Browsing by Author "Deshmukh, R"

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    Article Drought and Oxidative Stress in Flax (Linum usitatissimum L.) Entails Harnessing Non-Canonical Reference Gene for Precise Quantification of qRT-PCR Gene Expression
    (2023-04) Dash, PK; Rai, R; Pradhan, SK; Shivaraj, SM; Deshmukh, R
    Flax (Linum usitatissimum L.) is a self-pollinating, annual, diploid crop grown for multi utility purposes for its quality oil, shining bast fiber, and industrial solvent. Being a cool (Rabi) season crop, it is affected by unprecedented climatic changes such as high temperature, drought, and associated oxidative stress that, globally, impede its growth, production, and productivity. To precisely assess the imperative changes that are inflicted by drought and associated oxidative stress, gene expression profiling of predominant drought-responsive genes (AREB, DREB/CBF, and ARR) was carried out by qRT-PCR. Nevertheless, for normalization/quantification of data obtained from qRT-PCR results, a stable reference gene is mandatory. Here, we evaluated a panel of four reference genes (Actin, EF1a, ETIF5A, and UBQ) and assessed their suitability as stable reference genes for the normalization of gene expression data obtained during drought-induced oxidative stress in flax. Taking together, from the canonical expression of the proposed reference genes in three different genotypes, we report that EF1a as a stand-alone and EF1a and ETIF5A in tandem are suitable reference genes to be used for the real-time visualization of cellular impact of drought and oxidative stress on flax
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    Editorial: Genetic advancements for improving the plant tolerance to biotic and abiotic stresses
    (2024-05) Kulkarni, K; Vennapusa, A; Pandian, B; Deshmukh, R
    In this Research Topic on “Genetic advancements for improving the plant tolerance to biotic and abiotic stresses”, we have collated 12 articles (10 original research articles and two review articles) that highlight the potential insights into the physiological, molecular, and genetic factors involved in imparting abiotic and biotic stress tolerance in plants. This compilation highlights many recent findings, methods, and molecular genetic resources for crop improvement programs and contributes to enhancing agricultural productivity and sustainability.
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    Editorial: RNA plasticity: novel structures, shapes, modifications, and functions
    (2023-09) Kadam, U; Deshmukh, R; Tian, L
    This Research Topic on “RNA Plasticity: Novel Structures, Shapes, Modifications, and Functions” was constituted with a focus on various aspects of plant RNA biology including novel structures, modifications, and its biological roles as regulatory molecules. In applied biotechnology, novel designs drive technological innovations and advancements that help resolve contemporary society’s significant challenges. The diversified roles played by the different forms of RNA molecules in the past few decades exemplify its significant role in cellular regulation, as it acts as a messenger of information from genomic DNA to the production of distinct proteins as well as regulates unique biological processes via flexibility of RNA structure and functions.
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    Genomics-Assisted Breeding: A Powerful Breeding Approach for Improving Plant Growth and Stress Resilience
    (2024-05) Tyagi, A; Mir, Z; Almalki, M; Deshmukh, R; Ali, s
    Climate change biotic and abiotic stressors lead to unpredictable crop yield losses, threaten ing global food and nutritional security. In the past, traditional breeding has been instrumental in fulfilling food demand; however, owing to its low efficiency, dependence on environmental condi tions, labor intensity, and time consumption, it fails to maintain global food demand in the face of a rapidly changing environment and an expanding population. In this regard, plant breeders need to integrate multiple disciplines and technologies, such as genotyping, phenotyping, and envirotyping, in order to produce stress-resilient and high-yielding crops in a shorter time. With the technological revolution, plant breeding has undergone various reformations, for example, artificial selection breed ing, hybrid breeding, molecular breeding, and precise breeding, which have been instrumental in developing high-yielding and stress-resilient crops in modern agriculture. Marker-assisted selection, also known as marker-assisted breeding, emerged as a game changer in modern breeding and has evolved over time into genomics-assisted breeding (GAB). It involves genomic information of crops to speed up plant breeding in order to develop stress-resilient and high-yielding crops. The combination of speed breeding with genomic and phenomic resources enabled the identification of quantitative trait loci (QTLs)/genes quickly, thereby accelerating crop improvement efforts. In this review, we provided an update on rapid advancement in molecular plant breeding, mainly GAB, for efficient crop improvements. We also highlighted the importance of GAB for improving biotic and abiotic stress tolerance as well as crop productivity in different crop systems. Finally, we discussed how the expansion of GAB to omics-assisted breeding (OAB) will contribute to the development of future resilient crops.
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    Hemibiotrophic Phytophthora infestans Modulates the Expression of SWEET Genes in Potato (Solanum tuberosum L.)
    (2023-09) Kardile, HB; Karkute, SG; Challam, C; Sharma, NK; Shelake, RM; Kawar, PG; Patil, VU; Deshmukh, R
    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 haveimpliedtheinvolvementofpotatoSWEET genesinthemostdevastatinglateblight 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.
