Department of Biological Sciences
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Item Expression and functional analysis of rice genes involved in reproductive development and stress response(World Scientific, 2007) Sharma, RitaThe rice genome sequenced and annotated by the IRGSP has identified 37,544 protein-coding genes. In an effort to identify genes encoding transcription factors and signal transduction components, more than 7,000 genes belonging to 87 classes have been used to prepare a local database. Detailed analysis of genes for plant hormone response, CDPKs, C2H2 zinc-finger, and SET domain proteins unraveled interesting evolutionary aspects in relation to genes and the rice genome. A 51k microarray, SAGE analysis, and real-time polymerase chain reaction revealed differential expression of target genes during reproductive development and stress conditions. Several genes specific to reproductive floral organs and seed development have been identified. A large number of SAGE tags are observed from intergenic regions and antisense strands reflecting the unexplored transcription potential of the rice genome. Analysis of rice gene promoter activities has been undertaken in transgenic tobacco/Arabidopsis to demarcate regions conferring anther-/pollen-specific expression. OSISAP1, a gene coding for a stress-associated zinc-finger protein, and its promoter have been functionally validated in transgenic tobacco and rice. Genes for proteins interacting with OSISAP1 have also been found to be stress-inducible. Investigations on functional analysis of stress-responsive genes are in progress.Item Role of phytohormones in regulating agronomically important seed traits in crop plants(Elsevier, 2023) Sharma, RitaSeed development is a complex process that commences after double fertilization. Both forward and reverse genetic studies have revealed the critical roles of phytohormones in regulating seed development and the associated agronomic traits. The growing evidence points to the complex interactions among underlying genetic pathways due to hormone cross talk or shared signaling components. Moving forward to deconvolute these complex interactions requires an in-depth understanding of the genes regulating individual hormone pathways. Here, we summarize the multifaceted roles of key genes regulating biosynthesis and signaling of plant hormones, and the broad spectrum of mechanisms underpinning hormone action during seed development. The gain- and loss-of-function phenotypes associated with agronomically important seed traits, namely, seed size, weight, shape, number, longevity, and dormancy, provide compelling evidence for the plant hormones as crucial metabolic engineering targets to optimize seed traits in crop plants.Item Vulnerability and Resilience of Sorghum to Changing Climatic Conditions: Lessons from the Past and Hope for the Future(Springer, 2022-04) Sharma, Rita; Joshi, MukulClimate change poses a serious threat to crop productivity. The rise in CO2 levels, air temperature, soil salinity and variability in precipitation are the key factors that contribute to yield loss. Sorghum stands in the arid and semi-arid regions of the world that are particularly vulnerable to climate change. A comprehensive assessment of its vulnerability and resilience is required to adopt appropriate mitigation strategies. Here, we provide an overview of the projected and observed impact of the rise in temperature, CO2, salinity, drought and flooding stress on plant physiology, growth and development, and overall productivity of sorghum. While an increase in CO2 has been projected to enhance sorghum yields, a decrease in precipitation along with temperature rise would negatively impact sorghum productivity. Although sorghum is moderately tolerant to salinity and waterlogging, screening of germplasm for selection of improved varieties and development of tolerant cultivars is necessary for superior performance. The best agricultural practices, technological advances, and genetic enhancement desirable to mitigate the impact of climate change on sorghum productivity have been discussed.Item The endoplasmic reticulum-quality control component SDF2 is essential for XA21-mediated immunity in rice(Elsevier, 2013-09) Sharma, RitaPlant genomes contain large number of plasma membrane (PM)-localized immune receptors, also called pattern recognition receptors (PRRs). PRRs are synthesized in the endoplasmic reticulum (ER) and then translocated to the PM, where they recognize conserved pathogen-associated molecular patterns (PAMPs) and activate innate immune response. The rice XA21 immune receptor confers resistance to the Gram-negative bacterial pathogen, Xanthomonas oryzae pv. oryzae (Xoo). To identify components that mediate XA21-mediated signaling, we performed co-purification experiments using C-terminal GFP tagged XA21 protein. Several endoplasmic reticulum-quality control (ER-QC) proteins including stromal-derived factor 2 (SDF2) co-purified with XA21. Silencing of the SDF2 