R. solani and rice is known to be modulated by some WRKY transcription factors (TFs). However, genes and defense responses involved in incompatible interaction with R. solani remain unexplored, because no such interactions are known in any host plants. Recently, we demonstrated that Bd3‐1, an accession of the model grass Brachypodium distachyon, is resistant to R. solani and, upon inoculation with the fungus, undergoes rapid induction of genes responsive to the phytohormone salicylic acid (SA) that encode the WRKY TFs BdWRKY38 and BdWRKY44. Here, we show that endogenous SA and these WRKY TFs positively regulate this accession‐specific R. solani resistance. In contrast to a susceptible accession (Bd21), the infection process in the resistant accessions Bd3‐1 and Tek‐3 was suppressed at early stages before the development of fungal biomass and infection machinery. A comparative transcriptome analysis during pathogen infection revealed that putative WRKY‐dependent defense genes were induced faster in the resistant accessions than in Bd21. A gene regulatory network (GRN) analysis based on the transcriptome dataset demonstrated that BdWRKY38 was a GRN hub connected to many target genes specifically in resistant accessions, whereas BdWRKY44 was shared in the GRNs of all three accessions. Moreover, overexpression of BdWRKY38 increased R. solani resistance in Bd21. Our findings demonstrate that these resistant accessions can activate an incompatible host response to R. solani, and BdWRKY38 regulates this response by mediating SA signaling. Significance Statement: Rhizoctonia solani is a plant pathogenic fungus that causes sheath blight in grasses. In accordance with its necrotrophic lifestyle with a broad host range, the incompatible plant–R. solani interactions are not known in any host plants. Here, we demonstrate that such interactions could occur in the small grass Brachypodium distachyon, and BdWRKY38 is a key transcription factor that positively regulates this interaction by mediating the salicylic acid signaling pathway. [ABSTRACT FROM AUTHOR]

Summary: Climate change will increase frequency of drought and flooding, which threaten global crop productivity and food security. Rice (Oryza sativa) is unique in that it is able to grow in both flooded and upland conditions, which have large differences in the concentrations and chemical forms of mineral elements available to plants.To comprehensively understand the mechanisms of rice for coping with different water status, we performed ionomics and transcriptomics analysis of the roots, nodes and leaves of rice grown in flooded and upland conditions.Focusing the analysis on genes encoding proteins involved in transport functions for mineral elements, it was found that, although rice plants maintained similar levels of each element in the shoots for optimal growth, different transporters for mineral elements were utilised for nitrogen, iron, copper and zinc to deal with different soil water conditions. For example, under flooded conditions, rice roots take up nitrogen using transporters for both ammonium (OsAMT1/2) and nitrate (OsNPF2.4, OsNRT1.1A and OsNRT2.3), whereas under upland conditions, nitrogen uptake is mediated by different nitrate transporters (OsNRT1.1B and OsNRT1.5A).This study shows that rice possesses plastic transport systems for mineral elements in response to different water conditions (upland and flooding). [ABSTRACT FROM AUTHOR]

* Rhizoctonia solani is a soil-borne fungus causing sheath blight. In consistent with its necrotrophic life style, no rice cultivars fully resistant to R. solani are known, and agrochemical plant defense activators used for rice blast, which upregulate a phytohormonal salicylic acid (SA)-dependent pathway, are ineffective towards this pathogen. As a result of the unavailability of genetics, the infection process of R. solani remains unclear. * We used the model monocotyledonous plants Brachypodium distachyon and rice, and evaluated the effects of phytohormone-induced resistance to R. solani by pharmacological, genetic and microscopic approaches to understand fungal pathogenicity. * Pretreatment with SA, but not with plant defense activators used in agriculture, can unexpectedly induce sheath blight resistance in plants. SA treatment inhibits the advancement of R. solani to the point in the infection process in which fungal biomass shows remarkable expansion and specific infection machinery is developed. The involvement of SA in R. solani resistance is demonstrated by SA-deficient NahG transgenic rice and the sheath blight-resistant B. distachyon accessions, Bd3-1 and Gaz-4, which activate SA-dependent signaling on inoculation. * Our findings suggest a hemi-biotrophic nature of R. solani, which can be targeted by SA-dependent plant immunity. Furthermore, B. distachyon provides a genetic resource that can confer disease resistance against R. solani to plants. [ABSTRACT FROM AUTHOR]

Phosphate (Pi) deficiency is known to be a major limitation for symbiotic nitrogen fixation ( SNF), and hence legume crop productivity globally. However, very little information is available on the adaptive mechanisms, particularly in the important legume crop chickpea ( Cicer arietinum L.), which enable nodules to respond to low-Pi availability. Thus, to elucidate these mechanisms in chickpea nodules at molecular level, we used an RNA sequencing approach to investigate transcriptomes of the nodules in Mesorhizobium mediterraneum SWRI9-( Mm SWRI9)-chickpea and M. ciceri CP-31-( Mc CP-31)-chickpea associations under Pi-sufficient and Pi-deficient conditions, of which the Mc CP-31-chickpea association has a better SNF capacity than the Mm SWRI9-chickpea association during Pi starvation. Our investigation revealed that more genes showed altered expression patterns in Mm SWRI9-induced nodules than in Mc CP-31-induced nodules (540 vs. 225) under Pi deficiency, suggesting that the Pi-starvation-more-sensitive Mm SWRI9-induced nodules required expression change in a larger number of genes to cope with low-Pi stress than the Pi-starvation-less-sensitive Mc CP-31-induced nodules. The functional classification of differentially expressed genes ( DEGs) was examined to gain an understanding of how chickpea nodules respond to Pi starvation, caused by soil Pi deficiency. As a result, more DEGs involved in nodulation, detoxification, nutrient/ion transport, transcriptional factors, key metabolic pathways, Pi remobilization and signalling were found in Pi-starved Mm SWRI9-induced nodules than in Pi-starved Mc CP-31-induced nodules. Our findings have enabled the identification of molecular processes that play important roles in the acclimation of nodules to Pi deficiency, ultimately leading to the development of Pi-efficient chickpea symbiotic associations suitable for Pi-deficient soils. [ABSTRACT FROM AUTHOR]