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Erratic rainfall leading to flash flooding causes huge yield losses in lowland rice. The traditional varieties and landraces of rice possess variable levels of tolerance to submergence stress, but gene discovery and utilization of these resources has been limited to the Sub1A-1 allele from variety FR13A. Therefore, we analysed the allelic sequence variation in three Sub1 genes in a panel of 179 rice genotypes and its association with submergence tolerance. Population structure and diversity analysis based on a 36-plex genome wide genic-SNP assay grouped these genotypes into two major categories representing Indica and Japonica cultivar groups with further sub-groupings into Indica, Aus, Deepwater and Aromatic-Japonica cultivars. Targetted re-sequencing of the Sub1A, Sub1B and Sub1C genes identfied 7, 7 and 38 SNPs making 8, 9 and 67 SNP haplotypes, respectively. Haplotype networks and phylogenic analysis revealed evolution of Sub1B and Sub1A genes by tandem duplication and divergence of the ancestral Sub1C gene in that order. The alleles of Sub1 genes in tolerant reference variety FR13A seem to have evolved most recently. However, no consistent association could be found between the Sub1 allelic variation and submergence tolerance probably due to low minor allele frequencies and presence of exceptions to the known Sub1A-1 association in the genotype panel. We identified 18 cultivars with non-Sub1A-1 source of submergence tolerance which after further mapping and validation in bi-parental populations will be useful for development of superior flood tolerant rice cultivars.
Anuradha Singh; Yashi Singh; Ajay K. Mahato; Pawan K. Jayaswal; Sangeeta Singh; Renu Singh; Neera Yadav; Rakesh Singh; Rajesh Kumar; Endang M. Septiningsih; H. S. Balyan; Nagendra K. Singh; Vandna Rai. Allelic sequence variation in the Sub1A, Sub1B and Sub1C genes among diverse rice cultivars and its association with submergence tolerance. Scientific Reports 2020, 10, 1 -18.
AMA StyleAnuradha Singh, Yashi Singh, Ajay K. Mahato, Pawan K. Jayaswal, Sangeeta Singh, Renu Singh, Neera Yadav, Rakesh Singh, Rajesh Kumar, Endang M. Septiningsih, H. S. Balyan, Nagendra K. Singh, Vandna Rai. Allelic sequence variation in the Sub1A, Sub1B and Sub1C genes among diverse rice cultivars and its association with submergence tolerance. Scientific Reports. 2020; 10 (1):1-18.
Chicago/Turabian StyleAnuradha Singh; Yashi Singh; Ajay K. Mahato; Pawan K. Jayaswal; Sangeeta Singh; Renu Singh; Neera Yadav; Rakesh Singh; Rajesh Kumar; Endang M. Septiningsih; H. S. Balyan; Nagendra K. Singh; Vandna Rai. 2020. "Allelic sequence variation in the Sub1A, Sub1B and Sub1C genes among diverse rice cultivars and its association with submergence tolerance." Scientific Reports 10, no. 1: 1-18.
Pigeonpea is the second most important pulse legume crop for food and nutritional security of South Asia that requires accelerated breeding using high throughput genomic tools. Single nucleotide polymorphisms (SNPs) are highly suitable markers for this purpose because of their bi-allelic nature, reproducibility and high abundance in the genome. Here we report on development and use of a pigeonpea 62 K SNP chip array ‘CcSNPnks’ for Affymetrix GeneTitan® platform. The array was designed after filtering 645,662 genic-SNPs identified by re-sequencing of 45 diverse genotypes and has 62,053 SNPs from 9629 genes belonging to five different categories, including 4314 single-copy genes unique to pigeonpea, 4328 single-copy genes conserved between soybean and pigeonpea, 156 homologs of agronomically important cloned genes, 746 disease resistance and defense response genes and 85 multi-copy genes of pigeonpea. This fully genic chip has 28.94% exonic, 33.04% intronic, 27.56% 5′UTR and 10.46% 3′UTR SNPs and incorporates multiple SNPs per gene allowing gene haplotype network analysis. It was used successfully for the analysis of genetic diversity and population structure of 95 pigeonpea varieties and high resolution mapping of 11 yield related QTLs for number of branches, pod bearing length and number of seeds per pod in a biparental RIL population. As an accurate high-density genotyping tool, ‘CcSNPnks’ chip array will be useful for high resolution fingerprinting, QTL mapping and genome wide as well as gene-based association studies in pigeonpea.
Sangeeta Singh; Ajay K. Mahato; Pawan K. Jayaswal; Nisha Singh; Meenakshi Dheer; Preeti Goel; Ranjeet S. Raje; Jeshima K. Yasin; Rohini Sreevathsa; Vandna Rai; Kishor Gaikwad; Nagendra K. Singh. A 62K genic-SNP chip array for genetic studies and breeding applications in pigeonpea (Cajanus cajan L. Millsp.). Scientific Reports 2020, 10, 4960 -14.