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    Hemibiotrophic Phytophthora infestans Modulates the Expression of SWEET Genes in Potato (Solanum tuberosum L.)
    (2023-09) Kardile, H; Karkute, S; Sharma, N; Deshmukh, R
    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.
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    Pinpointing Genomic Regions and Candidate Genes Associated with Seed Oil and Protein Content in Soybean through an Integrative Transcriptomic and QTL Meta-Analysis
    (2022-12) Kumar, V; Goyal, V; Mandlik, R; Deshmukh, R
    Soybean with enriched nutrients has emerged as a prominent source of edible oil and protein. In the present study, a meta-analysis was performed by integrating quantitative trait loci (QTLs) information, region-specific association and transcriptomic analysis. Analysis of about a thousand QTLs previously identified in soybean helped to pinpoint 14 meta-QTLs for oil and 16 meta-QTLs for protein content. Similarly, region-specific association analysis using whole genome re-sequenced data was performed for the most promising meta-QTL on chromosomes 6 and 20. Only 94 out of 468 genes related to fatty acid and protein metabolic pathways identified within the meta QTL region were found to be expressed in seeds. Allele mining and haplotyping of these selected genes were performed using whole genome resequencing data. Interestingly, a significant haplotypic association of some genes with oil and protein content was observed, for instance, in the case of FAD2- 1B gene, an average seed oil content of 20.22% for haplotype 1 compared to 15.52% for haplotype 5 was observed. In addition, the mutation S86F in the FAD2-1B gene produces a destabilizing effect of (∆∆G Stability) −0.31 kcal/mol. Transcriptomic analysis revealed the tissue-specific expression of candidate genes. Based on their higher expression in seed developmental stages, genes such as sugar transporter, fatty acid desaturase (FAD), lipid transporter, major facilitator protein and amino acid transporter can be targeted for functional validation. The approach and information generated in the present study will be helpful in the map-based cloning of regulatory genes, as well as for marker-assisted breeding in soybean.
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    Reference Guided De Novo Genome Assembly of Transformation Pliable Solanum lycopersicum cv. Pusa Ruby
    (2023-02) Deshmukh, R; Vats, S; Kumar, V; Mandlik, R
    Solanum lycopersicum cv. Pusa Ruby (PR) is a superior tomato cultivar routinely used as a model tomato variety. Here, we report a reference-guided genome assembly for PR, covering 97.6% of the total single-copy genes in the solanales order. The PR genome contains 34,075 genes and 423,288 variants, out of which 127,131 are intragenic and 1232 are of high impact. The assembly was packaged according to PanSol guidelines (N50 = 60,396,827) with the largest scaffold measuring 85 megabases. The similarity of the PR genome assembly to Heinz1706, M82, and Fla.8924 was measured and the results suggest PR has the lowest affinity towards the hybrid Fla.8924. We then analyzed the regeneration efficiency of PR in comparison to another variety, Pusa Early Dwarf (PED). PR was found to have a high regeneration rate (45.51%) and therefore, we performed allele mining for genes associated with regeneration and found that only AGAMOUS-LIKE15 has a null mutation. Further, allele mining for fruit quality-related genes was also executed. The PR genome has an Ovate mutation leading to round fruit shape, causing economically undesirable fruit cracking. This genomic data can be potentially used for large scale crop improvement programs as well as functional annotation studies.
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    Saffron, a Potential Bridge between Nutrition and Disease Therapeutics: Global Health Challenges and Therapeutic Opportunities
    (2024-05) Mir, R; Tyagi, A; Hussain, S; Almalki, M; Zeyad, M; Deshmukh, R; Ali, S
    Plants are an important source of essential bioactive compounds that not only have a beneficial role in human health and nutrition but also act as drivers for shaping gut microbiome. However, the mechanism of their functional attributes is not fully understood despite their signif icance. One such important plant is Crocus sativus, also known as saffron, which possesses huge medicinal, nutritional, and industrial applications like food and cosmetics. The importance of this plant is grossly attributed to its incredible bioactive constituents such as crocins, crocetin, safranal, picrocrocin, and glycosides. These bioactive compounds possess a wide range of therapeutic activities against multiple human ailments. Since a huge number of studies have revealed negative unwanted side effects of modern-day drugs, the scientific communities at the global level are investigating a large number of medicinal plants to explore natural products as the best alternatives. Taken into consideration, the available research findings indicate that saffron has a huge scope to be further explored to establish alternative natural-product-based drugs for health benefits. In this review, we are providing an update on the role of bioactive compounds of saffron as therapeutic agents (human disorders and antimicrobial activity) and its nutritional values. We also highlighted the role of omics and metabolic engineering tools for increasing the content of key saffron bioactive molecules for its mass production. Finally, pre-clinical and clinical studies seem to be necessary to establish its therapeutic potential against human diseases.