Dev Mani Pandey

Effect of Growth Regulators on Photosynthesis, Transpiration and Related Parameters in Water Stressed Cotton

Gas exchange in Gossypium hirsutum L. cv. H-777 as affected by water deficit and growth regulators (IAA, GA3, BAP, ABA, ethrel) was examined. Sixty days after sowing, growth regulators in concentration 50 µM were applied as foliar spray and irrigation was withheld to get desired (moderate and severe) water deficit. All the parameters were measured on the third leaf from the top between 10:00 and 11:00. Net photosynthetic rate (PN), transpiration rate (E), stomatal conductance (gs), carboxylation efficiency (CE), and water potential (ψw) decreased significantly with the increasing water stress, however, water use efficiency (WUE) was unaffected. Foliar spray with IAA, GA3 and BAP partially counteracted the effect of water deficit on the above parameters except ψw, which became more negative. ABA and up to some extent ethrel increased WUE and maintained higher ψw, however, caused further decrease in PN, E, and gs.

Identification of new stress-induced microRNA and their targets in wheat using computational approach

MicroRNAs (miRNAs) are a class of short endogenous non-coding small RNA molecules of about 18–22 nucleotides in length. Their main function is to downregulate gene expression in different manners like translational repression, mRNA cleavage and epigenetic modification. Computational predictions have raised the number of miRNAs in wheat significantly using an EST based approach. Hence, a combinatorial approach which is amalgamation of bioinformatics software and perl script was used to identify new miRNA to add to the growing database of wheat miRNA. Identification of miRNAs was initiated by mining the EST (Expressed Sequence Tags) database available at National Center for Biotechnology Information. In this investigation, 4677 mature microRNA sequences belonging to 50 miRNA families from different plant species were used to predict miRNA in wheat. A total of five abiotic stress-responsive new miRNAs were predicted and named Ta-miR5653, Ta-miR855, Ta-miR819k, Ta-miR3708 and Ta-miR5156. In addition, four previously identified miRNA, i.e., Ta-miR1122, miR1117, Ta-miR1134 and Ta-miR1133 were predicted in newly identified EST sequence and 14 potential target genes were subsequently predicted, most of which seems to encode ubiquitin carrier protein, serine/threonine protein kinase, 40S ribosomal protein, F-box/kelch-repeat protein, BTB/POZ domain-containing protein, transcription factors which are involved in growth, development, metabolism and stress response. Our result has increased the number of miRNAs in wheat, which should be useful for further investigation into the biological functions and evolution of miRNAs in wheat and other plant species.

Physiological effects of plant hormones in cotton under drought

Effects of plant hormones indole-3-yl-acetic acid (IAA), gibberellic acid (GA), benzylaminopurine (BAP), abscisic acid (ABA) and ethrel (ETH) in 5 μM concentration on gas exchange, ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBPCO, EC 4.1.1.39) activity, pigment content and yield in cotton (Gossypium hirsutum L. cv. H-777) under drought were studied. At reproductive stage (55 – 60 d after sowing) these hormones were sprayed on shoots one day prior to stress imposition by withholding irrigation. The soil moisture of control plants was kept at field capacity. Net photosynthetic rate (PN), stomatal conductance (gs), transpiration rate (E), carboxylation efficiency (CE), water use efficiency (WUE), RuBPCO activity, boll number per plant, seed number per plant and lint mass per plant significantly decreased at drought while chlorophyll (Chl) b content and flower number per plant increased. ABA and ETH significantly reduced gas exchange parameters, Chl a and Chl b content. Detrimental drought effect on PN, gs, E, CE, RuBPCO and lint mass per plant was significantly alleviated by BAP and also its effect on seed number and lint mass per plant was significantly alleviated with the ABA treatment.

