Botany - Research Publications

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    Transcriptomic investigations of gene networks in response to arsenic accumulation in Brassica juncea (L.) Czern & Coss
    (Central University of Punjab, 2019) Thakur, Sapna; Bhardwaj, Pankaj
    Arsenic (As), a widespread toxic metalloid is class I carcinogen known to cause adverse health effects in human. In the present study, As accumulation potential and differential gene expression in B. juncea is investigated. The amount of arsenic accumulated varied in the range of 15.99 to 1138.70 mg/Kg on dry weight basis in five cultivars. A decrease in chlorophyll content and increase in membrane damage and enzymatic activities of antioxidants was observed with increase in As concentration in the B. juncea cultivars. Using maximum As accumulating cultivar (RLM514), a total of 10,870 significantly differentially expressed transcripts in response to As treatment were identified. Further, the pathway analysis revealed a large scale reprogramming of genes involving carbon metabolism (2.5%), plant hormone signaling (1.4%), and glutathione metabolism (0.6%). Moreover, a comparative account of Cd toxicity revealed a total of 11,294 transcripts to be significantly differentially expressed. The genes related to response to chemical, oxidative stress, transport, and secondary metabolism were upregulated whereas multicellular organismal development, developmental process, photosynthesis were downregulated by Cd treatment. Furthermore, 616 membrane transport proteins were found to be significantly differentially expressed. Cd-related transporters such as metal transporter (Nramp1), metal tolerance protein (MTPC2, MTP11), cadmiumtransporting ATPase, and plant cadmium resistance protein (PCR2, PCR6) were upregulated while cadmium/zinc- transporting ATPase (HMA2, HMA3, HMA4), highaffinity calcium antiporter (CAX1), and iron transport protein (IRT1) were downregulated by Cd treatment. Pathway analysis revealed signaling cascades including plant hormones signaling, MAPK signaling and Ca signaling was modulated suggesting their role in Cd-stress tolerance. The regulation overview using MapMan also revealed gene expression related to plant hormones, calcium regulation and MAP kinases were altered under Cd-stress.
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    Comparative Transcriptome Profiling Under Cadmium Stress Reveals the Uptake and Tolerance Mechanism in Brassica juncea
    (Springer, 2019) Thakur, Sapna; Choudhary, Shurti; Bhardwaj, Pankaj
    Cadmium (Cd) is a biologically non-essential and phytotoxic heavy metal pollutant. In this study, we estimated the Cd accumulation potential of Indian mustard and identified factors responsible for Cd uptake, tolerance, and detoxification. Eight transcriptomic libraries were sequenced and ??230 million good quality reads were generated. The alignment rate against B. juncea reference genome V1.5 varied in the range of 85.03-90.06%. Comparative expression analysis using DESeq2 revealed 11,294 genes to be significantly differentially expressed under Cd treatment. The agriGO singular enrichment analysis revealed genes related to response to chemical, oxidative stress, transport, and secondary metabolic process were upregulated, whereas multicellular organismal development, developmental process, and photosynthesis were downregulated by Cd treatment. Furthermore, 616 membrane transport proteins were found to be significantly differentially expressed. Cd-related transporters such as metal transporter (Nramp1), metal tolerance protein (MTPC2, MTP11), cadmium-transporting ATPase, and plant cadmium resistance protein (PCR2, PCR6) were upregulated whereas cadmium/zinc-transporting ATPase (HMA2, HMA3, HMA4), high-affinity calcium antiporter (CAX1), and iron transport protein (IRT1) were downregulated by Cd treatment. A total of 332 different gene-networks affected by Cd stress were identified using KAAS analysis. Various plant hormones signaling cascades were modulated suggesting their role in Cd stress tolerance. The regulation overview using MapMan analysis also revealed gene expression related to plant hormones, calcium regulation, and MAP kinases were altered under Cd stress.
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    Exploring microRNA profiles for circadian clock and flowering development regulation in Himalayan Rhododendron
    (Elsevier, 2018) Choudhary, Shruti; Thakur, Sapna; Majeed, Aasim; Bhardwaj, Pankaj
    miRNA is a non-coding, yet crucial entity in remodeling the genetic architecture. Rhododendron arboreum of Himalayas grows and even flower under fluctuating climate. sRNA from leaves of vegetative and reproductive periods was sequenced to elucidate its seasonal associations. Conserved (256) and novel (210) miRNAs and their precursors were located based on homology with plant databases and transcriptome of the species. 27,139 predicted targets were involved with metabolism, reproduction, and response to abiotic stimuli. A comparative analysis showed differential expression of 198 miRNAs with season-specific abundance of 103 miRNAs. Specific isoforms of 11 miRNA families exhibited a temporal expression and targeted different genes implying a complex regulation. The variable miRNA expression among the tissues of different conditions can be associated with the adaptability of the species, which will prove essential for further study on miRNAs mediating seasonal response. Moreover, exogenous cues also mediate phase transition via networking of flowering pathways and their components. In this context, 18 known families and 77 novel miRNAs modulating 117 genes crucial in circadian entrainment were filtered. A negative correlation was obtained between the expression of 18 of these miRNAs and their targets when tested through quantitative-PCR. It highlighted the role of miRNA-target pairs in perceiving environmental variabilities and monitoring flowering growth. Furthermore, a phylogenetic clustering was performed, which supported the lineage-specific evolution and function of putative miR156 sequence in the species. This documentation of genome-wide profiling of miRNA, their targets, and expression will enhance the understanding of developmental and climate-tolerance strategies in high-altitude trees.
