Browsing by Author "Ashutosh Rai"

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Conventional breeding approaches for abiotic stress management in horticultural crops
(Elsevier, 2021) Krishna Kumar Rai; Ajay Kumar; Ashutosh Rai; Ved Prakash Rai; Avinash Chandra Rai
Global warming due to climate change, adverse climatic conditions, and increasing attack of insect/pests has strongly impacted the growth, development, and reproduction of major horticultural crops that have posed a significant threat to global food and nutritional security. In this challenging scenario, advanced conventional breeding approaches are required to expedite the developments of stress-tolerant/resistant varieties with accelerated genetic gains. Also, along with the improved adaptation to adverse climatic conditions, new climate-resilient varieties should also be able to maintain appropriate levels of primary and secondary nutrients as well as enhanced productivity. Another conventional way to improve the production and productivity of major horticultural crops is to implement new cultivation techniques that are highly cost-effective and more efficient. Huge mapping populations such as recombinant inbred lines, near-isogenic lines and double haploids, molecular markers, marker-trait association, and mapping software are the pillars on which the conventional breeding approaches are based. In this chapter, we will be discussing conventional and marker-assisted breeding approaches for abiotic stress management in horticultural crops such as quantitative trait loci mapping, genome-wide association analysis, mutation breeding, and the importance and role of germplasm resources in the breeding of biotic and abiotic stress-tolerant/resistant crops with improved productivity. © 2021 Elsevier Inc.
De novo assembly of bitter gourd transcriptomes: Gene expression and sequence variations in gynoecious and monoecious lines
(Public Library of Science, 2015) Anjali Shukla; V.K. Singh; D.R. Bharadwaj; Rajesh Kumar; Ashutosh Rai; A.K. Rai; Raja Mugasimangalam; Sriram Parameswaran; Major Singh; P.S. Naik
Bitter gourd (Momordica charantia L.) is a nutritious vegetable crop of Asian origin, used as a medicinal herb in Indian and Chinese traditional medicine. Molecular breeding in bitter gourd is in its infancy, due to limited molecular resources, particularly on functional markers for traits such as gynoecy. We performed de novo transcriptome sequencing of bitter gourd using Illumina next-generation sequencer, from root, flower buds, stem and leaf samples of gynoecious line (Gy323) and a monoecious line (DRAR1). A total of 65,540 transcripts for Gy323 and 61,490 for DRAR1 were obtained. Comparisons revealed SNP and SSR variations between these lines and, identification of gene classes. Based on available transcripts we identified 80 WRKY transcription factors, several reported in responses to biotic and abiotic stresses; 56 ARF genes which play a pivotal role in auxin-regulated gene expression and development. The data presented will be useful in both functions studies and breeding programs in bitter gourd. © 2015 Shukla et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
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.
Engineered BcZAT12 gene mitigates salt stress in tomato seedlings
(Springer, 2021) Avinash Chandra Rai; Ashutosh Rai; Kavita Shah; Major Singh
In salt-prone areas, plant growth and productivity is adversely affected. In the present study, the ZT1-ZT6 transgenic tomato lines having BcZAT12 gene under the regulatory control of the stress inducible Bclea1 promoter were exposed to three salinity levels (50, 100 and 200 mM) at the four leaf stage for 10 days. The transgenic lines showed improved growth in stem height, leaf area, root length and shoot length under saline conditions, as compared to control. Moreover, ZT1 and ZT5 lines showed lower electrolyte leakage and decreased hydrogen peroxide formation, in combination with elevated relative water content, proline and chlorophyll levels. The enzyme activity of catalase was also enhanced in ZT1 and ZT5. These results poses the present lines as an attractive alternative for tomato cultivation in salinity-affected areas. © 2021, Prof. H.S. Srivastava Foundation for Science and Society.
Enhancement in Biological Availability of Vitamins by Nano-engineering and its Applications: An Update
(Bentham Science Publishers, 2024) Sadhna Mishra; Shalini Sahani; Shikha Pandhi; Arvind Kumar; Dipendra Kumar Mahato; Pradeep Kumar; Kaustubh Chandrakant Khaire; Ashutosh Rai
Vitamin nano-engineering has been accomplished by synthesizing various nanostructures to improve their stability, bioavailability, shelf life, and functioning. This review provides a detailed description of recent advances in the art of encapsulation with high efficiency through the use of practical and logistic nano-engineering techniques such as nanofibres, nanogels, nanobeads, nanotubes, nanoparticles, nanoliposomes, and many other nanostructures. To demonstrate the interaction of molecules with nano-forms, the bioavailability of several vitamins such as B, C, E, A, D, and others in the form of nanostructures is explored. This review will provide a thorough understanding of how to improve bioavailability and nanostructure selection to extend the utility, shelf life, and structural stability of vitamins. While nanoencapsulation can improve vitamin stability and distribution, the materials employed in nanotechnologies may offer concerns if they are not sufficiently tested for safety. If nanoparticles are not adequately designed and evaluated, they may cause inflammation, oxidative stress, or other unwanted effects. Researchers and makers of nanomaterials and medication delivery systems should adhere to established rules and regulations. Furthermore, long-term studies are required to monitor any negative consequences that may result from the use of nanostructure. © 2024 Bentham Science.
