Papers by Rahul Mahadev Shelake
Journal of Mycopathological Research, 2024
Plant growth promotion (PGP) and biocontrol activities of endophytes provide sustainable alternat... more Plant growth promotion (PGP) and biocontrol activities of endophytes provide sustainable alternatives to chemical use in agriculture. In this study, bacterial endophytes were isolated from the leaves, shoots and roots of cotton and pigeon pea plants. Using the Biolog system, microbial isolates were identified as members of the Bacillus genus in which cotton endophytic bacteria (CEB) isolatesCEB1 (B. safensis) and CEB2 (B. subtilis)found in the roots andCEB3 (B. amyloliquefaciens)were found in the shoots. Pigeon pea endophytic bacteria (PEB), PEB4 and PEB5 both identified as B. qingdaonensis which were derived from the roots. Among the tested strains for biocontrol activity, the CEB3 (B. amyloliquefaciens) strain exhibited maximum mycelial growth inhibition against various fungal plant pathogens. All analyzed bacterial endophytes possessed PGP activities and could produce indole-3-acetic acid (IAA), hydrogen cyanide (HCN), siderophore, ammonia, and P-solubilizing enzymes. CEB3 endophytic strains recorded maximum production of IAA, HCN, and siderophores compared to other endophytes. The seed priming dose of CEB3 applied at 6g/kg to finger millet recorded maximum shoot and root length, shoot and root weight, and the highest vigor index. Higher extracellular enzymatic activities were observed in all bacterial endophytes.
Molecular Biology Reports, Oct 10, 2023
Background Sesuvium portulacastrum is a facultative halophyte capable of thriving in a saline env... more Background Sesuvium portulacastrum is a facultative halophyte capable of thriving in a saline environment. Despite molecular studies conducted to unravel its salt adaptation mechanism, there is a paucity of information on the role of salt-responsive orthologs and microRNAs (miRNAs) in this halophyte. Here, we searched the orthology to identify salt-responsive orthologs and miRNA targets of Sesuvium using the Arabidopsis genome. Methods The relative fold change of orthologs, conserved miRNAs, and miRNA targets of Sesuvium was analyzed under 100 mM (LS) and 250 mM NaCl (HS) treatment at 24 h using qRT-PCR. The comparison between the expression of Sesuvium orthologs and Arabidopsis orthologs (Arabidopsis eFP browser database) was used to identify differentially expressed genes. Results Upon salt treatment, we found that SpCIPK3 (1.95-fold in LS and 2.90-fold in HS) in Sesuvium roots, and SpNHX7 (1.61-fold in LS and 6.39-fold in HS) and, SpSTPK2 (2.54-fold in LS and 7.65-fold in HS) in Sesuvium leaves were upregulated in a salt concentration-specific manner. In Arabidopsis, these genes were either downregulated or did not show significant variation, implicating its significance in the halophytic nature of Sesuvium. Furthermore, miRNAs like miR394a, miR396a, and miR397a exhibited a negative correlation with their targets—Frigida interacting protein 1, Cysteine proteinases superfamily protein, and Putative laccase, respectively under different salt treatments. Conclusion The study revealed that the high salt tolerance in Sesuvium is associated with distinct transcriptional reprogramming, hence, to gain holistic mechanistic insights, global-scale profiling is required.
Agriculture, 2024
Climate change has rapidly increased incidences of frequent extreme abiotic stresses, such as hea... more Climate change has rapidly increased incidences of frequent extreme abiotic stresses, such as heat, drought, salinity, and waterlogging. Each of these stressors negatively affects the cotton crop (Gossypium spp.) and results in significant yield decreases. Every stressful event causes specific changes in the metabolism and physiology of plants, which are linked to complex molecular alterations. Understanding the molecular mechanisms that regulate a plant’s response to stress is essential to developing stress-resistant cotton varieties that can withstand various stress factors. Gene expressions in response to multiple stresses have been studied and mapped. These genes include ion transporters and heat shock proteins, which are vital to allowing adaptive responses. These approaches showed the ability to employ advanced genome sequencing and multi-omics techniques to identify dynamic gene expression patterns and elucidate intricate regulatory networks. Using genetic variation in combination with molecular techniques, it would be possible to generate stress-resilient cotton varieties that would enable sustainable cotton output in the face of abiotic stresses. Here, we reviewed the effects of major abiotic stressors on cotton plants, such as heat, salinity, drought, heavy metals, and waterlogging. We also examine the vast network of proteins, genes, and stress-sensitive signaling pathways that help cotton tolerate abiotic stress.
