Optimal level of purple acid phosphatase5 is required for maintaining complete resistance to Pseudomonas syringae

High-throughput diagnostic markers for foliar fungal disease resistance and high oleic acid content in groundnut

BACKGROUND

Foliar diseases namely late leaf spot (LLS) and leaf rust (LR) reduce yield and deteriorate fodder quality in groundnut. Also the high oleic acid content has emerged as one of the most important traits for industries and consumers due to its increased shelf life and health benefits.

RESULTS

Genetic mapping combined with pooled sequencing approaches identified candidate resistance genes (LLSR1 and LLSR2 for LLS and LR1 for LR) for both foliar fungal diseases. The LLS-A02 locus housed LLSR1 gene for LLS resistance, while, LLS-A03 housed LLSR2 and LR1 genes for LLS and LR resistance, respectively. A total of 49 KASPs markers were developed from the genomic regions of important disease resistance genes, such as NBS-LRR, purple acid phosphatase, pentatricopeptide repeat-containing protein, and serine/threonine-protein phosphatase. Among the 49 KASP markers, 41 KASPs were validated successfully on a validation panel of contrasting germplasm and breeding lines. Of the 41 validated KASPs, 39 KASPs were designed for rust and LLS resistance, while two KASPs were developed using fatty acid desaturase (FAD) genes to control high oleic acid levels. These validated KASP markers have been extensively used by various groundnut breeding programs across the world which led to development of thousands of advanced breeding lines and few of them also released for commercial cultivation.

CONCLUSION

In this study, high-throughput and cost-effective KASP assays were developed, validated and successfully deployed to improve the resistance against foliar fungal diseases and oleic acid in groundnut. So far deployment of allele-specific and KASP diagnostic markers facilitated development and release of two rust- and LLS-resistant varieties and five high-oleic acid groundnut varieties in India. These validated markers provide opportunities for routine deployment in groundnut breeding programs.

Proteo-metabolomic Dissection of Extracellular Matrix Reveals Alterations in Cell Wall Integrity and Calcium Signaling Governs Wall-Associated Susceptibility during Stem Rot Disease in Jute

The plant surveillance system confers specificity to disease and immune states by activating distinct molecular pathways linked to cellular functionality. The extracellular matrix (ECM), a preformed passive barrier, is dynamically remodeled at sites of interaction with pathogenic microbes. Stem rot, caused by Macrophomina phaseolina, adversely affects fiber production in jute. However, how wall related susceptibility affects the ECM proteome and metabolome remains undetermined in bast fiber crops. Here, stem rot responsive quantitative temporal ECM proteome and metabolome were developed in jute upon M. phaseolina infection. Morpho-histological examination revealed that leaf shredding was accompanied by reactive oxygen species production in patho-stressed jute. Electron microscopy showed disease progression and ECM architecture remodeling due to necrosis in the later phase of fungal attack. Using isobaric tags for relative and absolute quantitative proteomics and liquid chromatography-tandem mass spectrometry, we identified 415 disease-responsive proteins involved in wall integrity, acidification, proteostasis, hydration, and redox homeostasis. The disease-related correlation network identified functional hubs centered on α-galactosidase, pectinesterase, and thaumatin. Gas chromatography-mass spectrometry analysis pointed toward enrichment of disease-responsive metabolites associated with the glutathione pathway, TCA cycle, and cutin, suberin, and wax metabolism. Data demonstrated that wall-degrading enzymes, structural carbohydrates, and calcium signaling govern rot responsive wall-susceptibility. Proteomics data were deposited in Pride (PXD046937; PXD046939).

Acid phosphatase involved in phosphate homeostasis in Brassica napus and the functional analysis of BnaPAP10s

Purple acid phosphatases (PAPs) are involved in activating the rhizosphere's organic phosphorus (P) and promoting P recycling during plant development, especially under the long-term P deficiency conditions in acid soil. However, the function of BnaPAPs in response to P deficiency stress in Brassica napus has rarely been explored. In this study, we found that the acid phosphatase activities (APA) of rapeseed shoot and root increased under P deficienct conditions. Genome-wide identification found that 82 PAP genes were unevenly distributed on 19 chromosomes in B. napus, which could be divided into eight subfamilies. The segmental duplication events were the main driving force for expansion during evolution, and the gene structures and conserved motifs of most members within the same subfamily were highly conservative. Moreover, the expression levels of 37 and 23 different expressed genes were induced by low P in leaf and root, respectively. BnaA09.PAP10a and BnaC09.PAP10a were identified as candidate genes via interaction networks. Significantly, both BnaPAP10a overexpression lines significantly increased root-related APA and total phosphate concentration under P deficiency and ATP supply conditions, thereby improving plant growth and root length. In summary, our results provided a valuable foundation for further study of BnaPAP functions.

