@article { ISI:000316759800020, title = {Genome-wide identification and characterization of microRNA genes and their targets in flax (Linum usitatissimum)}, journal = {Planta}, volume = {237}, number = {4}, year = {2013}, month = {APR}, pages = {1149-1161}, publisher = {SPRINGER}, address = {233 SPRING ST, NEW YORK, NY 10013 USA}, abstract = {

MicroRNAs (miRNAs) are small (20-24 nucleotide long) endogenous regulatory RNAs that play important roles in plant growth and development. They regulate gene expression at the post-transcriptional level by translational repression or target degradation and gene silencing. In this study, we identified 116 conserved miRNAs belonging to 23 families from the flax (Linum usitatissimum L.) genome using a computational approach. The precursor miRNAs varied in length; while most of the mature miRNAs were 21 nucleotide long, intergenic and showed conserved signatures of RNA polymerase II transcripts in their upstream regions. Promoter region analysis of the flax miRNA genes indicated prevalence of MYB transcription factor binding sites. Four miRNA gene clusters containing members of three phylogenetic groups were identified. Further, 142 target genes were predicted for these miRNAs and most of these represent transcriptional regulators. The miRNA encoding genes were expressed in diverse tissues as determined by digital expression analysis as well as real-time PCR. The expression of fourteen miRNAs and nine target genes was independently validated using the quantitative reverse transcription PCR (qRT-PCR). This study suggests that a large number of conserved plant miRNAs are also found in flax and these may play important roles in growth and development of flax.

}, keywords = {Digital expression analysis, Gene cluster, Linseed, miRNA, MiRNA target transcript, Promoter analysis}, issn = {0032-0935}, doi = {10.1007/s00425-012-1833-5}, author = {Barvkar, Vitthal T. and Pardeshi, Varsha C. and Kale, Sandip M. and Qiu, Shuqing and Rollins, Meaghen and Datla, Raju and Gupta, Vidya S. and Kadoo, Narendra Y.} } @article { ISI:000316557400002, title = {Genome-wide identification and characterization of nucleotide binding site leucine-rich repeat genes in linseed reveal distinct patterns of gene structure}, journal = {Genome}, volume = {56}, number = {2}, year = {2013}, month = {FEB}, pages = {91-99}, publisher = {CANADIAN SCIENCE PUBLISHING, NRC RESEARCH PRESS}, address = {1200 MONTREAL ROAD, BUILDING M-55, OTTAWA, ON K1A 0R6, CANADA}, abstract = {

Plants employ different disease-resistance genes to detect pathogens and to induce defense responses. The largest class of these genes encodes proteins with nucleotide binding site (NBS) and leucine-rich repeat (LRR) domains. To identify the putative NBS-LRR encoding genes from linseed, we analyzed the recently published linseed genome sequence and identified 147 NBS-LRR genes. The NBS domain was used for phylogeny construction and these genes were classified into two well-known families, non-TIR (CNL) and TIR related (TNL), and formed eight clades in the neighbor-joining bootstrap tree. Eight different gene structures were observed among these genes. An unusual domain arrangement was observed in the TNL family members, predominantly in the TNL-5 clade members belonging to class D. About 12\% of the genes observed were linseed specific. The study indicated that the linseed genes probably have an ancient origin with few progenitor genes. Quantitative expression analysis of five genes showed inducible expression. The in silico expression evidence was obtained for a few of these genes, and the expression was not correlated with the presence of any particular regulatory element or with unusual domain arrangement in those genes. This study will help in understanding the evolution of these genes, the development of disease resistant varieties, and the mechanism of disease resistance in linseed.

}, keywords = {Flax, in silico gene expression, motif analysis, NBS-LRR, Phylogenetic analysis, Promoter analysis}, issn = {0831-2796}, doi = {10.1139/gen-2012-0135}, author = {Kale, Sandip M. and Pardeshi, Varsha C. and Barvkar, Vitthal T. and Gupta, Vidya S. and Kadoo, Narendra Y.} } @article { ISI:000358630800013, title = {Genotype x environment interactions and QTL clusters underlying dough rheology traits in triticum aestivum L.}, journal = {Journal of Cereal Science}, volume = {64}, year = {2015}, month = {JUL}, pages = {82-91}, publisher = {ACADEMIC PRESS LTD- ELSEVIER SCIENCE LTD}, address = {24-28 OVAL RD, LONDON NW1 7DX, ENGLAND}, abstract = {