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    Genetic diversity and population structure of Melia azedarach in North-Western Plains of India
    (Springer Verlag, 2016) Thakur, Sapna; Choudhary, Shruti; Singh, Amandeep; Ahmad, Kamal; Sharma, Gagan; Majeed, Aasim; Bhardwaj, Pankaj
    Key message: Genetic structure amongM. azedarachpopulations was detected and two subpopulations were present among them. A significant ?isolation by distance? was found inM. azedarachpopulation in North-Western Plains of India. Abstract: Melia azedarach is an important forest tree with pharmaceutical, insecticidal, pesticidal, and commercial significance. It is a good reforestation tree because of its fast growth and drought hardy nature. Genetic variation in a species allows itself to adapt, evolve and respond to environmental stress. It provides the basis for survival of a species and critically influences its evolutionary potential. Assessment of genetic diversity is necessary for improvement and conservation of a species. For this, microsatellite markers are of particular interest given the attributes like co-dominance, reproducibility, hyper variability and abundance throughout the genome. In the present study, we analyzed the genetic diversity and population structure of M. azedarach, an ecologically imperative species growing in the North-Western Plains of India. We developed 43 microsatellite markers, of which 20 were subsequently employed for analysis of diversity and population structure among 33 populations encompassing 318 genotypes representing North-Western Plains of India. A moderate level of diversity (Na?=?5.1, Ho?=?0.506, He?=?0.712, I?=?1.386) was assessed. The highest value of ?K estimated using STRUCTURE indicated 2 subpopulations (K?=?2). AMOVA exhibited 73?% variation within populations and 12?% variation was found among regions. Significant positive correlation between geographical and genetic distance was found (Rxy?=?0.365, P?=?0.010). The present study lays a foundation on a better understanding of genetic dynamics of the species and reveals its diversity and population structure in North-Western Plains of India. ? 2016, Springer-Verlag Berlin Heidelberg.
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    Development and characterization of genomic microsatellite markers in Tinospora cordifolia
    (Springer India, 2017) Gargi, Madhuranjana; Thakur, Sapna; Anand, Shashi Shekhar; Choudhary, Shruti; Bhardwaj, Pankaj; Gargi, M.; Thakur, S.; Anand, S.S.; Choudhary, S.; Bhardwaj, P.
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    Development and characterization of genomic microsatellite markers in Prosopis cineraria
    (Elsevier B.V., 2017) Anand, Shashi Shekhar; Thakur, Sapna; Gargi, Madhuranjana; Choudhary, Shruti; Bhardwaj, Pankaj; Anand, S.S.; Thakur, S.; Gargi, M.; Choudhary, S.; Bhardwaj, P.
    Characterization of genetic diversity is a must for exploring the genetic resources for plant development and improvement. Prosopis cineraria is ecologically imperative species known for its innumerable biological benefits. Since there is a lack of genetic resources for the species, so it is crucial to unravel the population dynamics which will be very effective in plant improvement and conservation strategies. Of the 41 genomic microsatellite markers designed from (AG)n enriched library, 24 were subsequently employed for characterization on 30 genotypes of Indian arid region. A total of 93 alleles with an average 3.875 could be amplified by tested primer pairs. The average observed and expected heterozygosity was 0.5139 and 0.5786, respectively with 23 primer pairs showing significant deviations from Hardy-Weinberg equilibrium. Polymorphic information content average to 0.5102 and the overall polymorphism level was found to be 93.27%. STRUCTURE analysis and DARwin exhibited the presence of 4 clusters among 30 genotypes. ? 2017 The Authors
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    Development and characterization of genomic microsatellite markers in Rhododendron arboreum
    (Kluwer Academic Publishers, 2014) Choudhary, Shruti; Thakur, Sapna; Saini, Ram Gopal; Bhardwaj, Pankaj; Choudhary, S.; Thakur, S.; Saini, R.G.; Bhardwaj, P.
    Population genetics characteristics are the fundamentals of conservation and management practices. Rhododendronarboreum, a key biodiversity component inhabiting Indian Himalayas, suffers from overexploitation and global warming. Using biotin?streptavidin hybridization technique, 41 microsatellite markers were designed from an enriched DNA library to provide a genetic background and an insight into the population structure of the species. With a range of 2?14 alleles amplified from 38 loci, the populations were reported with observed and expected heterozygosity of 0.167?0.933 and 0.422?0.917 respectively. Some of the loci showed significant deviations from Hardy?Weinberg equilibrium and overall no linkage disequilibrium was detected. These markers will support genetic diversity and further genotyping studies in R. arboreum. ? 2014, Springer Science+Business Media Dordrecht.