Expression analysis of droughtinduced genes in wild tomato line (Solanum habrochaites)
(Indian Academy of Sciences, 2014) Ranjit Singh Gujjar; Moin Akhtar; Ashutosh Rai; Major Singh
Many plant genes are regulated in response to abiotic stresses such as drought, high salinity, heat and cold, and their gene products function in stress response and tolerance. The whole process of plant adaptation to these environmental stresses is controlled by orchestration of complex molecular networks. In the present study, eight genes showing significant difference of expression on exposure to artificial drought stress in tomato, were selected from the previously performed microarray experiment. Expression analysis of the genes was done semi-quantitatively as well as quantitatively under artificially imposed drought stress and the results were almost similar to those of microarray experiment. Tissue-specific analysis of the genes, performed on tolerant line, revealed fairly a similar pattern of expression in root, stem and leaf with notable differences in flower, which experienced the least influence of drought. The results confirmed that SlPRP16, SlCYP51-17, SlMCPI19 and SlGDSL20 were downregulated in both the lines with stronger downregulation in sensitive line. SlWRKY4 was downregulated in both the lines with more folds of downregulation in tolerant line. SlEFH12 and SlSNF4-15 were upregulated in tolerant line. SlUSPA9 was upregulated in both the lines with relatively more folds of upregulation in sensitive line.
Gene expression analysis of Solanum lycopersicum and Solanum habrochaites under drought conditions
(Elsevier Inc, 2016) Upama Mishra; Ashutosh Rai; Rajesh Kumar; Major Singh; Hausila Prasad Pandey
Drought is one of the limiting environmental factors that affect crop production worldwide. Understanding the molecular mechanism of drought stress is the key to developing drought tolerant crop. In this experiment we performed expression profiling of tomato plants under water deficit conditions using microarray technology. The data set we generated (available in the NCBI/GEO database under GSE22304) has been analyzed to identify genes that are involved in the regulation of tomato's responses to drought. © 2016.
Genetic diversity in Capsicum germplasm based on microsatellite and random amplified microsatellite polymorphism markers
(2013) Ved Prakash Rai; Rajesh Kumar; Sanjay Kumar; Ashutosh Rai; Sanjeet Kumar; Major Singh; Sheo Pratap Singh; Awadesh Bahadur Rai; Rajneesh Paliwal
A sound knowledge of the genetic diversity among germplasm is vital for strategic germplasm collection, maintenance, conservation and utilisation. Genomic simple sequence repeats (SSRs) and random amplified microsatellite polymorphism (RAMPO) markers were used to analyse diversity and relationships among 48 pepper (Capsicum spp.) genotypes originating from nine countries. These genotypes covered 4 species including 13 germplasm accessions, 30 improved lines of 4 domesticated species and 5 landraces derived from natural interspecific crosses. Out of 106 SSR markers, 25 polymorphic SSR markers (24 %) detected a total of 76 alleles (average, 3.04; range, 2-5). The average polymorphic information content (PIC) was 0.69 (range, 0.29-0.92). Seventeen RAMPO markers produced 87 polymorphic fragments with average PIC of 0.63 (range, 0.44-0.81). Dendrograms based on SSRs and RAMPOs generated two clusters. All 38 Capsicum annuum genotypes and an interspecific landrace clustered together, whereas nine non-annuum (three Capsicum frutescens, one Capsicum chinense, one Capsicum baccatum and four interspecific landraces) genotypes clustered separately. Genetic variation within non-annuum genotypes was greater than the C. annuum genotypes. Distinctness of interspecific derivative landraces grown in northeast India was validated; natural crossing between sympatric Capsicum species has been proposed as the mechanism of their origin. © 2013 Prof. H.S. Srivastava Foundation for Science and Society.