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

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

Bacterial leaf streak 1 encoding a mitogen-activated protein kinase confers resistance to bacterial leaf streak in rice

Bacterial leaf streak (BLS) is a major bacterial disease of rice. Utilization of host genetic resistance has become one of the most important strategies for controlling BLS. However, only a few resistance genes have been characterized. Previously, a recessive BLS resistance gene bls1 was roughly mapped on chromosome 6. Here, we further delineated bls1 to a 21 kb region spanning four genes. Genetic analysis confirmed that the gene encoding a mitogen-activated protein kinase (OsMAPK6) is the target of the allelic genes BLS1 and bls1. Overexpression of BLS1 weakened resistance to the specific Xanthomonas oryzae pv. oryzicola (Xoc) strain JZ-8, while low expression of bls1 increased resistance. However, both overexpression of BLS1 and low expression of bls1 could increase no-race-specific broad-spectrum resistance. These results indicate that BLS1 and bls1 negatively regulate race-specific resistance to Xoc strain JZ-8 but positively and negatively control broad-spectrum resistance, respectively. Subcellular localization demonstrated that OsMAPK6 was localized in the nucleus. RGA4, which is known to mediate resistance to Xoc, is the potential target of OsMAPK6. Overexpression of BLS1 and low expression of bls1 showed increase in salicylic acid and induced expression of defense-related genes, simultaneously increasing broad-spectrum resistance. Moreover, low expression of bls1 showed increase an in jasmonic acid and abscisic acid, in company with an increase in resistance to Xoc strain JZ-8. Collectively, our study provides new insights into the understanding of BLS resistance and facilitates the development of rice host-resistant cultivars.

Temperature Differentially Influences the Capacity of Trichoderma Species to Induce Plant Defense Responses in Tomato Against Insect Pests

Species of the ecological opportunistic, avirulent fungus, Trichoderma are widely used in agriculture for their ability to protect crops from the attack of pathogenic fungi and for plant growth promotion activity. Recently, it has been shown that they may also have complementary properties that enhance plant defense barriers against insects. However, the use of these fungi is somewhat undermined by their variable level of biocontrol activity, which is influenced by environmental conditions. Understanding the source of this variability is essential for its profitable and wide use in plant protection. Here, we focus on the impact of temperature on Trichoderma afroharzianum T22, Trichoderma atroviride P1, and the defense response induced in tomato by insects. The in vitro development of these two strains was differentially influenced by temperature, and the observed pattern was consistent with temperature-dependent levels of resistance induced by them in tomato plants against the aphid, Macrosiphum euphorbiae, and the noctuid moth, Spodoptera littoralis. Tomato plants treated with T. afroharzianum T22 exhibited enhanced resistance toward both insect pests at 25°C, while T. atroviride P1 proved to be more effective at 20°C. The comparison of plant transcriptomic profiles generated by the two Trichoderma species allowed the identification of specific defense genes involved in the observed response, and a selected group was used to assess, by real-time quantitative reverse transcription PCR (qRT-PCR), the differential gene expression in Trichoderma-treated tomato plants subjected to the two temperature regimens that significantly affected fungal biological performance. These results will help pave the way toward a rational selection of the most suitable Trichoderma isolates for field applications, in order to best face the challenges imposed by local environmental conditions and by extreme climatic shifts due to global warming.

Genome-wide analysis of H3K4me3 and H3K27me3 modifications due to Lr28 for leaf rust resistance in bread wheat (Triticum aestivum)

Present study revealed a complex relationship among histone H3 methylation (examined using H3K4/K27me3 marks), cytosine DNA methylation and differential gene expression during Lr28 mediated leaf rust resistance in wheat. During the present study, genome-wide histone modifications were examined in a pair of near isogenic lines (NILs) (with and without Lr28 in the background of cv. HD2329). The two histone marks used included H3K4me3 (an activation mark) and H3K27me3 (a repression mark). The results were compared with levels of expression (using RNA-seq) and DNA methylation (MeDIP) data obtained using the same pair of NILs. Some of the salient features of the present study include the following: (i) large scale differential binding sites (DBS) were available for only H3K4me3 in the susceptible cultivar, but for both H3K4me3 and H3K27me3 in its resistant NIL; (ii) DBSs for H3K27me3 mark were more abundant (> 80%) in intergenic regions, whereas DBSs for H3K4me3 were distributed in all genomic regions including exons, introns, intergenic, TTS (transcription termination sites) and promoters; (iii) fourteen (14) genes associated with DBSs showed co-localization for both the marks; (iv) only a small fraction (7% for H3K4me3 and 12% for H3K27me3) of genes associated with DBSs matched with the levels of gene expression inferred from RNA-seq data; (v) validation studies using qRT-PCR were conducted on 26 selected representative genes; results for only 11 genes could be validated. The proteins encoded by important genes involved in promoting infection included domains generally carried by R gene proteins such as Mlo like protein, protein kinases and purple acid phosphatase. Similarly, proteins encoded by genes involved in resistance included those carrying domains for lectin kinase, R gene, aspartyl protease, etc. Overall, the results suggest a very complex network of downstream genes that are expressed during compatible and incompatible interactions; some of the genes identified during the present study may be used in future validation studies involving RNAi/overexpression approaches.