AMA StyleSangeeta Singh, Ajay K. Mahato, Pawan K. Jayaswal, Nisha Singh, Meenakshi Dheer, Preeti Goel, Ranjeet S. Raje, Jeshima K. Yasin, Rohini Sreevathsa, Vandna Rai, Kishor Gaikwad, Nagendra K. Singh. A 62K genic-SNP chip array for genetic studies and breeding applications in pigeonpea (Cajanus cajan L. Millsp.). Scientific Reports. 2020; 10 (1):4960-14.
Chicago/Turabian StyleSangeeta Singh; Ajay K. Mahato; Pawan K. Jayaswal; Nisha Singh; Meenakshi Dheer; Preeti Goel; Ranjeet S. Raje; Jeshima K. Yasin; Rohini Sreevathsa; Vandna Rai; Kishor Gaikwad; Nagendra K. Singh. 2020. "A 62K genic-SNP chip array for genetic studies and breeding applications in pigeonpea (Cajanus cajan L. Millsp.)." Scientific Reports 10, no. 1: 4960-14.
Jain Ajay; Rai Vandna. CRISPR-Cas systems ushered in an era of facile DNA-free genome editing. Seminars in Cell & Developmental Biology 2019, 96, 1 -3.
AMA StyleJain Ajay, Rai Vandna. CRISPR-Cas systems ushered in an era of facile DNA-free genome editing. Seminars in Cell & Developmental Biology. 2019; 96 ():1-3.
Chicago/Turabian StyleJain Ajay; Rai Vandna. 2019. "CRISPR-Cas systems ushered in an era of facile DNA-free genome editing." Seminars in Cell & Developmental Biology 96, no. : 1-3.
Crop productivity in rice is harshly limited due to high concentration of salt in the soil. To understand the intricacies of the mechanism it is important to unravel the key pathways operating inside the plant cell. Emerging state-of-the art technologies have provided the tools to discover the key components inside the plant cell for salt tolerance. Among the molecular entities, transcription factors and/or other important components of sensing and signaling cascades have been the attractive targets and the role of NHX and SOS1 transporters amply described. Not only marker assisted programs but also transgenic approaches by using reverse genetic strategies (knockout or knockdown) or overexpression have been extensively used to engineer rice crop. CRISPR/Cas is an attractive paradigm and provides the feasibility for manipulating several genes simultaneously. Here, in this review we highlight some of the molecular entities that could be potentially targeted for generating rice amenable to sustain growth under high salinity conditions by employing CRISPR/Cas. We also try to address key questions for rice salt stress tolerance other than what is already known.
Sufia Farhat; Neha Jain; Nisha Singh; Rohini Sreevathsa; Prasanta K. Dash; Rhitu Rai; Sandeep Yadav; Pramod Kumar; Ananda K. Sarkar; Ajay Jain; Nagendra K Singh; Vandna Rai. CRISPR-Cas9 directed genome engineering for enhancing salt stress tolerance in rice. Seminars in Cell & Developmental Biology 2019, 96, 91 -99.
AMA StyleSufia Farhat, Neha Jain, Nisha Singh, Rohini Sreevathsa, Prasanta K. Dash, Rhitu Rai, Sandeep Yadav, Pramod Kumar, Ananda K. Sarkar, Ajay Jain, Nagendra K Singh, Vandna Rai. CRISPR-Cas9 directed genome engineering for enhancing salt stress tolerance in rice. Seminars in Cell & Developmental Biology. 2019; 96 ():91-99.
Chicago/Turabian StyleSufia Farhat; Neha Jain; Nisha Singh; Rohini Sreevathsa; Prasanta K. Dash; Rhitu Rai; Sandeep Yadav; Pramod Kumar; Ananda K. Sarkar; Ajay Jain; Nagendra K Singh; Vandna Rai. 2019. "CRISPR-Cas9 directed genome engineering for enhancing salt stress tolerance in rice." Seminars in Cell & Developmental Biology 96, no. : 91-99.
Among abiotic stresses, salt stress adversely affects growth and development in rice. Contrasting salt tolerant (CSR27), and salt sensitive (MI48) rice varieties provided information on an array of genes that may contribute for salt tolerance of rice. Earlier studies on transcriptome and proteome profiling led to the identification of salt stress-induced serine hydroxymethyltransferase-3 (SHMT3) gene. In the present study, the SHMT3 gene was isolated from salt-tolerant (CSR27) rice. OsSHMT3 exhibited salinity-stress induced accentuated and differential expression levels in different tissues of rice. OsSHMT3 was overexpressed in Escherichia coli and assayed for enzymatic activity and modeling protein structure. Further, Arabidopsis transgenic plants overexpressing OsSHMT3 exhibited tolerance toward salt stress. Comparative analyses of OsSHMT3 vis a vis wild type by ionomic, transcriptomic, and metabolic profiling, protein expression and analysis of various traits revealed a pivotal role of OsSHMT3 in conferring tolerance toward salt stress. The gene can further be used in developing gene-based markers for salt stress to be employed in marker assisted breeding programs. HIGHLIGHTS - The study provides information on mechanistic details of serine hydroxymethyl transferase gene for its salt tolerance in rice.