Identification of transcription factors in tomato, potentially related to early blight resistance at invasion in host tissue using, microarray expression profiling
(Elsevier B.V., 2016) Priti Upadhyay; Showkat Hussain Ganie; Ashutosh Rai; Major Singh; Brajesh Sinha
Tomato early blight is an important threat due to its capacity to reduce the production in all major tomato producing areas. Molecular mechanisms underlying resistance to the causal organism are not well known. Therefore, we aimed to study tomato – Alternaria solani system to search the transcription factors and pathways which, are responsible for resistance to this fungi using, affymetrix gene chip for tomato. three hundred ninety five transcription factors were found to be differentially expressed at 24 h after inoculation with A. solani in the resistant genotype, EC-520,061, of tomato. Also, Zinc Finger Proteins, Ribosomal binding unit S4 and Auxin responsive transcription factors were found to play significant role in resistance. Their expression has enhanced the pathogenesis related proteins and also other proteins as well, which, have direct role in stopping the penetration of mycelia in host plant. © 2016 South African Association of Botanists
Microarray analyses during early stage of the tomato/Alternaria solani interaction
(Elsevier Inc., 2015) Priti Upadhyay; Ashutosh Rai; Rajesh Kumar; Major Singh; Brajesh Sinha
Tomato early blight is an important threat and it has capacity to reduce the production in all major tomato producing areas. Molecular mechanism underlying the resistance against this is not well known. Therefore we studied this system to search the possible mechanism of resistance, which includes pathogenesis related protein, and pathways and transcription factors, which are responsible for resistance against this pathogen using affymetrix gene chip for tomato. Their differential expressions have enhanced the biochemical and other related products, which have, direct or indirect role in stopping the penetration of mycelia in the host plant. © 2015 The Authors. Published by Elsevier Inc.
Plant growth promotion and differential expression of defense genes in chilli pepper against Colletotrichum truncatum induced by Trichoderma asperellum and T. harzianum
(BioMed Central Ltd, 2023) Mukesh Yadav; Kumari Divyanshu; Manish Kumar Dubey; Ashutosh Rai; Sunil Kumar; Yashoda Nandan Tripathi; Vaishali Shukla; Ram Sanmukh Upadhyay
Background: Trichoderma asperellum and T. harzianum were assessed in this study as a potential biological control against Colletotrichum truncatum. C. truncatum is a hemibiotrophic fungus that causes anthracnose disease in chilli thereby affecting plant growth and fruit yield. Scanning electron microscope (SEM) technique showed the beneficial interaction between chilli root-Trichoderma spp. inducing the plant growth promotion, mechanical barrier, and defense network under C. truncatum challenged conditions. Methods: Seeds bio-primed with T. asperellum, T. harzianum, and T. asperellum + T. harzianum promoted the plant growth parameters and strengthening of physical barrier via lignification on the wall of vascular tissues. Seed primed with bioagents were used for exploring the molecular mechanism of defense response in pepper against anthracnose to assess the temporal expression of six defense genes in the Surajmukhi variety of Capsicum annuum. QRT-PCR demonstrated induction of defense responsive genes in chilli pepper bioprimed with Trichoderma spp. such as plant defensin 1.2 (CaPDF1.2), superoxide dismutase (SOD), ascorbate peroxidase (APx), guaiacol peroxidase (GPx), pathogenesis related proteins PR-2 and PR-5. Results: The results showed that bioprimed seeds were assessed for T. asperellum, T. harzianum, and T. asperellum + T. harzianum-chilli root colonization interaction under in vivo conditions. The results of the scanning electron microscope revealed that T. asperellum, T. harzianum and T. asperellum + T. harzianum interact with chilli roots directly via the development of plant-Trichoderma interaction system. Seeds bio-primed with bioagents promoted the plant growth parameters, fresh and dry weight of shoot and root, plant height, leaf area index, number of leaves, stem diameter and strengthening of physical barrier via lignification on the wall of vascular tissues and expression of six defense related genes in pepper against anthracnose. Conclusions: Application of T. asperellum and T. harzianum and in combination of treatments enhanced the plant growth. Further, as seeds bioprimed with T. asperellum, T. harzianum and in combination with treatment of T. asperellum + T. harzianum induced the strengthening of the cell wall by lignification and expression of six defense related genes CaPDF1.2, SOD, APx, GPx, PR-2 and PR-5 in pepper against C. truncatum. Our study contributed for better disease management through biopriming with T. asperellum, T. harzianum and T. asperellum + T. harzianum. The biopriming possess enormous potential to promote plant growth, modulate the physical barrier, and induced the defense related genes in chilli pepper against anthracnose. © 2023, The Author(s).
