Department of Biological Sciences
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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 Comparative phylogenomic analysis provides insights into TCP gene functions in Sorghum(Springer Nature, 2016-12) Sharma, RitaSorghum is a highly efficient C4 crop with potential to mitigate challenges associated with food, feed and fuel. TCP proteins are of particular interest for crop improvement programs due to their well-demonstrated roles in crop domestication and shaping plant architecture thereby, affecting agronomic traits. We identified 20 TCP genes from Sorghum. Except SbTCP8, all are either intronless or contain introns in the untranslated regions. Comparative phylogenetic analysis of Arabidopsis, rice, Brachypodium and Sorghum TCP proteins revealed two distinct classes categorized into ten sub-clades. Sub-clade F is dicot-specific, whereas A2, G1 and I1 groups only contained genes from grasses. Sub-clade B was missing in Sorghum, whereas group A1 was missing in rice indicating species-specific divergence of TCP proteins. TCP proteins of Sorghum are enriched in disorder promoting residues with class I containing higher percent disorder than class II proteins. Seven pairs of paralogous TCP genes were identified from Sorghum, five of which seem to predate Rice-Sorghum divergence. All of them have diverged in their expression. Based on the expression and orthology analysis, five Sorghum genes have been shortlisted for further investigation for their roles in regulating plant morphology. Whereas, three genes have been identified as candidates for engineering abiotic stress tolerance.Item MicroRNAs as targets for engineering biofuel feedstock Sorghum(Springer, 2017-12) Sharma, RitaSorghum is a highly efficient C4 crop, with enormous potential as a biofuel feedstock. Fermentable sugars that accumulate in sorghum stalks, high biomass, drought tolerance and adaptability to diverse climates are some of the key attributes of sorghum. However, sustainable production of renewable fuels through large scale plantation of sorghum needs targeted research efforts at several fronts. One of the promising areas is manipulating gene expression to engineer traits-of-interest. In the recent past, microRNAs have emerged as important targets for engineering complex agronomical traits, including biomass yields, sugar accumulation, flowering time, drought tolerance, disease resistance, micronutrient homeostasis, etc., in several crop plants. Both homology-based bioinformatics, and experimental approaches viz. miRNA microarrays and small RNA sequencing have been utilised to gain insights into the role of miRNAs in regulating bioenergy-related traits in sorghum. Through this review, we provide a comprehensive overview of the information available till date about the miRNA-related research in sorghum and propose the prospective directions for future endeavours in this area.Item Small RNA profiling from meiotic and post-meiotic anthers reveals prospective miRNA-target modules for engineering male fertility in sorghum(Elsevier, 2020-03) Sharma, RitaUnderstanding male gametophyte development is essential to augment hybrid production in sorghum. Although small RNAs are known to critically influence anther/pollen development, their roles in sorghum reproduction have not been deciphered yet. Here, we report small RNA profiling and high-confidence annotation of microRNAs (miRNAs) from meiotic and post-meiotic anthers in sorghum. We identified 262 miRNAs (82 known and 180 novel), out of which 58 (35 known and 23 novel) exhibited differential expression between two stages. Out of 35 differentially expressed known miRNAs, 13 are known to regulate anther/pollen development in other plant species. We also demonstrated conserved spatiotemporal patterns of 21- and 24-nt phasiRNAs and their respective triggers, miR2118 and miR2275, in sorghum anthers as evidenced in other monocots. miRNA target identification yielded 5622 modules, of which 46 modules comprising 16 known and 8 novel miRNA families with 38 target genes are prospective candidates for engineering male fertility in grasses.Item Transcriptional trajectories of anther development provide candidates for engineering male fertility in sorghum(Springer Nature, 2020-01) Sharma, RitaSorghum is a self-pollinated crop with multiple economic uses as cereal, forage, and biofuel feedstock. Hybrid breeding is a cornerstone for sorghum improvement strategies that currently relies on cytoplasmic male sterile lines. To engineer genic male sterility, it is imperative to examine the genetic components regulating anther/pollen development in sorghum. To this end, we have performed transcriptomic analysis from three temporal stages of developing anthers that correspond to meiotic, microspore and mature pollen stages. A total of 5286 genes were differentially regulated among the three anther stages with 890 of them exhibiting anther-preferential expression. Differentially expressed genes could be clubbed into seven distinct developmental trajectories using K-means clustering. Pathway mapping revealed that genes involved in cell cycle, DNA repair, regulation of transcription, brassinosteroid and auxin biosynthesis/signalling exhibit peak expression in meiotic anthers, while those regulating abiotic stress, carbohydrate metabolism, and transport were enriched in microspore stage. Conversely, genes associated with protein degradation, post-translational modifications, cell wall biosynthesis/modifications, abscisic acid, ethylene, cytokinin and jasmonic acid biosynthesis/signalling were highly expressed in mature pollen stage. High concurrence in transcriptional dynamics and cis-regulatory elements of differentially expressed genes in rice and sorghum confirmed conserved developmental pathways regulating anther development across species. Comprehensive literature survey in conjunction with orthology analysis and anther-preferential accumulation enabled shortlisting of 21 prospective candidates for in-depth characterization and engineering male fertility in sorghum.Item Phylogenomic Analysis of R2R3 MYB Transcription Factors in Sorghum and their Role in Conditioning Biofuel Syndrome(Bentham Science, 2020) Sharma, RitaLarge scale cultivation of sorghum for food, feed, and biofuel requires concerted efforts for engineering multipurpose cultivars with optimised agronomic traits. Due to their vital role in regulating the biosynthesis of