Pragya Mishra; Ajay Jain; Teruhiro Takabe; Yoshito Tanaka; Manisha Negi; Nisha Singh; Neha Jain; Vagish Mishra; R. Maniraj; S. L. Krishnamurthy; Rohini Sreevathsa; Nagendra K. Singh; Vandna Rai. Heterologous Expression of Serine Hydroxymethyltransferase-3 From Rice Confers Tolerance to Salinity Stress in E. coli and Arabidopsis. Frontiers in Plant Science 2019, 10, 1 .
AMA StylePragya Mishra, Ajay Jain, Teruhiro Takabe, Yoshito Tanaka, Manisha Negi, Nisha Singh, Neha Jain, Vagish Mishra, R. Maniraj, S. L. Krishnamurthy, Rohini Sreevathsa, Nagendra K. Singh, Vandna Rai. Heterologous Expression of Serine Hydroxymethyltransferase-3 From Rice Confers Tolerance to Salinity Stress in E. coli and Arabidopsis. Frontiers in Plant Science. 2019; 10 ():1.
Chicago/Turabian StylePragya Mishra; Ajay Jain; Teruhiro Takabe; Yoshito Tanaka; Manisha Negi; Nisha Singh; Neha Jain; Vagish Mishra; R. Maniraj; S. L. Krishnamurthy; Rohini Sreevathsa; Nagendra K. Singh; Vandna Rai. 2019. "Heterologous Expression of Serine Hydroxymethyltransferase-3 From Rice Confers Tolerance to Salinity Stress in E. coli and Arabidopsis." Frontiers in Plant Science 10, no. : 1.
Bacillus thuringiensis insecticidal proteins (Bt ICPs) are reliable and valuable options for pest management in crops. Protein engineering of Bt ICPs is a competitive alternative for resistance management in insects. The primary focus of the study was to reiterate the translational utility of a protein-engineered chimeric Cry toxin, Cry1AcF, for its broad spectrum insecticidal efficacy using molecular modeling and docking studies. In-depth bioinformatic analysis was undertaken for structure prediction of the Cry toxin as the ligand and aminopeptidase1 receptors (APN1) from Helicoverpa armigera (HaAPN1) and Spodoptera litura (SlAPN1) as receptors, followed by interaction studies using protein-protein docking tools. The study revealed feasible interactions between the toxin and the two receptors through H-bonding and hydrophobic interactions. Further, molecular dynamics simulations substantiated the stability of the interactions, proving the broad spectrum efficacy of Cry1AcF in controlling H. armigera and S. litura. These findings justify the utility of protein-engineered toxins in pest management.
Maniraj Rathinam; Karthik Kesiraju; Shweta Singh; Vinutha Thimmegowda; Vandna Rai; Debasis Pattanayak; Rohini Sreevathsa. Molecular Interaction-Based Exploration of the Broad Spectrum Efficacy of a Bacillus thuringiensis Insecticidal Chimeric Protein, Cry1AcF. Toxins 2019, 11, 143 .
AMA StyleManiraj Rathinam, Karthik Kesiraju, Shweta Singh, Vinutha Thimmegowda, Vandna Rai, Debasis Pattanayak, Rohini Sreevathsa. Molecular Interaction-Based Exploration of the Broad Spectrum Efficacy of a Bacillus thuringiensis Insecticidal Chimeric Protein, Cry1AcF. Toxins. 2019; 11 (3):143.
Chicago/Turabian StyleManiraj Rathinam; Karthik Kesiraju; Shweta Singh; Vinutha Thimmegowda; Vandna Rai; Debasis Pattanayak; Rohini Sreevathsa. 2019. "Molecular Interaction-Based Exploration of the Broad Spectrum Efficacy of a Bacillus thuringiensis Insecticidal Chimeric Protein, Cry1AcF." Toxins 11, no. 3: 143.
In earlier studies at IIRR, Hyderabad, screening of ∼2000 EMS mutants of the rice variety Nagina22 (N22) resulted in the identification of 11 loss-of-function mutants with zero grain yield in Pi-deprived soil under field condition. Among these mutants, NH101 was selected for comparative analyses with N22 for various morphophysiological and/or molecular traits during growth in a hydroponic system (7 d) and in a pot soil (50% flowering) under different Pi regime. The total length of the seminal and adventitious roots, agronomic traits (panicle length and unfilled spikelet/panicle), activities of the antioxidant enzymes (SOD, POD, and APX), and the relative expression levels of the genes involved in the maintenance of Pi homeostasis (MPH) i.e., OsPHR2, SPX1/2 OsPT4, 6, and 8 showed significant increase in the Pi-deprived mutant compared with N22. Whereas, some of the traits showed significant reduction in NH101 than N22 such as number of tillers and filled spikelets/panicle, yield, contents of Pi and externally secreted APase, activity of CAT, and the relative expression levels of MPH genes i.e., OsmiR399a, OsPHO1;2, OsIPS1, OsPAP10a, OsPT2, 9, and 10. The study highlighted wide spectrum differential effects of the mutation in NH101 on various traits that play important roles governing the maintenance of Pi homeostasis. This mutant thus provides a rich repository of genetic material amenable for the identification of the genes that are pivotal for Pi use efficiency.