Genetic dissection of dough rheology traits (DRT) in hexaploid wheat was carried out using nine mixograph characters evaluated in two consecutive years in three agro-climatic zones in India in an RIL population (HI977 x HD2329). Pearson correlations determined in each year-location indicated 15 stable trait inter-relationships among them but inconsistent correlations with loaf volume (LV) were observed. Using AMMI analysis we derived patterns in G x E interactions (GEI) indicating 6-47\% contribution for the DRT. Composite interval mapping using a linkage map of 202 SSR markers identified 144 DRT QTLs of which, 96 were detected in single- and the rest in two to five year-locations. Sixteen QTL clusters located on ten chromosomes were identified and only three of them on chromosomes 1B, 5B and 6D involved LV QTLs. For each trait, majority of the DRT QTLs detected in single as well as multiple environments showed location-specificity and suggested that owing to GEI, breeding for wheat dough quality might need careful selection of QTLs targeted for individual agro-climatic zones. The inconsistent correlations of DRT and LV and differential locations of their QTLs in this population corroborated that using dough rheological traits alone to predict LV might pose challenges during wheat improvement. (C) 2015 Elsevier Ltd. All rights reserved.

}, keywords = {AMMI analysis, Dough rheology, Mixograph, QTL}, issn = {0733-5210}, doi = {10.1016/j.jcs.2015.05.002}, author = {Prashant, Ramya and Mani, Elangovan and Rai, Richa and Gupta, R. K. and Tiwari, Ratan and Dholakia, Bhushan B. and Oak, Manoj and Roeder, Marion and Kadoo, Narendra Y. and Gupta, Vidya} } @article {44479, title = {GA3 application in grapes (Vitis vinifera L.) modulates different sets of genes at cluster emergence, full bloom, and berry stage as revealed by RNA sequence-based transcriptome analysis}, journal = {Functional \& Integrative Genomics}, volume = {18}, year = {2018}, month = {JUL}, pages = {439{\textendash}455}, abstract = {In grapes (Vitis vinifera L.), exogenous gibberellic acid (GA3) is applied at different stages of bunch development to achieve desirable bunch shape and berry size in seedless grapes used for table purpose. RNA sequence-based transcriptome analysis was used to understand the mechanism of GA3 action at cluster emergence, full bloom, and berry stage in table grape variety Thompson Seedless. At cluster emergence, rachis samples were collected at 6 and 24 h after application of GA3, whereas flower clusters and berry samples were collected at 6, 24, and 48 h after application at full bloom and 3{\textendash}4 mm berry stages. Seven hundred thirty-three genes were differentially expressed in GA3-treated samples. At rachis and flower cluster stage respectively, 126 and 264 genes were found to be significantly differentially expressed within 6 h of GA3 application. The number of DEG reduced considerably at 24 h. However, at berry stage, major changes occurred even at 24 h and a number of DEGs at 6 and 24 h were 174 and 191, respectively. As compared to upregulated genes, larger numbers of genes were downregulated. Stage-specific response to the GA3 application was observed as evident from the unique set of DEGs at each stage and only a few common genes among three stages. Among the DEGs, 67 were transcription factors. Functional categorization and enrichment analysis revealed that several transcripts involved in sucrose and hexose metabolism, hormone and secondary metabolism, and abiotic and biotic stimuli were enriched in response to application of GA3. A high correlation was recorded for real-time PCR and transcriptome data for selected DEGs, thus indicating the robustness of transcriptome data obtained in this study for understanding the GA3 response at different stages of berry development in grape. Chromosomal localization of DEGs and identification of polymorphic microsatellite markers in selected genes have potential for their use in breeding for varieties with improved bunch architecture.}, keywords = {Bunch architecture, GA3 response, Microsatellite markers, RNA seq, Transcription factors, Vitis vinifera}, issn = {1438-793X}, doi = {10.1007/s10142-018-0605-0}, author = {Upadhyay, Anuradha and Maske, Smita and Jogaiah, Satisha and Kadoo, Narendra Y. and Gupta, Vidya S.} } @article {47484, title = {Global study of MFS superfamily transporters in arabidopsis and grapes reveals their functional diversity in plants}, journal = {Plant Gene}, volume = {18}, year = {2019}, month = {JUN }, type = {Article}, abstract = {The Major Facilitator Superfamily (MFS) is the largest superfamily of secondary transporters present in all organisms, from prokaryotes to higher eukaryotes, that facilitates transport of diverse molecules like sugars, vitamins, amino-acids, hormones, etc. across cell membranes. The superfamily was further expanded to MFS Superfamily (MFSS) to integrate MFS with nine more families. The present study revealed their land plant specific diversity through identification across six species from unicellular alga to higher flowering plants. We identified 71, 131, 254, 260, 213 and 203 MFSS transporters in Chlamydomonas reinhardtii, Physcomitrella patens, Selaginella moellendorffii, Oryza sativa (var. Japonica), Arabidopsis thaliana and Vitis vinifera, respectively and classified them into MFSS families and subfamilies based on their transporter classification identifiers (TCIDs). Detailed analysis of 20 land plant specific subfamilies was conducted in A. thaliana and V. vinifera. Phylogenetic and gene duplication studies revealed the expansion of sugar porter and proton dependent oligopeptide transporter families in Arabidopsis and grape. The subcellular localization of the majority of the transporters was predicted to be in the plasma membrane. Furthermore, the microarray expression analysis of MFSS transporters from Arabidopsis and grapes revealed their multi-tissue-specificity and differential regulation under biotic and abiotic stress conditions. Studies of the transmembrane topology highlighted the presence of central cytoplasmic loop along with family specific topological variations that were evident from phylogenetic analysis. Overall, this study adds to the knowledge of functional and structural diversity and evolution of MFSS transporters in plants and opens the scope for detailed physiological and functional studies on these proteins.}, doi = {10.1016/j.plgene.2019.100179}, author = {Patil, Sucheta S. and Prashant, Ramya and Kadoo, Narendra Y. and Upadhyay, Anuradha and Gupta, Vidya S.} } @article {46917, title = {Gibberellic acid induces unique molecular responses in {\textquoteleft}thompson seedless{\textquoteright} grapes as revealed by non-targeted metabolomics}, journal = {Journal of Plant Growth Regulation}, volume = {40}, year = {2021}, month = {FEB}, pages = {293-304}, type = {Article}, abstract = {