genes in the XA21 rice genetic background compromises resistance to Xoo but does not affect plant growth and development.Item Functional delineation of rice MADS29 reveals its role in embryo and endosperm development by affecting hormone homeostasis(OUP, 2013) Sharma, RitaRice MADS29 has recently been reported to cause programmed cell death of maternal tissues, the nucellus, and the nucellar projection during early stages of seed development. However, analyses involving OsMADS29 protein expression domains and characterization of OsMADS29 gain-of-function and knockdown phenotypes revealed novel aspects of its function in maintaining hormone homeostasis, which may have a role in the development of embryo and plastid differentiation and starch filling in endosperm cells. The MADS29 transcripts accumulated to high levels soon after fertilization; however, protein accumulation was found to be delayed by at least 4 days. Immunolocalization studies revealed that the protein accumulated initially in the dorsal-vascular trace and the outer layers of endosperm, and subsequently in the embryo and aleurone and subaleurone layers of the endosperm. Ectopic expression of MADS29 resulted in a severely dwarfed phenotype, exhibiting elevated levels of cytokinin, thereby suggesting that cytokinin biosynthesis pathway could be one of the major targets of OsMADS29. Overexpression of OsMADS29 in heterologous BY2 cells was found to mimic the effects of exogenous application of cytokinins that causes differentiation of proplastids to starch-containing amyloplasts and activation of genes involved in the starch biosynthesis pathway. Suppression of MADS29 expression by RNAi severely affected seed set. The surviving seeds were smaller in size, with developmental abnormalities in the embryo and reduced size of endosperm cells, which also contained loosely packed starch granules. Microarray analysis of overexpression and knockdown lines exhibited altered expression of genes involved in plastid biogenesis, starch biosynthesis, cytokinin signalling and biosynthesis.Item Construction of a rice glycoside hydrolase phylogenomic database and identification of targets for biofuel research(Frontiers, 2013-08) Sharma, RitaGlycoside hydrolases (GH) catalyze the hydrolysis of glycosidic bonds in cell wall polymers and can have major effects on cell wall architecture. Taking advantage of the massive datasets available in public databases, we have constructed a rice phylogenomic database of GHs (http://ricephylogenomics.ucdavis.edu/cellwalls/gh/). This database integrates multiple data types including the structural features, orthologous relationships, mutant availability, and gene expression patterns for each GH family in a phylogenomic context. The rice genome encodes 437 GH genes classified into 34 families. Based on pairwise comparison with eight dicot and four monocot genomes, we identified 138 GH genes that are highly diverged between monocots and dicots, 57 of which have diverged further in rice as compared with four monocot genomes scanned in this study. Chromosomal localization and expression analysis suggest a role for both whole-genome and localized gene duplications in expansion and diversification of GH families in rice. We examined the meta-profiles of expression patterns of GH genes in twenty different anatomical tissues of rice. Transcripts of 51 genes exhibit tissue or developmental stage-preferential expression, whereas, seventeen other genes preferentially accumulate in actively growing tissues. When queried in RiceNet, a probabilistic functional gene network that facilitates functional gene predictions, nine out of seventeen genes form a regulatory network with the well-characterized genes involved in biosynthesis of cell wall polymers including cellulose synthase and cellulose synthase-like genes of rice. Two-thirds of the GH genes in rice are up regulated in response to biotic and abiotic stress treatments indicating a role in stress adaptation. Our analyses identify potential GH targets for cell wall modification.Item De Novo Assembly and Characterization of Stress Transcriptome in a Salinity-Tolerant Variety CS52 of Brassica juncea(PLOS Biology, 2015-05) Sharma, RitaOilseed mustard, Brassica juncea, exhibits high levels of genetic variability for salinity tolerance. To obtain the global view of transcriptome and investigate the molecular basis of salinity tolerance in a salt-tolerant variety CS52 of B. juncea, we performed transcriptome sequencing of control and salt-stressed seedlings. De novo assembly of 184 million high-quality paired-end reads yielded 42,327 unique transcripts longer than 300 bp with RPKM ≥1. When compared with non-redundant proteins, we could annotate 67% unigenes obtained in our study. Based on the mapping to expressed sequence tags (ESTs), 52.6% unigenes are novel compared to EST data available for B. juncea and constituent genomes. Differential expression analysis revealed altered expression of 1469 unigenes in response to salinity stress. Of these, 