Poli Yugandhar; Yafei Sun; Lu Liu; Manisha Negi; Veronica Nallamothu; Shubin Sun; Sarla Neelamraju; Vandna Rai; Ajay Jain. Characterization of the loss-of-function mutant NH101 for yield under phosphate deficiency from EMS-induced mutants of rice variety Nagina22. Plant Physiology and Biochemistry 2018, 130, 1 -13.
AMA StylePoli Yugandhar, Yafei Sun, Lu Liu, Manisha Negi, Veronica Nallamothu, Shubin Sun, Sarla Neelamraju, Vandna Rai, Ajay Jain. Characterization of the loss-of-function mutant NH101 for yield under phosphate deficiency from EMS-induced mutants of rice variety Nagina22. Plant Physiology and Biochemistry. 2018; 130 ():1-13.
Chicago/Turabian StylePoli Yugandhar; Yafei Sun; Lu Liu; Manisha Negi; Veronica Nallamothu; Shubin Sun; Sarla Neelamraju; Vandna Rai; Ajay Jain. 2018. "Characterization of the loss-of-function mutant NH101 for yield under phosphate deficiency from EMS-induced mutants of rice variety Nagina22." Plant Physiology and Biochemistry 130, no. : 1-13.
Rice, a staple food crop, is often subjected to drought and salinity stresses thereby limiting its yield potential. Since there is a cross talk between these abiotic stresses, identification of common and/or overlapping regulatory elements is pivotal for generating rice cultivars that showed tolerance towards them. Analysis of the gene interaction network (GIN) facilitates identifying the role of individual genes and their interactions with others that constitute important molecular determinants in sensing and signaling cascade governing drought and/or salinity stresses. Identification of the various cis-regulatory elements of the genes constituting GIN is equally important. Here, in this study graphical Gaussian model (GGM) was used for generating GIN for an array of genes that were differentially regulated during salinity and/or drought stresses to contrasting rice cultivars (salt-tolerant [CSR11], salt-sensitive [VSR156], drought-tolerant [Vandana], drought-sensitive [IR64]). Whole genome transcriptom profiling by using microarray were employed in this study. Markov Chain completed co-expression analyses of differentially expressed genes using Dynamic Bayesian Network, Probabilistic Boolean Network and Steady State Analysis. A compact GIN was identified for commonly co-expressed genes during salinity and drought stresses with three major hubs constituted by Myb2 transcription factor (TF), phosphoglycerate kinase and heat shock protein (Hsp). The analysis suggested a pivotal role of these genes in salinity and/or drought stress responses. Further, analysis of cis-regulatory elements (CREs) of commonly differentially expressed genes during salinity and drought stresses revealed the presence of 20 different motifs.
Pragya Mishra; Nisha Singh; Ajay Jain; Neha Jain; Vagish Mishra; Pushplatha G; Kiran P. Sandhya; Nagendra Kumar Singh; Vandna Rai; Hyderabad Ocimum Biosolutions. Identification of cis-regulatory elements associated with salinity and drought stress tolerance in rice from co-expressed gene interaction networks. Bioinformation 2018, 14, 123 -131.
AMA StylePragya Mishra, Nisha Singh, Ajay Jain, Neha Jain, Vagish Mishra, Pushplatha G, Kiran P. Sandhya, Nagendra Kumar Singh, Vandna Rai, Hyderabad Ocimum Biosolutions. Identification of cis-regulatory elements associated with salinity and drought stress tolerance in rice from co-expressed gene interaction networks. Bioinformation. 2018; 14 (3):123-131.
Chicago/Turabian StylePragya Mishra; Nisha Singh; Ajay Jain; Neha Jain; Vagish Mishra; Pushplatha G; Kiran P. Sandhya; Nagendra Kumar Singh; Vandna Rai; Hyderabad Ocimum Biosolutions. 2018. "Identification of cis-regulatory elements associated with salinity and drought stress tolerance in rice from co-expressed gene interaction networks." Bioinformation 14, no. 3: 123-131.
Anuradha Singh; Vandna Rai; Endang Septiningsih; Harendra S. Balyan. Genetics, Physiological Mechanisms and Breeding of Flood-Tolerant Rice ( Oryza sativa L.). Plant and Cell Physiology 2017, 1 .
AMA StyleAnuradha Singh, Vandna Rai, Endang Septiningsih, Harendra S. Balyan. Genetics, Physiological Mechanisms and Breeding of Flood-Tolerant Rice ( Oryza sativa L.). Plant and Cell Physiology. 2017; ():1.