Peroxisomes: versatile organelles with diverse roles in plants

Peroxisomes are small, ubiquitous organelles that are delimited by a single membrane and lack genetic material. However, these simple-structured organelles are highly versatile in morphology, abundance and protein content in response to various developmental and environmental cues. In plants, peroxisomes are essential for growth and development and perform diverse metabolic functions, many of which are carried out coordinately by peroxisomes and other organelles physically interacting with peroxisomes. Recent studies have added greatly to our knowledge of peroxisomes, addressing areas such as the diverse proteome, regulation of division and protein import, pexophagy, matrix protein degradation, solute transport, signaling, redox homeostasis and various metabolic and physiological functions. This review summarizes our current understanding of plant peroxisomes, focusing on recent discoveries. Current problems and future efforts required to better understand these organelles are also discussed. An improved understanding of peroxisomes will be important not only to the understanding of eukaryotic cell biology and metabolism, but also to agricultural efforts aimed at improving crop performance and defense.

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

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

AtPAP2, a Unique Member of the PAP Family, Functions in the Plasma Membrane

Purple acid phosphatases (PAPs) play various physiological roles in plants. AtPAP2 was previously shown to localize to both chloroplasts and mitochondria and to modulate carbon metabolism in Arabidopsis. Over-expression of AtPAP2 resulted in faster growth and increased biomass in several plant species, indicating its great potential for crop improvement of phosphate use and yield. Here, we studied the localization of AtPAP2 by transient expression in tobacco leaves. The results showed AtPAP2 was localized to the plasma membrane through the secretory pathway, which is different from previous studies. We also found that AtPAP2 had a close relationship with fungal PAP2-like proteins based on phylogenetic analysis. In addition, the C-terminal transmembrane domain conserved in land plants is unique among other AtPAPs except AtPAP9, which is a close homolog of AtPAP2. Taken together, our results provide information for further study of AtPAP2 in understanding its special function in crop improvement.

The Soybean Purple Acid Phosphatase GmPAP14 Predominantly Enhances External Phytate Utilization in Plants

Induction and secretion of acid phosphatases (APases) is considered to be an important strategy for improving plant growth under conditions of low inorganic phosphate (Pi). Purple acid phosphatases (PAPs), are an important class of plant APases that could be secreted into the rhizosphere to utilize organic phosphorus (Po) for plant growth and development. To date, only a few members of the PAP family have been identified in soybean. In this paper, we identified a secreted PAP in soybean, GmPAP14, and investigated its role in utilizing external phytate, the main form of organic phosphorus in the soil. An analysis of its expression and promoter showed that GmPAP14 was mainly expressed in the root and was strongly induced following Po treatment, during which its expression expanded from meristematic to maturation zones and root hairs. In vitro enzyme assays indicated that GmPAP14 had a relatively high phytase activity. Furthermore, GmPAP14 overexpression increased secreted APase activities and phytase activities, leading to the improved use of external plant phytate, higher phosphorus content, and increased shoot weight. Thus, these results confirmed that GmPAP14 is an important gene induced in response to Po, and that it predominantly participates in utilizing external Po to enhance plant growth and development.

Transcriptome and proteome analyses provide insight into laticifer's defense of Euphorbia tirucalli against pests

The cytoplasm of laticifers, which are plant cells specialized for rubber production and defense against microbes and herbivores, is a latex. Although laticifers share common functions, the protein constituents of latexes are highly variable among plant species and even among organs. In this study, transcriptomic and proteomic analyses of Euphorbia tirucalli's (Euphorbiaceae) latex were conducted to determine the molecular basis of the laticifer's functions in this plant. The hybrid de novo assembly of Illumina mRNA-seq and expressed sequence tags obtained by Sanger's sequencing revealed 26,447 unigenes. A unigene similar to Arabidopsis embryo-specific protein 3 (AT5G62200), which is a PLAT domain-containing protein, and rubber elongation factor showed the highest expression levels. The proteome analysis, studied by liquid chromatography-mass spectrometry with the de novo assembled unigenes as the database, revealed 161 proteins in the latex, 107 of which were not detected in the stem. A gene ontology analysis indicated that the laticifer's proteome was enriched with proteins related to proteolysis, phosphatase, defense against various environmental stresses and lipid metabolisms. D-mannose-binding lectin, ricin (which lacked the N-terminal conserved ribosome-inactivating protein domain), chitinase and peroxidase were highly accumulated, as confirmed by two-dimensional polyacrylamide gel electrophoresis. Thus, the lectins and chitinase may be the major defensive proteins against pests, and the other defense-related proteins and transcripts detected in latex may work in coordination with them. Highly expressing unigenes with unknown functions are candidate novel defense- or rubber production-related genes.