Springer eBooks, 2019
Biological control agents (BCAs) are gaining more attention as alternatives to the chemical pesti... more Biological control agents (BCAs) are gaining more attention as alternatives to the chemical pesticides for management of pests and diseases in agricultures. It offers an ecofriendly way for plant health management (PHM), and it also helps to reduce the excessive use of toxic chemicals or pesticides. The BCAs considered as the most promising technology for sustainable agriculture. Various beneficial BCAs have been known for PHM but need effective adoption together with standardization of bioformulations for field applications. The mechanisms of BCAs in PHM mainly include direct (parasitism, hyperparasitism, commensalism), indirect (competition, systemic acquired or induced systemic resistance), or mixed antagonistic modes (production of antibiotics, siderophores, lytic enzyme, and volatile organic substances). Apart from their role in plant growth promotion, plant growth-promoting rhizobacteria (PGPR) and fungi (PGPF) also act as BCAs that function through either of the mechanisms. The PGPR/PGPF possesses many traits that serve them as potential BCAs, and therefore possess great promise for successful application in sustainable agriculture. In this chapter, different approaches for BCAs applications and their mechanism in PHM especially for disease and pest (DP) management are discussed. Also, the relationship between the PGPR/PGPF diversity and their application in biological control is discussed. Furthermore, we have summarized the global-Indian scenario of current research including state-of-the-art technological advances in PGPR/PGPF-mediated DP management.
In Vitro Cellular & Developmental Biology - Plant, 2011
... from male floral meristems of Musa spp. cultivars Virupakshi and Sirumalai Shelake Rahul Maha... more ... from male floral meristems of Musa spp. cultivars Virupakshi and Sirumalai Shelake Rahul Mahadev & Angappan Kathithachalam & Murugan Marimuthu ... References Al-Amin MD; Karim MR; Amin MR; Rahman S.; Mamun AN M. In vitro micropropagation of banana (Musa spp.). ...
Plant Physiology and Biochemistry, Sep 30, 2023
Plant species have evolved diverse metabolic pathways to effectively respond to internal and exte... more Plant species have evolved diverse metabolic pathways to effectively respond to internal and external signals throughout their life cycle, allowing adaptation to their sessile and phototropic nature. These pathways selectively activate specific metabolic processes, producing plant secondary metabolites (PSMs) governed by genetic and environmental factors. Humans have utilized PSM-enriched plant sources for millennia in medicine and nutraceuticals. Recent technological advances have significantly contributed to discovering metabolic pathways and related genes involved in the biosynthesis of specific PSM in different food crops and medicinal plants. Consequently, there is a growing demand for plant materials rich in nutrients and bioactive compounds, marketed as “superfoods”. To meet the industrial demand for superfoods and therapeutic PSMs, modern methods such as system biology, omics, synthetic biology, and genome editing (GE) play a crucial role in identifying the molecular players, limiting steps, and regulatory circuitry involved in PSM production. Among these methods, clustered regularly interspaced short palindromic repeats-CRISPR associated protein (CRISPR/Cas) is the most widely used system for plant GE due to its simple design, flexibility, precision, and multiplexing capabilities. Utilizing the CRISPR-based toolbox for metabolic engineering (ME) offers an ideal solution for developing plants with tailored preventive (nutraceuticals) and curative (therapeutic) metabolic profiles in an ecofriendly way. This review discusses recent advances in understanding the multifactorial regulation of metabolic pathways, the application of CRISPR-based tools for plant ME, and the potential research areas for enhancing plant metabolic profiles.
Plants, 2024
Climate change presents numerous challenges for agriculture, including frequent events of plant a... more Climate change presents numerous challenges for agriculture, including frequent events of plant abiotic stresses such as elevated temperatures that lead to heat stress (HS). As the primary driving factor of climate change, HS threatens global food security and biodiversity. In recent years, HS events have negatively impacted plant physiology, reducing plant’s ability to maintain disease resistance and resulting in lower crop yields. Plants must adapt their priorities toward defense mechanisms to tolerate stress in challenging environments. Furthermore, selective breeding and long-term domestication for higher yields have made crop varieties vulnerable to multiple stressors, making them more susceptible to frequent HS events. Studies on climate change predict that concurrent HS and biotic stresses will become more frequent and severe in the future, potentially occurring simultaneously or sequentially. While most studies have focused on singular stress effects on plant systems to examine how plants respond to specific stresses, the simultaneous occurrence of HS and biotic stresses pose a growing threat to agricultural productivity. Few studies have explored the interactions between HS and plant–biotic interactions. Here, we aim to shed light on the physiological and molecular effects of HS and biotic factor interactions (bacteria, fungi, oomycetes, nematodes, insect pests, pollinators, weedy species, and parasitic plants), as well as their combined impact on crop growth and yields. We also examine recent advances in designing and developing various strategies to address multi-stress scenarios related to HS and biotic factors.