Chicago/Turabian StyleAnuradha Singh; Vandna Rai; Endang Septiningsih; Harendra S. Balyan. 2017. "Genetics, Physiological Mechanisms and Breeding of Flood-Tolerant Rice ( Oryza sativa L.)." Plant and Cell Physiology , no. : 1.
Soil salinity is one of the major constraints limiting productivity of crop plants. In present study, effect of NaCl (150mM) on high-affinity potassium transporters (HKTs) were investigated into four contrasting rice genotypes salttolerant (CSR11, CSR27) and salt-sensitive (MI48 and VSR156). Salinity stress significantly reduced growth of VSR156 and MI48 whereas, only slight reduction was observed in CSR11 and CSR27. Under NaCl stress, OsHKTs group I transcripts were significantly up-regulated in saltsensitive varieties in comparison with salt-tolerant. However, OsHKTs group II showed higher expression in salt-tolerant one in comparison with sat-sensitive. These results suggested the differential expression of OsHKT group I and II genes and hence, their differential behavior in response to salt stress. Our study, elucidate the role of seven OsHKT genes in shoot and root for salt tolerance in rice plant. Top
Pragya Mishra; Vagish Mishra; Nagendra Kumar Singh; Vandna Rai. Gene expression dynamics of HKT family genes in salt-tolerant and salt-sensitive indica rice cultivars. Indian Journal of Genetics and Plant Breeding (The) 2017, 77, 364 .
AMA StylePragya Mishra, Vagish Mishra, Nagendra Kumar Singh, Vandna Rai. Gene expression dynamics of HKT family genes in salt-tolerant and salt-sensitive indica rice cultivars. Indian Journal of Genetics and Plant Breeding (The). 2017; 77 (3):364.
Chicago/Turabian StylePragya Mishra; Vagish Mishra; Nagendra Kumar Singh; Vandna Rai. 2017. "Gene expression dynamics of HKT family genes in salt-tolerant and salt-sensitive indica rice cultivars." Indian Journal of Genetics and Plant Breeding (The) 77, no. 3: 364.
Soil salinity is a major constraint to rice production in large inland and coastal areas around the world. Modern high yielding rice varieties are particularly sensitive to high salt stress. There are salt tolerant landraces and traditional varieties of rice but with limited information on genomic regions (QTLs) and genes responsible for their tolerance. Here we describe a method for rapid identification of QTLs for reproductive stage salt tolerance in rice using bulked segregant analysis (BSA) of bi-parental recombinant inbred lines (RIL). The number of RILs required for the creation of two bulks with extreme phenotypes was optimized to be thirty each. The parents and bulks were genotyped using a 50K SNP chip to identify genomic regions showing homogeneity for contrasting alleles of polymorphic SNPs in the two bulks. The method was applied to ‘CSR11/MI48’ RILs segregating for reproductive stage salt tolerance. Genotyping of the parents and RIL bulks, made on the basis of salt sensitivity index for grain yield, revealed 6,068 polymorphic SNPs and 21 QTL regions showing homogeneity of contrasting alleles in the two bulks. The method was validated further with ‘CSR27/MI48’ RILs used earlier for mapping salt tolerance QTLs using low-density SSR markers. BSA with 50K SNP chip revealed 5,021 polymorphic loci and 34 QTL regions. This not only confirmed the location of previously mapped QTLs but also identified several new QTLs, and provided a rapid way to scan the whole genome for mapping QTLs for complex agronomic traits in rice.
Sushma Tiwari; Krishnamurthy Sl; Vinod Kumar; Balwant Singh; Atmakuri Ramakrishna Rao; Amitha Mithra Sv; Vandna Rai; Ashok Kumar Singh; Nagendra K. Singh. Mapping QTLs for Salt Tolerance in Rice (Oryza sativa L.) by Bulked Segregant Analysis of Recombinant Inbred Lines Using 50K SNP Chip. PLOS ONE 2016, 11, e0153610 -e0153610.
AMA StyleSushma Tiwari, Krishnamurthy Sl, Vinod Kumar, Balwant Singh, Atmakuri Ramakrishna Rao, Amitha Mithra Sv, Vandna Rai, Ashok Kumar Singh, Nagendra K. Singh. Mapping QTLs for Salt Tolerance in Rice (Oryza sativa L.) by Bulked Segregant Analysis of Recombinant Inbred Lines Using 50K SNP Chip. PLOS ONE. 2016; 11 (4):e0153610-e0153610.
Chicago/Turabian StyleSushma Tiwari; Krishnamurthy Sl; Vinod Kumar; Balwant Singh; Atmakuri Ramakrishna Rao; Amitha Mithra Sv; Vandna Rai; Ashok Kumar Singh; Nagendra K. Singh. 2016. "Mapping QTLs for Salt Tolerance in Rice (Oryza sativa L.) by Bulked Segregant Analysis of Recombinant Inbred Lines Using 50K SNP Chip." PLOS ONE 11, no. 4: e0153610-e0153610.