Hormonal Regulation of Photosynthetic Enzymes in Cotton under Water Stress

Activities of ribulose bisphosphate carboxylase/oxygenase (RuBPCO), phosphoenolpyruvate carboxylase (PEPC), and carbonic anhydrase (CA) were determined in leaves of cotton (Gossypium hirsutum L. cv. H-777) subjected to 8-d waterlogging (WL) at the vegetative stage, or to drought (D) at the reproductive stage, or to interaction of both stresses. The soil moisture of control plants was kept at field capacity. One day prior to stress various growth hormones (5 μM) were sprayed up to runoff. WL reduced RuBPCO and CA activities, while PEPC activity increased. Upon D, RuBPCO and PEPC activities were reduced while CA activity was increased. Imposition of both stresses increased activities of all three enzymes. Effect of stresses on enzyme activity was alleviated by benzylaminopurine (BAP), but indol-3-yl-acetic acid was more promoting under interactive stress. No CA activity with BAP was observed during interactive stress.

Identification of miRNAs in sorghum by using bioinformatics approach

MicroRNAs (miRNAs) regulate gene expression mainly by post-transcriptional gene silencing (PTGS) and in some cases by transcriptional genes silencing (TGS). miRNAs play critical roles in developmental processes, nutrient homeostasis, abiotic stress and pathogen responses of plants. In contrast to the large number of miRNAs predicted in cereal model plant rice, only 148 miRNAs were predicted in sorghum till date (miRBase release 17). This suggested that miRNAs identified in sorghum is far from saturation. Hence, we developed a bioinformatics pipeline using an in-house PERL script and publicly available structure prediction tools to identify miRNAs and their target genes from publically available Expressed Sequence Tags (EST) and Genomic Survey Sequence (GSS). About 1,379 known and unique plant miRNAs from 33 different crops were used to predict new miRNAs in sorghum. We identified 31 new miRNAs belonging to 10 different miRNA families. We predicted 72 potential target genes for 31 miRNAs, and most of these target genes are predicted to be involved in plant growth and development. These newly identified miRNAs add to the growing database of miRNA and lay the foundation for further understanding of miRNA function in sorghum plant development.

Transcriptional Regulatory Network Analysis of MYB Transcription Factor Family Genes in Rice.

MYB transcription factor (TF) is one of the largest TF families and regulates defense responses to various stresses, hormone signaling as well as many metabolic and developmental processes in plants. Understanding these regulatory hierarchies of gene expression networks in response to developmental and environmental cues is a major challenge due to the complex interactions between the genetic elements. Correlation analyses are useful to unravel co-regulated gene pairs governing biological process as well as identification of new candidate hub genes in response to these complex processes. High throughput expression profiling data are highly useful for construction of co-expression networks. In the present study, we utilized transcriptome data for comprehensive regulatory network studies of MYB TFs by “top-down” and “guide-gene” approaches. More than 50% of OsMYBs were strongly correlated under 50 experimental conditions with 51 hub genes via “top-down” approach. Further, clusters were identified using Markov Clustering (MCL). To maximize the clustering performance, parameter evaluation of the MCL inflation score (I) was performed in terms of enriched GO categories by measuring F-score. Comparison of co-expressed cluster and clads analyzed from phylogenetic analysis signifies their evolutionarily conserved co-regulatory role. We utilized compendium of known interaction and biological role with Gene Ontology enrichment analysis to hypothesize function of coexpressed OsMYBs. In the other part, the transcriptional regulatory network analysis by “guide-gene” approach revealed 40 putative targets of 26 OsMYB TF hubs with high correlation value utilizing 815 microarray data. The putative targets with MYB-binding cis-elements enrichment in their promoter region, functional co-occurrence as well as nuclear localization supports our finding. Specially, enrichment of MYB binding regions involved in drought-inducibility implying their regulatory role in drought response in rice. Thus, the co-regulatory network analysis facilitated the identification of complex OsMYB regulatory networks, and candidate target regulon genes of selected guide MYB genes. The results contribute to the candidate gene screening, and experimentally testable hypotheses for potential regulatory MYB TFs, and their targets under stress conditions.