Molecular Breeding, 2024
Tomato (Solanum lycopersicum L.) is one of the most important crops in the world for its fruit pr... more Tomato (Solanum lycopersicum L.) is one of the most important crops in the world for its fruit production. Advances in cutting-edge techniques have enabled the development of numerous critical traits related to the quality and quantity of tomatoes. Genetic engineering techniques, such as gene transformation and gene editing, have emerged as powerful tools for generating new plant varieties with superior traits. In this study, we induced parthenocarpic traits in a population of elite tomato (ET) lines. At first, the adaptability of ET lines to genetic transformation was evaluated to identify the best-performing lines by transforming the SlANT1 gene overexpression cassette and then later used to produce the SlIAA9 knockout lines using the CRISPR/Cas9 system. ET5 and ET8 emerged as excellent materials for these techniques and showed higher efficiency. Typical phenotypes of knockout sliaa9 were clearly visible in G0 and G1 plants, in which simple leaves and parthenocarpic fruits were observed. The high efficiency of the CRISPR/Cas9 system in developing new tomato varieties with desired traits in a short period was demonstrated by generating T-DNA-free homozygous sliaa9 knockout plants in the G1 generation. Additionally, a simple artificial fertilization method was successfully applied to recover seed production from parthenocarpic plants, securing the use of these varieties as breeding materials.
Euphytica, 2024
Tomato (Solanum lycopersicum L.) is the second most important vegetable crop after potatoes, and ... more Tomato (Solanum lycopersicum L.) is the second most important vegetable crop after potatoes, and global demands have been steadily increasing in recent years. Conventional and modern breeding techniques have been applied to breed and domesticate tomato varieties to meet the need for higher yield or superior agronomical traits that allow them to sustain under different climatic conditions. In the current study, we applied bulk population breeding by crossing eight tomato accessions procured from the Asian Vegetable Research and Development Center with three heat-resistant tomato inbred lines from Vietnam and generated ten elite tomato (ET) lines in the F8 generation. The individual F8 lines exhibited robust vigor and adaptability to climatic conditions of North Vietnam. Among the ten lines, ET1 and ET3 displayed indeterminate growth. ET2 showed semi-determinate, while all the other lines had determinate growth. The different ET lines showed distinctive superior agronomical traits, including early maturing (ET4, ET7, and ET10), highly efficient fruit set (ET1), higher yield (ET1, ET8, ET10), jointless pedicels (ET2), and partial parthenocarpy (ET9). Molecular analysis revealed that the ET3 line consisted of Ty-1 and Ty-3 loci that positively contribute to Tomato yellow leaf curl virus resistance in tomato plants. The elite tomato lines developed in this study would contribute significantly to the Vietnamese and Asian gene pool for improved tomato production and would be a valuable resource for various breeding goals.