Differentially expressed antioxidant enzymes, amino acids and proteins in contrasting rice genotypes, and co-location of their genes in the QTLs mapped using bi-parental population, indicated their role in salt tolerance. Soil salinity is a major environmental constraint limiting rice productivity. Salt-tolerant 'CSR27', salt-sensitive 'MI48'and their extreme tolerant and sensitive recombinant inbred line (RIL) progenies were used for the elucidation of salt stress tolerance metabolic pathways. Salt stress-mediated biochemical and molecular changes were analyzed in the two parents along with bulked-tolerant (BT) and bulked-sensitive (BS) extreme RILs. The tolerant parent and BT RILs suffered much lower reduction in the chlorophyll as compared to their sensitive counterparts. Activities of antioxidant enzymes superoxide dismutase (SOD) and peroxidase (POD) and non-enzymatic antioxidant ascorbic acid were much higher in salt-stressed CSR27 and BT RILs than MI48 and BS RILs. Further, the tolerant lines showed significant enhancement in the levels of amino acids methionine and proline in response to salt stress in comparison to the sensitive lines. Similarly, the tolerant genotypes showed minimal reduction in cysteine content whereas sensitive genotypes showed a sharp reduction. Real time PCR analysis confirmed the induction of methionine biosynthetic pathway (MBP) enzymes cystathionine-β synthase (CbS), S-adenosyl methionine synthase (SAMS), S-adenosyl methionine decarboxylase (SAMDC) and serine hydroxymethyl transferase (SHMT) genes in tolerant lines, suggesting potential role of the MBP in conferring salt tolerance in rice variety CSR27. Proteome profiling also confirmed higher expression of SOD, POD and plastidic CbS and other proteins in the tolerant lines, whose genes were co-located in the QTL intervals for salt tolerance mapped in the RIL population. The study signifies integrated biochemical-molecular approach for identifying salt tolerance genes for genetic improvement for stress tolerant rice varieties.
Pragya Mishra; Vagish Mishra; Teruhiro Takabe; Vandna Rai; Nagendra Kumar Singh. Elucidation of salt-tolerance metabolic pathways in contrasting rice genotypes and their segregating progenies. Plant Cell Reports 2016, 35, 1273 -1286.
AMA StylePragya Mishra, Vagish Mishra, Teruhiro Takabe, Vandna Rai, Nagendra Kumar Singh. Elucidation of salt-tolerance metabolic pathways in contrasting rice genotypes and their segregating progenies. Plant Cell Reports. 2016; 35 (6):1273-1286.
Chicago/Turabian StylePragya Mishra; Vagish Mishra; Teruhiro Takabe; Vandna Rai; Nagendra Kumar Singh. 2016. "Elucidation of salt-tolerance metabolic pathways in contrasting rice genotypes and their segregating progenies." Plant Cell Reports 35, no. 6: 1273-1286.
Nagendra Kumar Singh; Balwant Singh; Shefali Mishra; Nisha Singh; Kabita Panda; Vandna Rai. Indian Wild Rice: Diversity, Population Structure, Trait Value and Relation with Cultivated Rice. Indian Journal of Plant Genetic Resources 2016, 29, 366 .
AMA StyleNagendra Kumar Singh, Balwant Singh, Shefali Mishra, Nisha Singh, Kabita Panda, Vandna Rai. Indian Wild Rice: Diversity, Population Structure, Trait Value and Relation with Cultivated Rice. Indian Journal of Plant Genetic Resources. 2016; 29 (3):366.
Chicago/Turabian StyleNagendra Kumar Singh; Balwant Singh; Shefali Mishra; Nisha Singh; Kabita Panda; Vandna Rai. 2016. "Indian Wild Rice: Diversity, Population Structure, Trait Value and Relation with Cultivated Rice." Indian Journal of Plant Genetic Resources 29, no. 3: 366.
A halotolerant cyanobacterium Aphanothece halophytica thrives in extreme salinity with accumulation of a potent osmoprotectant glycine betaine. Recently, this cyanobacterium was shown to accumulate sunscreen molecule mycosporine-2-glycine significantly at high salinity. In this study, we investigated effects of nitrate and amino acid provision on the accumulation of glycine betaine and mycosporine-2-glycine. With elevated nitrate concentrations at high salinity, intracellular levels of both metabolites were enhanced. Six-fold high nitrate concentration increased the relative amounts of glycine betaine and mycosporine-2-glycine to be 1.5 and 2.0 folds compared with control condition. Increased levels were time- and dose-dependent manner. Exogenous supply of glycine/serine at high salinity resulted in the similar trends as observed in excess nitrate experiment. Intracellular level of glycine betaine increased ∼1.6 folds with glycine/serine supplementation. These supplementations also caused the increased level of mycosporine-2-glycine, namely 1.4 and 2 folds by glycine and serine, respectively. The transcription of glycine betaine and mycosporine-2-glycine biosynthetic genes was strongly induced under high-nitrate-salt condition. These results suggest the dependence of glycine betaine and mycosporine-2-glycine productions on substrate availability, and the effect of nitrate was possibly associated with stimulation of osmoprotectant increment in this extremophile.
