Browsing by Author "Prabhakar Mohan Singh"

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A novel insight into transcriptional and epigenetic regulation underlying sex expression and flower development in melon (Cucumis melo L.)
(John Wiley and Sons Inc, 2021) Mohd Aamir; Pradip Karmakar; Vinay Kumar Singh; Sarvesh Pratap Kashyap; Sudhakar Pandey; Binod Kumar Singh; Prabhakar Mohan Singh; Jagdish Singh
Melon (Cucumis melo L.) is an important cucurbit and has been considered as a model plant for studying sex determination. The four most common sexual morphotypes in melon are monoecious (A-G-M), gynoecious (−-ggM-), andromonoecious (A-G-mm), and hermaphrodite (--ggmm). Sex expression in melons is complex, as the genes and associated networks that govern the sex expression are not fully explored. Recently, RNA-seq transcriptomic profiling, ChIP-qPCR analysis integrated with gene ontology annotation and Kyoto Encyclopedia of Genes and Genomes pathways predicted the differentially expressed genes including sex-specific ACS and ACO genes, in regulating the sex-expression, phytohormonal cross-talk, signal transduction, and secondary metabolism in melons. Integration of transcriptional control through genetic interaction in between the ACS7, ACS11, and WIP1 in epistatic or hypostatic manner, along with the recruitment of H3K9ac and H3K27me3, epigenetically, overall determine sex expression. Alignment of protein sequences for establishing phylogenetic evolution, motif comparison, and protein–protein interaction supported the structural conservation while presence of the conserved hydrophilic and charged residues across the diverged evolutionary group predicted the functional conservation of the ACS protein. Presence of the putative cis-binding elements or DNA motifs, and its further comparison with DAP-seq-based cistrome and epicistrome of Arabidopsis, unraveled strong ancestry of melons with Arabidopsis. Motif comparison analysis also characterized putative genes and transcription factors involved in ethylene biosynthesis, signal transduction, and hormonal cross-talk related to sex expression. Overall, we have comprehensively reviewed research findings for a deeper insight into transcriptional and epigenetic regulation of sex expression and flower development in melons. © 2021 Scandinavian Plant Physiology Society
De novo assembly, differential gene expression and pathway analyses for anthracnose resistance in chilli (Capsicum annuum L.)
(Springer, 2022) Rajesh Kumar; Ashutosh Rai; Avinash Chandra Rai; Vinay Kumar Singh; Major Singh; Prabhakar Mohan Singh; Jagdish Singh
Chilli (Capsicum annuum L.) is one of the most important vegetable as well as spice crops grown worldwide for its wide usage. Production of chilli is profoundly affected by anthracnose disease which is one of the most serious and destructive fungal diseases of chilli, especially in tropical and subtropical regions causing around 60–80% yield loss under severe infection. In order to understand the pattern of gene expression and development of molecular markers in chilli for management of anthracnose disease, transcriptome analysis of a resistant (IIVRC-452) and susceptible (Pusa Jwala) genotypes was carried out. Transcriptome data yielded a total of 53,921,012 and 50,079,890 reads with HQ bases 5.18 GB and 4.78 GB of FASTAq sequences and were used for de novo assembly of transcriptome for IIVRC-452 and Pusa Jwala, respectively. More than 50 thousand unigenes were identified in each genotype and around 40,000 of them could be annotated with 30% cut off identity. Digital gene expression analysis revealed a total of 3124 transcripts differentially expressed in resistant and susceptible lines. A total of 871 differential transcripts were annotated and 814 differential genes were present in both resistant and susceptible lines. Furthermore, five key candidate genes (CaLOX, CaLAG-1, CaPG, CaCYP76A2, and CaSAP-13) in pathogen-responsive pathway were identified by quantitative real-time PCR (qRT-PCR). Transcriptome data generated in the present study is a valuable resource for focused investigation on plant–pathogen-interaction, to study the pathways involved in resistance mechanism and to identify markers for use in resistance breeding programmes. © 2021, Society for Plant Biochemistry and Biotechnology.