BMB Reports, 2024
Directed evolution (DE) of desired locus by targeted random mutagenesis (TRM) tools is a powerful... more Directed evolution (DE) of desired locus by targeted random mutagenesis (TRM) tools is a powerful approach for generating genetic variations with novel or improved functions, particularly in complex genomes. TRM-based DE involves developing a mutant library of targeted DNA sequences and screening the variants for the desired properties. However, DE methods have for a long time been confined to bacteria and yeasts. Lately, CRISPR/Cas and DNA deaminase-based tools that circumvent enduring barriers such as longer life cycle, small library sizes, and low mutation rates have been developed to facilitate DE in native genetic environments of multicellular organisms. Notably, deaminase-based base editing-TRM (BE-TRM) tools have greatly expanded the scope and efficiency of DE schemes by enabling base substitutions and randomization of targeted DNA sequences. BE-TRM tools provide a robust platform for the continuous molecular evolution of desired proteins, metabolic pathway engineering, creation of a mutant library of desired locus to evolve novel functions, and other applications, such as predicting mutants conferring antibiotic resistance. This review provides timely updates on the recent advances in BE-TRM tools for DE, their applications in biology, and future directions for further improvements. [BMB Reports 2024; 57(1): 30-39]
Research Square (Research Square), Jun 13, 2023
Tomato (Solanum lycopersicum L.) is one of the most important crops in the world for its fruit pr... more Tomato (Solanum lycopersicum L.) is one of the most important crops in the world for its fruit production. Advances in cutting-edge techniques have enabled the development of numerous critical traits related to the quality and quantity of tomatoes. Genetic engineering techniques, such as gene transformation and gene editing, have emerged as powerful tools for generating new plant varieties with superior traits. In this study, we induced parthenocarpic traits in a population of elite tomato (ET) lines. At rst, the adaptability of ET lines to genetic transformation was evaluated to identify the best-performing lines by transforming the SlANT1 gene overexpression cassette and then later used to produce the SlIAA9 knockout lines using the CRISPR/Cas9 system. ET5 and ET8 emerged as excellent materials for these techniques and showed higher e ciency. Typical phenotypes of knockout sliaa9 were clearly visible in G0 and G1 plants, in which simple leaves and parthenocarpic fruits were observed. The high e ciency of the CRISPR/Cas9 system in developing new tomato varieties with desired traits in a short period was demonstrated by generating T-DNA-free homozygous sliaa9 knockout plants in the G1 generation. Additionally, a simple arti cial fertilization method was successfully applied to recover seed production from parthenocarpic plants, securing the use of these varieties as breeding materials.
Molecular Biology Reports , 2023
Background
Sesuvium portulacastrum is a facultative halophyte capable of thriving in a saline env... more Background
Sesuvium portulacastrum is a facultative halophyte capable of thriving in a saline environment. Despite molecular studies conducted to unravel its salt adaptation mechanism, there is a paucity of information on the role of salt-responsive orthologs and microRNAs (miRNAs) in this halophyte. Here, we searched the orthology to identify salt-responsive orthologs and miRNA targets of Sesuvium using the Arabidopsis genome.
Methods
The relative fold change of orthologs, conserved miRNAs, and miRNA targets of Sesuvium was analyzed under 100 mM (LS) and 250 mM NaCl (HS) treatment at 24 h using qRT-PCR. The comparison between the expression of Sesuvium orthologs and Arabidopsis orthologs (Arabidopsis eFP browser database) was used to identify differentially expressed genes.
Results
Upon salt treatment, we found that SpCIPK3 (1.95-fold in LS and 2.90-fold in HS) in Sesuvium roots, and SpNHX7 (1.61-fold in LS and 6.39-fold in HS) and, SpSTPK2 (2.54-fold in LS and 7.65-fold in HS) in Sesuvium leaves were upregulated in a salt concentration-specific manner. In Arabidopsis, these genes were either downregulated or did not show significant variation, implicating its significance in the halophytic nature of Sesuvium. Furthermore, miRNAs like miR394a, miR396a, and miR397a exhibited a negative correlation with their targets—Frigida interacting protein 1, Cysteine proteinases superfamily protein, and Putative laccase, respectively under different salt treatments.
Conclusion
The study revealed that the high salt tolerance in Sesuvium is associated with distinct transcriptional reprogramming, hence, to gain holistic mechanistic insights, global-scale profiling is required.
Plants, 2023
Sugar Efflux transporters (SWEET) are involved in diverse biological processes of plants. Pathoge... more Sugar Efflux transporters (SWEET) are involved in diverse biological processes of plants. Pathogens have exploited them for nutritional gain and subsequently promote disease progression. Recent studies have implied the involvement of potato SWEET genes in the most devastating late blight disease caused by Phytophthora infestans. Here, we identified and designated 37 putative SWEET genes as StSWEET in potato. We performed detailed in silico analysis, including gene structure, conserved domains, and phylogenetic relationship. Publicly available RNA-seq data was harnessed to retrieve the expression profiles of SWEET genes. The late blight-responsive SWEET genes were identified from the RNA-seq data and then validated using quantitative real-time PCR. The SWEET gene expression was studied along with the biotrophic (SNE1) and necrotrophic (PiNPP1) marker genes of P. infestans. Furthermore, we explored the co-localization of P. infestans resistance loci and SWEET genes. The results indicated that nine transporter genes were responsive to the P. infestans in potato. Among these, six transporters, namely StSWEET10, 12, 18, 27, 29, and 31, showed increased expression after P. infestans inoculation. Interestingly, the observed expression levels aligned with the life cycle of P. infestans, wherein expression of these genes remained upregulated during the biotrophic phase and decreased later on. In contrast, StSWEET13, 14, and 32 didn’t show upregulation in inoculated samples suggesting non-targeting by pathogens. This study underscores these transporters as prime P. infestans targets in potato late blight, pivotal in disease progression, and potential candidates for engineering blight-resistant potato genotypes.