Compact clusters and small berry size are the major problems associated with the commercialization of table grapes. The application of gibberellic acid 3 (GA(3)) has been a long-followed practice to overcome these issues. To analyze the molecular response of {\textquoteleft}Thompson Seedless{\textquoteright} grapes to GA(3) treatment, we investigated the metabolomes of its rachises, clusters, and berries, 6 h and 24 h after the treatment. Metabolite profiling using non-targeted metabolomics approach revealed several metabolites, including arginine, proline, tyrosine, kaempferol, resveratrol, catechin, and so on as possible biomarkers of GA(3) treatment in grapes. GA(3) treatment greatly impacted the alanine, aspartate, and glutamate metabolism pathways, and the GA(3)-mediated alterations in the levels of certain plant growth regulators and primary metabolites were in accordance with important growth and developmental processes in grapes. This study highlights the effect of GA(3) on the profiles of certain polyphenols impacting the flavone and flavonol biosynthesis pathways and hence the nutritional aspect of grapes. The results of this study would be useful to develop self-elongating varieties simplifying the grape cultivation.

}, keywords = {Biosynthetic pathways, GA(3) response, GA(3) signaling, Sultana grapes, Untargeted metabolomics}, issn = {0721-7595}, doi = {10.1007/s00344-020-10102-7, Early Access Date = MAR 2020}, author = {Jadhav, Uma and Mundhe, Swapnil and Kumar, Yashwant and Jogaiah, Satisha and Upadhyay, Anuradha and Gupta, Vidya S. and Kadoo, Narendra Y.} } @article {47802, title = {Gibberellic acid induces unique molecular responses in {\textquoteleft}thompson seedless{\textquoteright} grapes as revealed by non-targeted metabolomics}, journal = {Journal of Plant Growth Regulation}, volume = {40}, year = {2021}, month = {FEB}, pages = {293 - 304}, type = {Article}, abstract = {Compact clusters and small berry size are the major problems associated with the commercialization of table grapes. The application of gibberellic acid 3 (GA3) has been a long-followed practice to overcome these issues. To analyze the molecular response of {\textquoteleft}Thompson Seedless{\textquoteright} grapes to GA3 treatment, we investigated the metabolomes of its rachises, clusters, and berries, 6~h and 24~h after the treatment. Metabolite profiling using non-targeted metabolomics approach revealed several metabolites, including arginine, proline, tyrosine, kaempferol, resveratrol, catechin, and so on as possible biomarkers of GA3 treatment in grapes. GA3 treatment greatly impacted the alanine, aspartate, and glutamate metabolism pathways, and the GA3-mediated alterations in the levels of certain plant growth regulators and primary metabolites were in accordance with important growth and developmental processes in grapes. This study highlights the effect of GA3 on the profiles of certain polyphenols impacting the flavone and flavonol biosynthesis pathways and hence the nutritional aspect of grapes. The results of this study would be useful to develop self-elongating varieties simplifying the grape cultivation.}, isbn = {1435-8107}, doi = {10.1007/s00344-020-10102-7}, author = {Jadhav, Uma and Mundhe, Swapnil and Kumar, Yashwant and Jogaiah, Satisha and Upadhyay, Anuradha and Gupta, Vidya S. and Kadoo, Narendra Y.} }