Metabolomics-Driven Mining of Metabolite Resources: Applications and Prospects for Improving Vegetable Crops
(MDPI, 2022) Dhananjaya Pratap Singh; Mansi Singh Bisen; Renu Shukla; Ratna Prabha; Sudarshan Maurya; Yesaru S. Reddy; Prabhakar Mohan Singh; Nagendra Rai; Tribhuwan Chaubey; Krishna Kumar Chaturvedi; Sudhir Srivastava; Mohammad Samir Farooqi; Vijai Kumar Gupta; Birinchi K. Sarma; Anil Rai; Tusar Kanti Behera
Vegetable crops possess a prominent nutri-metabolite pool that not only contributes to the crop performance in the fields, but also offers nutritional security for humans. In the pursuit of identifying, quantifying and functionally characterizing the cellular metabolome pool, biomolecule separation technologies, data acquisition platforms, chemical libraries, bioinformatics tools, databases and visualization techniques have come to play significant role. High-throughput metabolomics unravels structurally diverse nutrition-rich metabolites and their entangled interactions in vegetable plants. It has helped to link identified phytometabolites with unique phenotypic traits, nutri-functional characters, defense mechanisms and crop productivity. In this study, we explore mining diverse metabolites, localizing cellular metabolic pathways, classifying functional biomolecules and establishing linkages between metabolic fluxes and genomic regulations, using comprehensive metabolomics deciphers of the plant’s performance in the environment. We discuss exemplary reports covering the implications of metabolomics, addressing metabolic changes in vegetable plants during crop domestication, stage-dependent growth, fruit development, nutri-metabolic capabilities, climatic impacts, plant-microbe-pest interactions and anthropogenic activities. Efforts leading to identify biomarker metabolites, candidate proteins and the genes responsible for plant health, defense mechanisms and nutri-rich crop produce are documented. With the insights on metabolite-QTL (mQTL) driven genetic architecture, molecular breeding in vegetable crops can be revolutionized for developing better nutritional capabilities, improved tolerance against diseases/pests and enhanced climate resilience in plants. © 2022 by the authors.
Untargeted Metabolomics of Alternaria solani-Challenged Wild Tomato Species Solanum cheesmaniae Revealed Key Metabolite Biomarkers and Insight into Altered Metabolic Pathways
(MDPI, 2023) Dhananjaya Pratap Singh; Mansi Singh Bisen; Ratna Prabha; Sudarshan Maurya; Suresh Reddy Yerasu; Renu Shukla; Jagesh Kumar Tiwari; Krishna Kumar Chaturvedi; Md. Samir Farooqi; Sudhir Srivastava; Anil Rai; Birinchi Kumar Sarma; Nagendra Rai; Prabhakar Mohan Singh; Tusar Kanti Behera; Mohamed A. Farag
Untargeted metabolomics of moderately resistant wild tomato species Solanum cheesmaniae revealed an altered metabolite profile in plant leaves in response to Alternaria solani pathogen. Leaf metabolites were significantly differentiated in non-stressed versus stressed plants. The samples were discriminated not only by the presence/absence of specific metabolites as distinguished markers of infection, but also on the basis of their relative abundance as important concluding factors. Annotation of metabolite features using the Arabidopsis thaliana (KEGG) database revealed 3371 compounds with KEGG identifiers belonging to biosynthetic pathways including secondary metabolites, cofactors, steroids, brassinosteroids, terpernoids, and fatty acids. Annotation using the Solanum lycopersicum database in PLANTCYC PMN revealed significantly upregulated (541) and downregulated (485) features distributed in metabolite classes that appeared to play a crucial role in defense, infection prevention, signaling, plant growth, and plant homeostasis to survive under stress conditions. The orthogonal partial least squares discriminant analysis (OPLS-DA), comprising a significant fold change (≥2.0) with VIP score (≥1.0), showed 34 upregulated biomarker metabolites including 5-phosphoribosylamine, kaur-16-en-18-oic acid, pantothenate, and O-acetyl-L-homoserine, along with 41 downregulated biomarkers. Downregulated metabolite biomarkers were mapped with pathways specifically known for plant defense, suggesting their prominent role in pathogen resistance. These results hold promise for identifying key biomarker metabolites that contribute to disease resistive metabolic traits/biosynthetic routes. This approach can assist in mQTL development for the stress breeding program in tomato against pathogen interactions. © 2023 by the authors.