Plant Physiology and Biochemistry, 2023
Plant species have evolved diverse metabolic pathways to effectively respond to internal and exte... more Plant species have evolved diverse metabolic pathways to effectively respond to internal and external signals throughout their life cycle, allowing adaptation to their sessile and phototropic nature. These pathways selectively activate specific metabolic processes, producing plant secondary metabolites (PSMs) governed by genetic and environmental factors. Humans have utilized PSM-enriched plant sources for millennia in medicine and nutraceuticals. Recent technological advances have significantly contributed to discovering metabolic pathways and related genes involved in the biosynthesis of specific PSM in different food crops and medicinal plants. Consequently, there is a growing demand for plant materials rich in nutrients and bioactive compounds, marketed as “superfoods”. To meet the industrial demand for superfoods and therapeutic PSMs, modern methods such as system biology, omics, synthetic biology, and genome editing (GE) play a crucial role in identifying the molecular players, limiting steps, and regulatory circuitry involved in PSM production. Among these methods, clustered regularly interspaced short palindromic repeats-CRISPR associated protein (CRISPR/Cas) is the most widely used system for plant GE due to its simple design, flexibility, precision, and multiplexing capabilities. Utilizing the CRISPR-based toolbox for metabolic engineering (ME) offers an ideal solution for developing plants with tailored preventive (nutraceuticals) and curative (therapeutic) metabolic profiles in an ecofriendly way. This review discusses recent advances in understanding the multifactorial regulation of metabolic pathways, the application of CRISPR-based tools for plant ME, and the potential research areas for enhancing plant metabolic profiles.
Mutation Breeding for Sustainable Food Production and Climate Resilience, 2023
Tomato (Solanum lycopersicum L.) is one of the most important crops in the world for its fruit pr... more Tomato (Solanum lycopersicum L.) is one of the most important crops in the world for its fruit production. Many critical characteristics related to the quality and quantity of tomatoes have been developed using cutting-edge techniques. Recently, genetic techniques such as gene transformation and gene editing have emerged as powerful tools to promptly generate new plant varieties with superior traits. In this study, we successfully induced parthenocarpy traits in a population of elite tomato (ET) lines. The ET lines were screened for their adaptability to new genetic techniques to determine the lines that performed best by applying ANT1 gene transformation and IAA9 knock-out using the CRISPR/Cas9 system. ET5 and ET8 emerged as excellent materials for these techniques due to their high efficiency in applying those modern techniques. Phenotypes of knock-out iaa9 were clearly shown in T-0 and T-1 plants, in which simple leaves and parthenocarpic fruits were observed. We generated T-DNA-...
bioRxiv (Cold Spring Harbor Laboratory), Nov 28, 2022
Tomato (Solanum lycopersicum L.) is the second most important vegetable crop after potatoes, and ... more Tomato (Solanum lycopersicum L.) is the second most important vegetable crop after potatoes, and global demands have been steadily increasing in recent years. Conventional breeding has been applied to breed and domesticate tomato varieties to meet the need for higher yield or superior agronomical traits that allow to sustain under different climatic conditions. In the current study, we applied bulk population breeding by crossing eight tomato accessions procured from the Asian Vegetable Research and Development Center (AVRDC) with three heat-resistant tomato inbred lines from Vietnam and generated ten elite tomato (ET) lines in the F8 generation. The individual F8 lines exhibited robust vigor and adaptability to Vietnamese climate conditions. Among the ten lines, ET1 and ET3 displayed indeterminate growth. ET2 showed semideterminate, while all the other lines had determinate growth. The different ET lines showed distinctive superior agronomical traits, including early maturing (ET4, ET7, and ET10), highly efficient fruit set (ET1), higher yield (ET1, ET8, ET10), jointless pedicels (ET2), and partial parthenocarpy (ET9). Molecular analysis revealed that the ET3 line consisted of Ty-1 and Ty-3 loci that positively contribute to Tomato yellow leaf curl virus (TYCLV) resistance in tomato plants. The elite tomato lines developed in this study would contribute significantly to the Vietnamese and Asian gene pool for improved tomato production and may be a valuable resource for various breeding goals.