Rungaroon Waditee-Sirisattha; Hakuto Kageyama; Minoru Fukaya; Vandna Rai; Teruhiro Takabe. Nitrate and amino acid availability affects glycine betaine and mycosporine-2-glycine in response to changes of salinity in a halotolerant cyanobacterium Aphanothece halophytica. FEMS Microbiology Letters 2015, 362, fnv198 .
AMA StyleRungaroon Waditee-Sirisattha, Hakuto Kageyama, Minoru Fukaya, Vandna Rai, Teruhiro Takabe. Nitrate and amino acid availability affects glycine betaine and mycosporine-2-glycine in response to changes of salinity in a halotolerant cyanobacterium Aphanothece halophytica. FEMS Microbiology Letters. 2015; 362 (23):fnv198.
Chicago/Turabian StyleRungaroon Waditee-Sirisattha; Hakuto Kageyama; Minoru Fukaya; Vandna Rai; Teruhiro Takabe. 2015. "Nitrate and amino acid availability affects glycine betaine and mycosporine-2-glycine in response to changes of salinity in a halotolerant cyanobacterium Aphanothece halophytica." FEMS Microbiology Letters 362, no. 23: fnv198.
Pigeonpea is an important legume crop with high protein content. However, it is often subjected to various abiotic and biotic stresses. Proteomics is a state-of-the-art technique used to analyze the protein profiling of a tissue for deciphering the molecular entities that could be manipulated for developing crops resistant to these stresses. In this context, developing a comprehensive proteome profile from different vegetative and reproductive tissues has become mandatory. Although several protein extraction protocols from different tissues of diverse plant species have been reported, there is no report for pigeonpea. Here, we report tissue-specific protein extraction protocols representing vegetative (young leaves), and reproductive (flowers and seeds) organs and their subsequent analysis on 2-dimensional gel electrophoresis. The study explicitly demonstrated that the efficacy of a particular protein extraction protocol is dependent on the different tissues, such as leaves, flowers and seeds that differ in their structure and metabolic constituents. For instance, phenol-based protocol showed an efficacy towards higher protein yield, better spot resolution and a minimal streaking on 2-DE gel for both leaves and flowers. Protein extraction from seeds was best achieved by employing phosphate-TCA-acetone protocol.
Nisha Singh; Neha Ejain; Ram Ekumar; Ajay Ejain; Nagendra Kumar Singh; Vandna Erai. A comparative method for protein extraction and 2-D gel electrophoresis from different tissues of Cajanus cajan. Frontiers in Plant Science 2015, 6, 606 .
AMA StyleNisha Singh, Neha Ejain, Ram Ekumar, Ajay Ejain, Nagendra Kumar Singh, Vandna Erai. A comparative method for protein extraction and 2-D gel electrophoresis from different tissues of Cajanus cajan. Frontiers in Plant Science. 2015; 6 ():606.
Chicago/Turabian StyleNisha Singh; Neha Ejain; Ram Ekumar; Ajay Ejain; Nagendra Kumar Singh; Vandna Erai. 2015. "A comparative method for protein extraction and 2-D gel electrophoresis from different tissues of Cajanus cajan." Frontiers in Plant Science 6, no. : 606.
Salinity induced physiological changes were investigated in two BC2F6–7 high yielding rice introgression lines (ILs) derived from advanced backcross populations of O. sativa (IR58025A/KMR3) × O. rufipogon. Plants were subjected to 150 mM NaCl treatment throughout the germination stage to early seedling stage for 10 days. The study revealed high root bleeding rate in K 198 under NaCl stress. The shoot length and dry weight reduction over control was drastic in K 198 under 150 mM NaCl treatment. Analysis of Na+ ion depicted ion exclusion mechanism in K 478 and high accumulation in K 198 when exposed to high concentration of NaCl. Significant differences were noticed in the activity of antioxidant enzymes amongst the introgression lines. Superoxide dismutase and ascorbate peroxidase activity increased in both introgression lines but the increase was more significant in K 478 under salinity (150 mM NaCl) condition. Catalase activity decreased under stress in both introgression lines. Activity of peroxidase increased in both ILs but K 478 showed significantly high activity. Our study on early seedling growth, accumulation of Na+ and activities of antioxidant enzymes indicated that the introgression line K 478 was considerably tolerant to salinity stress and this high yielding introgression line would further be used in developing salinity tolerant varieties.