Process optimization for the manufacture of lemon based beverage from hydrolyzed whey
(Springer, 2014) Sudhir Singh; Priti Khemariya; Ashutosh Rai
Whey obtained during the manufacture of Cheddar cheese and paneer was lactose hydrolyzed to develop lemon based whey beverage. The lactose present in whey was hydrolyzed by Maxilact L-2000 lactase enzyme. Maximum (85-90%) hydrolysis in cheese and paneer whey was optimized with enzyme concentration of 0.4% at pH 6.75 after incubation at 40°C for 3 h. The sweetness level in hydrolyzed whey was equivalent to 2.5% sucrose solution. Response surface methodology was used to optimize the levels of sugar, lemon juice, lemon flavor and stabilizer i.e. carboxyl methyl cellulose (CMC). The most acceptable lemon based beverage contained 8, 4, 0.1 and 0.05% of sugar, lemon juice, lemon flavor and CMC, respectively. The beverage had greater acceptability to judges after heat treatment at 90°C for 2 min than the heat treatment of 5 psi for 5 min. © 2011 Association of Food Scientists & Technologists (India).
Stress Tolerance in Horticultural Crops: Challenges and Mitigation Strategies
(Elsevier, 2021) Avinash Chandra Rai; Ashutosh Rai; Krishna Kumar Rai; Ved Prakash Rai; Ajay Kumar
Stress Tolerance in Horticultural Crops: Challenges and Mitigation Strategies explores concepts, strategies and recent advancements in the area of abiotic stress tolerance in horticultural crops, highlighting the latest advances in molecular breeding, genome sequencing and functional genomics approaches. Further sections present specific insights on different aspects of abiotic stress tolerance from classical breeding, hybrid breeding, speed breeding, epigenetics, gene/quantitative trait loci (QTL) mapping, transgenics, physiological and biochemical approaches to OMICS approaches, including functional genomics, proteomics and genomics assisted breeding. Due to constantly changing environmental conditions, abiotic stress such as high temperature, salinity and drought are being understood as an imminent threat to horticultural crops, including their detrimental effects on plant growth, development, reproduction, and ultimately, on yield. This book offers a comprehensive resource on new developments that is ideal for anyone working in the field of abiotic stress management in horticultural crops, including researchers, students and educators. © 2021 Elsevier Inc.
Transcriptomic characterization of Trichoderma harzianum T34 primed tomato plants: assessment of biocontrol agent induced host specific gene expression and plant growth promotion
(BioMed Central Ltd, 2023) Mohd Aamir; V. Shanmugam; Manish Kumar Dubey; Fohad Mabood Husain; Mohd Adil; Waquar Akhter Ansari; Ashutosh Rai; Pankaj Sah
In this study, we investigated the intricate interplay between Trichoderma and the tomato genome, focusing on the transcriptional and metabolic changes triggered during the late colonization event. Microarray probe set (GSE76332) was utilized to analyze the gene expression profiles changes of the un-inoculated control (tomato) and Trichoderma-tomato interactions for identification of the differentially expressed significant genes. Based on principal component analysis and R-based correlation, we observed a positive correlation between the two cross-comaparable groups, corroborating the existence of transcriptional responses in the host triggered by Trichoderma priming. The statistically significant genes based on different p-value cut-off scores [(p adj-values or q-value); p adj-value < 0.05], [(p cal-values); p cal-value < 0.05; p cal < 0.01; p cal < 0.001)] were cross compared. Through cross-comparison, we identified 156 common genes that were consistently significant across all probability thresholds, and showing a strong positive corelation between p-value and q-value in the selected probe sets. We reported TD2, CPT1, pectin synthase, EXT-3 (extensin-3), Lox C, and pyruvate kinase (PK), which exhibited upregulated expression, and Glb1 and nitrate reductase (nii), which demonstrated downregulated expression during Trichoderma-tomato interaction. In addition, microbial priming with Trichoderma resulted into differential expression of transcription factors related to systemic defense and flowering including MYB13, MYB78, ERF2, ERF3, ERF5, ERF-1B, NAC, MADS box, ZF3, ZAT10, A20/AN1, polyol sugar transporter like zinc finger proteins, and a novel plant defensin protein. The potential bottleneck and hub genes involved in this dynamic response were also identified. The protein–protein interaction (PPI) network analysis based on 25 topmost DEGS (p cal-value < 0.05) and the Weighted Correlation Gene Network Analysis (WGCNA) of the 1786 significant DEGs (p cal-value < 0.05) we reported the hits associated with carbohydrate metabolism, secondary metabolite biosynthesis, and the nitrogen metabolism. We conclude that the Trichoderma-induced microbial priming re-programmed the host genome for transcriptional response during the late colonization event and were characterized by metabolic shifting and biochemical changes specific to plant growth and development. The work also highlights the relevance of statistical parameters in understanding the gene regulatory dynamics and complex regulatory networks based on differential expression, co-expression, and protein interaction networks orchestrating the host responses to beneficial microbial interactions. © 2023, The Author(s).