mBio, 2023
Genome-editing (GE) techniques like base editing are ideal for introducing novel gain-of-function... more Genome-editing (GE) techniques like base editing are ideal for introducing novel gain-of-function mutations and in situ protein evolution. Features of base editors (BEs) such as higher efficacy, relaxed protospacer adjacent motif (PAM), and a broader editing window enables diversification of user-defined targeted locus. Cytosine (CBE) or adenine (ABE) BEs alone can only alter C-toT or A-to-G in target sites. In contrast, dual BEs (ACBEs) can concurrently generate C-toT and A-to-G modifications. Although BE tools have recently been applied in microbes, there is no report of ACBE for microbial GE. In this study, we engineered four improved ACBEs (iACBEs) tethering highly active CBE and ABE variants that can introduce synchronized C-toT and A-to-G mutations in targeted loci. iACBE4 generated by evoCDA1-ABE9e fusion demonstrated a broader editing window (positions 26 to 15) and is also compatible with the multiplex editing approach in Escherichia coli. We further show that the iACBE4-NG containing PAM-relaxed nCas9-NG expands the targeting scope beyond NGG (N-A/G/C/T) PAM. As a proof-of-concept, iACBE was effectively utilized to identify previously unknown mutations in the rpoB gene, conferring gain-of-function, i.e., rifampicin resistance. The iACBE tool would expand the CRISPR-GE toolkit for microbial genome engineering and synthetic biology.
Frontiers in Plant Science, 2023
Plasmodesmata (PD) play a critical role in symplasmic communication, coordinating plant activitie... more Plasmodesmata (PD) play a critical role in symplasmic communication, coordinating plant activities related to growth & development, and environmental stress responses. Most developmental and environmental stress signals induce reactive oxygen species (ROS)-mediated signaling in the apoplast that causes PD closure by callose deposition. Although the apoplastic ROS signals are primarily perceived at the plasma membrane (PM) by receptor-like kinases (RLKs), such components involved in PD regulation are not yet known. Here, we show that an Arabidopsis NOVEL CYS-RICH RECEPTOR KINASE (NCRK), a PDlocalized protein, is required for plasmodesmal callose deposition in response to ROS stress. We identified the involvement of NCRK in callose accumulation at PD channels in either basal level or ROS-dependent manner. Loss-of-function mutant (ncrk) of NCRK induces impaired callose accumulation at the PD under the ROS stress resembling a phenotype of the PD-regulating GLUCAN SYNTHASE-LIKE 4 (gsl4) knockout plant. The overexpression of transgenic NCRK can complement the callose and the PD permeability phenotypes of ncrk mutants but not kinaseinactive NCRK variants or Cys-mutant NCRK, in which Cys residues were mutated in Cys-rich repeat ectodomain. Interestingly, NCRK mediates plasmodesmal permeability in mechanical injury-mediated signaling pathways regulated by GSL4. Furthermore, we show that NCRK interacts with calmodulin-like protein 41 (CML41) and GSL4 in response to ROS stress. Altogether, our data indicate that NCRK functions as an upstream regulator of PD callose accumulation in response to ROS-mediated stress signaling pathways.