G. Pushpalatha; D. Subrahmanyam; K. Sreenu; T. Ram; L. V. Subbarao; B. Parmar; Archana Giri; N. Sarla; Vandna Rai. Effect of salt stress on seedling growth and antioxidant enzymes in two contrasting rice introgression lines. Indian Journal of Plant Physiology 2013, 18, 360 -366.
AMA StyleG. Pushpalatha, D. Subrahmanyam, K. Sreenu, T. Ram, L. V. Subbarao, B. Parmar, Archana Giri, N. Sarla, Vandna Rai. Effect of salt stress on seedling growth and antioxidant enzymes in two contrasting rice introgression lines. Indian Journal of Plant Physiology. 2013; 18 (4):360-366.
Chicago/Turabian StyleG. Pushpalatha; D. Subrahmanyam; K. Sreenu; T. Ram; L. V. Subbarao; B. Parmar; Archana Giri; N. Sarla; Vandna Rai. 2013. "Effect of salt stress on seedling growth and antioxidant enzymes in two contrasting rice introgression lines." Indian Journal of Plant Physiology 18, no. 4: 360-366.
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Suresh Tula; Mohammad Wahid Ansari; A. Prasad Babu; G Pushpalatha; K Sreenu; N Sarla; Narendra Tuteja; Vandna Rai. Physiological Assessment and Allele Mining in Rice Cultivars for Salinity and Drought Stress Tolerance. Vegetos 2013, 26, 219 .
AMA StyleSuresh Tula, Mohammad Wahid Ansari, A. Prasad Babu, G Pushpalatha, K Sreenu, N Sarla, Narendra Tuteja, Vandna Rai. Physiological Assessment and Allele Mining in Rice Cultivars for Salinity and Drought Stress Tolerance. Vegetos. 2013; 26 (2s):219.
Chicago/Turabian StyleSuresh Tula; Mohammad Wahid Ansari; A. Prasad Babu; G Pushpalatha; K Sreenu; N Sarla; Narendra Tuteja; Vandna Rai. 2013. "Physiological Assessment and Allele Mining in Rice Cultivars for Salinity and Drought Stress Tolerance." Vegetos 26, no. 2s: 219.
Vandna Rai; Teruhiro Takabe. Transporters and Abiotic Stress Tolerance in Plants. Improving Crop Resistance to Abiotic Stress 2012, 507 -522.
AMA StyleVandna Rai, Teruhiro Takabe. Transporters and Abiotic Stress Tolerance in Plants. Improving Crop Resistance to Abiotic Stress. 2012; ():507-522.
Chicago/Turabian StyleVandna Rai; Teruhiro Takabe. 2012. "Transporters and Abiotic Stress Tolerance in Plants." Improving Crop Resistance to Abiotic Stress , no. : 507-522.
In plants, betaine is synthesized upon abiotic stress via choline oxidation, in which choline monooxygenase (CMO) is a key enzyme. Although it had been thought that betaine synthesis is well regulated to protect abiotic stress, it is shown here that an exogenous supply of precursors such as choline, serine, and glycine in the betaine-accumulating plant Amaranthus tricolor further enhances the accumulation of betaine under salt stress, but not under normal conditions. Addition of isonicotinic acid hydrazide, an inhibitor of glycine decarboxylase, inhibited the salinity-induced accumulation of betaine. Salt-induced accumulation of A. tricolor CMO (AmCMO) and betaine was much slower in roots than in leaves, and a transient accumulation of proline was observed in the roots. Antisense expression of AmCMO mRNA suppressed the salt-induced accumulation of AmCMO and betaine, but increased the level of choline ∼2– 3-fold. This indicates that betaine synthesis is highly regulated by AmCMO expression. The genomic DNA, including the upstream region (1.6 kbp), of AmCMO was isolated. Deletion analysis of the AmCMO promoter region revealed that the 410 bp fragment upstream of the translation start codon contains the sequence responsive to salt stress. These data reveal that the promoter sequence of CMO, in addition to precursor supply, is important for the accumulation of betaine in the betaine-accumulating plant A. tricolor.
Nazmul H. Bhuiyan; Akira Hamada; Nana Yamada; Vandna Rai; Takashi Hibino; Teruhiro Takabe. Regulation of betaine synthesis by precursor supply and choline monooxygenase expression in Amaranthus tricolor. Journal of Experimental Botany 2007, 58, 4203 -4212.
AMA StyleNazmul H. Bhuiyan, Akira Hamada, Nana Yamada, Vandna Rai, Takashi Hibino, Teruhiro Takabe. Regulation of betaine synthesis by precursor supply and choline monooxygenase expression in Amaranthus tricolor. Journal of Experimental Botany. 2007; 58 (15-16):4203-4212.
Chicago/Turabian StyleNazmul H. Bhuiyan; Akira Hamada; Nana Yamada; Vandna Rai; Takashi Hibino; Teruhiro Takabe. 2007. "Regulation of betaine synthesis by precursor supply and choline monooxygenase expression in Amaranthus tricolor." Journal of Experimental Botany 58, no. 15-16: 4203-4212.