Identification of conserved drought stress responsive gene-network across tissues and developmental stages in rice

Identification of genes that are coexpressed across various tissues and environmental stresses is biologically interesting, since they may play coordinated role in similar biological processes. Genes with correlated expression patterns can be best identified by using coexpression network analysis of transcriptome data. In the present study, we analyzed the temporal-spatial coordination of gene expression in root, leaf and panicle of rice under drought stress and constructed network using WGCNA and Cytoscape. Total of 2199 differentially expressed genes (DEGs) were identified in at least three or more tissues, wherein 88 genes have coordinated expression profile among all the six tissues under drought stress. These 88 highly coordinated genes were further subjected to module identification in the coexpression network. Based on chief topological properties we identified 18 hub genes such as ABC transporter, ATP-binding protein, dehydrin, protein phosphatase 2C, LTPL153 - Protease inhibitor, phosphatidylethanolaminebinding protein, lactose permease-related, NADP-dependent malic enzyme, etc. Motif enrichment analysis showed the presence of ABRE cis-elements in the promoters of > 62% of the coordinately expressed genes. Our results suggest that drought stress mediated upregulated gene expression was coordinated through an ABA-dependent signaling pathway across tissues, at least for the subset of genes identified in this study, while down regulation appears to be regulated by tissue specific pathways in rice.

Stress-induced degradation of D1 protein and its photoprotection by DCPIP in isolated thylakoid membranes of barley leaf

Effects of various stress treatments such as NaCl, hydrogen peroxide, hydroxyl free radical, and high irradiance (HI, 1 000 µmol m−2 s−1) on the photosystem (PS) 2 mediated electron transport rate and the degradation of D1 protein in the thylakoid membranes of barley were studied. The applied stresses caused significant reduction in the PS 2-mediated electron transport and a degradation of D1 protein that was highest during the HI-treatment. Presence of 2,6-dichlorophenol indophenol (DCPIP), which is an artificial electron acceptor from water, significantly minimizes the HI-induced deleterious effect on the PS 2-mediated electron transport rate, disarrangement of PS machinery, and degradation of the D1 protein. HI in the absence of an acceptor resulted in production of reactive oxygen species due to electron transfer to oxygen.

Identification and annotation of abiotic stress responsive candidate genes in peanut ESTs.

Peanut (Arachis hypogaea L.) ranks fifth among the world oil crops and is widely grown in India and neighbouring countries. Due to its large and unknown genome size, studies on genomics and genetic modification of peanut are still scanty as compared to other model crops like Arabidopsis, rice, cotton and soybean. Because of its favourable cultivation in semi-arid regions, study on abiotic stress responsive genes and its regulation in peanut is very much important. Therefore, we aim to identify and annotate the abiotic stress responsive candidate genes in peanut ESTs. Expression data of drought stress responsive corresponding genes and EST sequences were screened from dot blot experiments shown as heat maps and supplementary tables, respectively as reported by Govind et al. (2009). Some of the screened genes having no information about their ESTs in above mentioned supplementary tables were retrieved from NCBI. A phylogenetic analysis was performed to find a group of utmost similar ESTs for each selected gene. Individual EST of the said group were further searched in peanut ESTs (1,78,490 whole EST sequences) using stand alone BLAST. For the prediction as well as annotation of abiotic stress responsive selected genes, various tools (like Vec-Screen, Repeat Masker, EST-Trimmer, DNA Baser, WISE2 and I-TASSER) were used. Here we report the predicted result of Contigs, domain as well as 3D structure for HSP 17.3KDa protein, DnaJ protein and Type 2 Metallothionein protein.

Dynamic changes of photosynthetic pigments in soybean callus under high irradiance

Dynamic changes of neoxanthin (NEO), violaxanthin (VIO), anteraxanthin (ANT), zeaxanthin (ZEA), chlorophyll (Chl) a, Chl b, α-carotene, β-carotene, and their behaviour under increasing duration of high irradiance (HI) were investigated in the soybean hypocotyl callus culture. The calli were induced on solid (1.1 % agar) MS medium (pH 5.8) supplemented with 4.52 μM 2,4-D, 2.32 μM kinetin, and 3 % sucrose. After 30 d of culture, the green calli were irradiated with “white light” (133W m−2) for 0, 3.5, and 24 h. HPLC profiles were separated on a C18 column. With increasing duration of HI, the content of total carotenoids (Cars) increased, but the ratio of Chl a+b/Cars decreased. With lengthening the duration of HI, there was induction of ZEA. Contents of ANT, α-carotene, and β-carotene remained nearly constant, but ratio of ZEA/Chl a+b increased with lengthening the HI duration.