587, mainly associated with ROS detoxification, sulfur assimilation and calcium signaling pathways, are up regulated. Notable of these is RSA1 (SHORT ROOT IN SALT MEDIUM 1) INTERACTING TRANSCRIPTION FACTOR 1 (RITF1) homolog up regulated by >100 folds in response to stress. RITF1, encoding a bHLH transcription factor, is a positive regulator of SOS1 and several key genes involved in scavenging of salt stress-induced reactive oxygen species (ROS). Further, we performed comparative expression profiling of key genes implicated in ion homeostasis and sequestration (SOS1, SOS2, SOS3, ENH1, NHX1), calcium sensing pathway (RITF1) and ROS detoxification in contrasting cultivars for salinity tolerance, B. juncea and B. nigra. The results revealed higher transcript accumulation of most of these genes in B. juncea var. CS52 compared to salt-sensitive cultivar even under normal growth conditions. Together, these findings reveal key pathways and signaling components that contribute to salinity tolerance in B. juncea var. CS52.Item Phylogenomics databases for facilitating functional genomics in rice(Springer, 2015-07) Sharma, RitaThe completion of whole genome sequence of rice (Oryza sativa) has significantly accelerated functional genomics studies. Prior to the release of the sequence, only a few genes were assigned a function each year. Since sequencing was completed in 2005, the rate has exponentially increased. As of 2014, 1,021 genes have been described and added to the collection at The Overview of functionally characterized Genes in Rice online database (OGRO). Despite this progress, that number is still very low compared with the total number of genes estimated in the rice genome. One limitation to progress is the presence of functional redundancy among members of the same rice gene family, which covers 51.6 % of all non-transposable element-encoding genes. There remain a significant portion or rice genes that are not functionally redundant, as reflected in the recovery of loss-of-function mutants. To more accurately analyze functional redundancy in the rice genome, we have developed a phylogenomics databases for six large gene families in rice, including those for glycosyltransferases, glycoside hydrolases, kinases, transcription factors, transporters, and cytochrome P450 monooxygenases. In this review, we introduce key features and applications of these databases. We expect that they will serve as a very useful guide in the post-genomics era of research.Item Targeted Switchgrass BAC Library Screening and Sequence Analysis Identifies Predicted Biomass and Stress Response-Related Genes(Springer, 2015-08) Sharma, RitaTo identify switchgrass homologs of rice genes, known/predicted to control biomass and stress response-related traits, we screened 96,000 clones from two switchgrass bacterial artificial chromosome (BAC) libraries. Full-length sequencing of 311 BAC clones revealed sequence for ∼3.2 % (51.7 Mb) of the switchgrass genome, coding for 3948 genes. A comparison with Arabidopsis and five grass genomes revealed that switchgrass genes share the highest number of homologs with rice (95.5 %) followed by foxtail millet (91.7 %) and Sorghum (91.5 %). One hundred eighteen of the annotated genes are unique to switchgrass. Gene annotation and ontology analysis revealed 695 genes belonging to gene families targeted in the screening. These include 350 kinase, 203 glycosyltransferase (GT), 109 glycoside hydrolase (GH), and 33 ethylene responsive transcription factor (ERF) family genes. Rice homologs of 65 genes, identified here, have demonstrated roles in bioenergy-relevant traits. These include 14 GT2 family genes involved in the synthesis of cellulose and hemicelluloses. Comparative expression analysis in six switchgrass organs revealed a conserved expression pattern for three cellulose synthase (CesA1, CesA2, and CesA9) and five cellulose-synthase-like genes (CslA2, CslA11, CslC1, CslD4, and CslE6). CslF genes that encode mixed linkage glucans are expressed in wider range of tissues in switchgrass compared with rice.Item Overexpression of Rice Wall-Associated Kinase 25 (OsWAK25) Alters Resistance to Bacterial and Fungal Pathogens(PLOS Biology, 2016-01) Sharma, RitaWall-associated kinases comprise a sub-family of receptor-like kinases that function in plant growth and stress responses. Previous studies have shown that the rice wall-associated kinase, OsWAK25, interacts with a diverse set of proteins associated with both biotic and abiotic stress responses. Here, we show that wounding and BTH treatments induce OsWAK25 transcript expression in rice. We generated OsWAK25 overexpression lines and show that these lines exhibit a lesion mimic phenotype and enhanced expression of rice NH1 (NPR1 homolog 1), OsPAL2, PBZ1 and PR10. Furthermore, these lines show resistance to the hemibiotrophic pathogens, Xanthomonas oryzae pv. oryzae (Xoo) and Magnaporthe oryzae, yet display increased susceptibility to necrotrophic fungal pathogens, Rhizoctonia solani and Cochliobolus miyabeanus.