Browsing by Author "Dhaka, N"

Now showing 1 - 3 of 3
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    Genome-wide in silico analysis of long intergenic non-coding RNAs from rice peduncles at the heading stage
    (2021-10) Kandpal, M; Dhaka, N; Sharma, R
    Long intergenic non-coding RNAs (lincRNAs) belong to the category of long non-coding RNAs (lncRNAs), originated from intergenic regions, which do not code for proteins. LincRNAs perform prominent role in regulation of gene expression during plant development and stress response by directly interacting with DNA, RNA, or proteins, or triggering production of small RNA regulatory molecules. Here, we identified 2973 lincRNAs and investigated their expression dynamics during pedun cle elongation in two Indian rice cultivars, Pokkali and Swarna, at the time of heading. Differential expression analysis revealed common and cultivar-specific expression patterns, which we utilized to infer the lincRNA candidates with potential involvement in peduncle elongation and panicle exsertion. Their putative targets were identified using in silico prediction methods followed by pathway mapping and literature-survey based functional analysis. Further, to infer the mechanism of action, we identified the lincRNAs which potentially act as miRNA precursors or target mimics.
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    Integrated analysis of transcriptomic and small RNA sequencing data provides miRNA candidates for engineering agronomically important seed traits in Brassica juncea
    (2023-11) Jain, R; Dhaka, N; Yadav, P; Sharma, M
    Brassica juncea L. is an important oilseed crop that yields edible oil and biofuel. Improving B. juncea seed traits is a primary breeding target, but these traits are genetically complex. MicroRNAs (miRNAs) regulate seed devel opment by modulating gene expression at the post-transcriptional or translational level and are excellent can didates for improving seed traits. However, the roles of miRNAs in B. juncea seed development are yet to be investigated. Here, we report small RNA profiling and miRNA identification from developing seeds of two contrasting varieties of B. juncea, Early Heera2 (EH2) and Pusa Jaikisan (PJK). We identified 326 miRNAs, including 127 known and 199 novel miRNAs, of which 103 exhibited inter-varietal differential expression. Integrating miRNAome and our previous transcriptome data identified 13,683 putative miRNA-target modules. Segregation of differentially expressed miRNAs into different groups based on variety-wise upregulation, fol lowed by comprehensive functional analysis of targets using pathway mapping, gene ontology, transcription factor mapping, and candidate gene analysis, revealed at least 11, 6, and 7 miRNAs as robust candidates for the regulation of seed size, seed coat color, and oil content, respectively. Further, co-localization with previously reported quantitative trait loci (QTL) proffered 29 and 15 miRNAs overlapping with seed weight and oil content QTLs, respectively. Our study is the first comprehensive report of miRNAome expression dynamics from developing seeds and provides candidate miRNAs and target genes for engineering seed traits in B. juncea.
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    Integrated analysis of transcriptomic and small RNA sequencing data provides miRNA candidates for engineering agronomically important seed traits in Brassica juncea
    (2023-11) Jain, R; Dhaka, N; Yadav, P; Sharma, MK; Danish, MD; Sharma, S; Kumari, S
    Brassica juncea L. is an important oilseed crop that yields edible oil and biofuel. Improving B. juncea seed traits is a primary breeding target, but these traits are genetically complex. MicroRNAs (miRNAs) regulate seed devel opment by modulating gene expression at the post-transcriptional or translational level and are excellent can didates for improving seed traits. However, the roles of miRNAs in B. juncea seed development are yet to be investigated. Here, we report small RNA profiling and miRNA identification from developing seeds of two contrasting varieties of B. juncea, Early Heera2 (EH2) and Pusa Jaikisan (PJK). We identified 326 miRNAs, including 127 known and 199 novel miRNAs, of which 103 exhibited inter-varietal differential expression. Integrating miRNAome and our previous transcriptome data identified 13,683 putative miRNA-target modules. Segregation of differentially expressed miRNAs into different groups based on variety-wise upregulation, fol lowed by comprehensive functional analysis of targets using pathway mapping, gene ontology, transcription factor mapping, and candidate gene analysis, revealed at least 11, 6, and 7 miRNAs as robust candidates for the regulation of seed size, seed coat color, and oil content, respectively. Further, co-localization with previously reported quantitative trait loci (QTL) proffered 29 and 15 miRNAs overlapping with seed weight and oil content QTLs, respectively. Our study is the first comprehensive report of miRNAome expression dynamics from developing seeds and provides candidate miRNAs and target genes for engineering seed traits in B. juncea.