phenylpropanoid-derived compounds, biomass composition, biotic, and abiotic stress response, R2R3-MYB family transcription factors are ideal targets for improving environmental resilience and economic value of sorghum.Item Phylogenomic Analysis of R2R3 MYB Transcription Factors in Sorghum and their Role in Conditioning Biofuel Syndrome(Bentham Science, 2020) Sharma, RitaBackground: Large scale cultivation of sorghum for food, feed, and biofuel requires concerted efforts for engineering multipurpose cultivars with optimised agronomic traits. Due to their vital role in regulating the biosynthesis of phenylpropanoid-derived compounds, biomass composition, biotic, and abiotic stress response, R2R3-MYB family transcription factors are ideal targets for improving environmental resilience and economic value of sorghum. Methods: We used diverse computational biology tools to survey the sorghum genome to identify R2R3-MYB transcription factors followed by their structural and phylogenomic analysis. We used inhouse generated as well as publicly available high throughput expression data to analyse the R2R3 expression patterns in various sorghum tissue types. Results: We have identified a total of 134 R2R3-MYB genes from sorghum and developed a framework to predict gene functions. Collating information from the physical location, duplication, structural analysis, orthologous sequences, phylogeny, and expression patterns revealed the role of duplications in clade-wise expansion of the R2R3-MYB family as well as intra-clade functional diversification. Using publicly available and in-house generated RNA sequencing data, we provide MYB candidates for conditioning biofuel syndrome by engineering phenylpropanoid biosynthesis and sugar signalling pathways in sorghum.Item Comparative phylogenomic analysis provides insights into TCP gene functions in Sorghum(Nature, 2016) Sharma, RitaSorghum is a highly efficient C4 crop with potential to mitigate challenges associated with food, feed and fuel. TCP proteins are of particular interest for crop improvement programs due to their well-demonstrated roles in crop domestication and shaping plant architecture thereby, affecting agronomic traits. We identified 20 TCP genes from Sorghum. Except SbTCP8, all are either intronless or contain introns in the untranslated regions. Comparative phylogenetic analysis of Arabidopsis, rice, Brachypodium and Sorghum TCP proteins revealed two distinct classes categorized into ten sub-clades. Sub-clade F is dicot-specific, whereas A2, G1 and I1 groups only contained genes from grasses. Sub-clade B was missing in Sorghum, whereas group A1 was missing in rice indicating species-specific divergence of TCP proteins. TCP proteins of Sorghum are enriched in disorder promoting residues with class I containing higher percent disorder than class II proteins. Seven pairs of paralogous TCP genes were identified from Sorghum, five of which seem to predate Rice-Sorghum divergence. All of them have diverged in their expression. Based on the expression and orthology analysis, five Sorghum genes have been shortlisted for further investigation for their roles in regulating plant morphology. Whereas, three genes have been identified as candidates for engineering abiotic stress tolerance.Item MicroRNAs as targets for engineering biofuel feedstock Sorghum(Springer, 2017) Sharma, RitaSorghum is a highly efficient C4 crop, with enormous potential as a biofuel feedstock. Fermentable sugars that accumulate in sorghum stalks, high biomass, drought tolerance and adaptability to diverse climates are some of the key attributes of sorghum. However, sustainable production of renewable fuels through large scale plantation of sorghum needs targeted research efforts at several fronts. One of the promising areas is manipulating gene expression to engineer traits-of-interest. In the recent past, microRNAs have emerged as important targets for engineering complex agronomical traits, including biomass yields, sugar accumulation, flowering time, drought tolerance, disease resistance, micronutrient homeostasis, etc., in several crop plants. Both homology-based bioinformatics, and experimental approaches viz. miRNA microarrays and small RNA sequencing have been utilised to gain insights into the role of miRNAs in regulating bioenergy-related traits in sorghum. Through this review, we provide a comprehensive overview of the information available till date about the miRNA-related research in sorghum and propose the prospective directions for future endeavours in this area.Item Transcriptional trajectories of anther development provide candidates for engineering male fertility in sorghum(Nature, 2020) Sharma, RitaSorghum is a self-pollinated crop with multiple economic uses as cereal, forage, and biofuel feedstock. Hybrid breeding is a cornerstone for sorghum improvement strategies that currently relies on cytoplasmic male sterile lines. To engineer genic male sterility, it is imperative to examine the genetic components regulating anther/pollen development in sorghum. To this end, we have performed transcriptomic analysis from three temporal stages of developing anthers that correspond to meiotic, microspore and mature pollen stages. A total of 5286 genes were differentially regulated among the three anther stages with 890 of them exhibiting anther-preferential expression. Differentially expressed genes could be clubbed into seven distinct developmental trajectories using K-means clustering. Pathway mapping revealed that genes involved in cell cycle, DNA repair, regulation of transcription, brassinosteroid and auxin biosynthesis/signalling exhibit peak expression in meiotic anthers, while those regulating abiotic stress, carbohydrate metabolism, and transport were enriched in microspore stage. Conversely, genes associated with protein degradation, post-translational modifications, cell wall biosynthesis/modifications, abscisic acid, ethylene, cytokinin and jasmonic acid biosynthesis/signalling were highly expressed in mature pollen stage. High concurrence in transcriptional dynamics and cis-regulatory elements of differentially expressed genes in rice and sorghum confirmed conserved developmental pathways regulating anther development across species. Comprehensive literature survey in conjunction with orthology analysis and anther-preferential accumulation enabled shortlisting of 21 prospective candidates for in-depth characterization and engineering male fertility in sorghum.