Frontiers in Agronomy, 2023
Editorial on the Research Topic Soil-plant-microbe interactions: An innovative approach towards i... more Editorial on the Research Topic Soil-plant-microbe interactions: An innovative approach towards improving soil health and plant growth The loss of soil health is one of the major obstacles to attaining agricultural sustainability. This loss is typically caused by the adoption of poor farming practices and the excessive use of chemicals, such as fertilizers and pesticides (Kumar et al., 2017; Kumar et al., 2018). One potential strategy to stop this deterioration in soil quality is the application of microbial inoculants to the soil or plant parts (Banik et al., 2019). Understanding how microbes function in the plant-soil system's biogeochemical cycling, as well as in processes like the reduction of toxins, nutrient dynamics, antioxidant activity, systemic induction of resistance, pathogen suppression, etc., is essential if we are to fully utilize their potential (Govindasamy et al., 2008). In addition to improving product quality and environmental health, these interactions will lessen the toxicity of synthetic chemicals and other pollutants. This special issue covers the aspects related to the relationship between soil, plants, and microbes to enhance soil health and plant growth, which is especially helpful for comprehending the sustainability of agricultural systems. In this Research Topic, the prevalence and potential management strategies of plant diseases in horticulture crops, including tomato fusarium wilt, apple replant disease (ARD), and kiwifruit early decline syndrome, have been examined. The factors of kiwifruit early decline syndrome were triggered due to the interaction between climatic conditions and agronomic soil management. Hence, properly managing these conditions might be useful to suppress the kiwifruit early decline syndrome (Bardi et al.). Whereas ARD disease was overcome by creating a new microbial community structure favorable to plant growth when ZnO-NPs were added to the soil (Pan et al.). On the other hand, Chaturvedi et al. highlighted the application of bacterial endophyte consortium to protect the photosynthetic system in tomato against fusarium wilt. Rhizospheric and endophytic beneficial microorganisms play a crucial role in promoting plant growth and improving soil health. The rhizospheric microbes improve Frontiers in Agronomy frontiersin.org 01
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Papers by Rahul Mahadev Shelake
Sesuvium portulacastrum is a facultative halophyte capable of thriving in a saline environment. Despite molecular studies conducted to unravel its salt adaptation mechanism, there is a paucity of information on the role of salt-responsive orthologs and microRNAs (miRNAs) in this halophyte. Here, we searched the orthology to identify salt-responsive orthologs and miRNA targets of Sesuvium using the Arabidopsis genome.
Methods
The relative fold change of orthologs, conserved miRNAs, and miRNA targets of Sesuvium was analyzed under 100 mM (LS) and 250 mM NaCl (HS) treatment at 24 h using qRT-PCR. The comparison between the expression of Sesuvium orthologs and Arabidopsis orthologs (Arabidopsis eFP browser database) was used to identify differentially expressed genes.
Results
Upon salt treatment, we found that SpCIPK3 (1.95-fold in LS and 2.90-fold in HS) in Sesuvium roots, and SpNHX7 (1.61-fold in LS and 6.39-fold in HS) and, SpSTPK2 (2.54-fold in LS and 7.65-fold in HS) in Sesuvium leaves were upregulated in a salt concentration-specific manner. In Arabidopsis, these genes were either downregulated or did not show significant variation, implicating its significance in the halophytic nature of Sesuvium. Furthermore, miRNAs like miR394a, miR396a, and miR397a exhibited a negative correlation with their targets—Frigida interacting protein 1, Cysteine proteinases superfamily protein, and Putative laccase, respectively under different salt treatments.
Conclusion
The study revealed that the high salt tolerance in Sesuvium is associated with distinct transcriptional reprogramming, hence, to gain holistic mechanistic insights, global-scale profiling is required.
Sesuvium portulacastrum is a facultative halophyte capable of thriving in a saline environment. Despite molecular studies conducted to unravel its salt adaptation mechanism, there is a paucity of information on the role of salt-responsive orthologs and microRNAs (miRNAs) in this halophyte. Here, we searched the orthology to identify salt-responsive orthologs and miRNA targets of Sesuvium using the Arabidopsis genome.
Methods
The relative fold change of orthologs, conserved miRNAs, and miRNA targets of Sesuvium was analyzed under 100 mM (LS) and 250 mM NaCl (HS) treatment at 24 h using qRT-PCR. The comparison between the expression of Sesuvium orthologs and Arabidopsis orthologs (Arabidopsis eFP browser database) was used to identify differentially expressed genes.
Results
Upon salt treatment, we found that SpCIPK3 (1.95-fold in LS and 2.90-fold in HS) in Sesuvium roots, and SpNHX7 (1.61-fold in LS and 6.39-fold in HS) and, SpSTPK2 (2.54-fold in LS and 7.65-fold in HS) in Sesuvium leaves were upregulated in a salt concentration-specific manner. In Arabidopsis, these genes were either downregulated or did not show significant variation, implicating its significance in the halophytic nature of Sesuvium. Furthermore, miRNAs like miR394a, miR396a, and miR397a exhibited a negative correlation with their targets—Frigida interacting protein 1, Cysteine proteinases superfamily protein, and Putative laccase, respectively under different salt treatments.
Conclusion
The study revealed that the high salt tolerance in Sesuvium is associated with distinct transcriptional reprogramming, hence, to gain holistic mechanistic insights, global-scale profiling is required.