Browsing by Author "Singh, Ashok Kumar"

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Differential RNA editing of mitochondrial genes in WA-cytoplasmic based male sterile line pusa 6A, and its maintainer and restorer lines
(Elsevier B.V., 2019) Ngangkham, Umakanta; Parida, Swarup K.; Singh, Ashok Kumar; Mohapatra, Trilochan
RNA editing changes the nucleotides at the transcript level of mitochondrial genes which results in synthesis of functional proteins. This study was designed to find the editing sites which could be implicated in male fertility restoration and to develop editing based markers for differentiation of cytoplasmic male sterility and maintainer lines from each other. DNA and RNA from young panicles were isolated from three-line system of hybrid rice PRH10, wild abortive (WA) cytoplasm based male sterile (A line Pusa 6A), maintainer (B line Pusa 6B) and restorer (R line PRR78) lines. Pusa 6A and PRR78 having the same WA cytoplasm are allo-nuclear and iso-cytpolasmic lines. The genomic and cDNA amplicons for eight mitochondrial genes (18SrRNA, atp6, atp9, cobII, coxI, coxIII, nadI and rps3) were sequenced and compared. Differences in genomic and cDNA sequences were considered as editing. Two hundred and thirty editing sites having base substitution or insertion/deletion were identified with the highest in 18SrRNA (5.74%) and the lowest in coxI (0.60%). The highest editing sites were observed in fertile maintainer Pusa 6B followed by PRR78 and Pusa 6A, of which random five editing sites in five different rice mitochondrial transcripts namely atp9, cobII, coxIII, rps3 and 18SrRNA were chosen and validated through cleaved amplified polymorphism sequence (CAPS) analysis and found to be partially edited in four genes. The identical editing sites of different mitochondrial genes from maintainer and restorer lines might reflect their possible contribution to fertility restoration of sterile WA cytoplasm.
Expression dynamics of metabolic and regulatory components across stages of panicle and seed development in indica rice
(Springer, 2012) Sharma, Rita; Agarwal, Pinky; Ray, Swatismita; Deveshwar, Priyanka; Sharma, Pooja; Sharma, Niharika; Nijhawan, Aashima; Jain, Mukesh; Singh, Ashok Kumar; Singh, Vijay Pal; Khurana, Jitendra Paul; Tyagi, Akhilesh K.; Kapoor, Sanjay
Carefully analyzed expression profiles can serve as a valuable reference for deciphering gene functions. We exploited the potential of whole genome microarrays to measure the spatial and temporal expression profiles of rice genes in 19 stages of vegetative and reproductive development. We could verify expression of 22,980 genes in at least one of the tissues. Differential expression analysis with respect to five vegetative tissues and preceding stages of development revealed reproductive stage-preferential/-specific genes. By using subtractive logic, we identified 354 and 456 genes expressing specifically during panicle and seed development, respectively. The metabolic/hormonal pathways and transcription factor families playing key role in reproductive development were elucidated after overlaying the expression data on the public databases and manually curated list of transcription factors, respectively. During floral meristem differentiation (P1) and male meiosis (P3), the genes involved in jasmonic acid and phenylpropanoid biosynthesis were significantly upregulated. P6 stage of panicle, containing mature gametophytes, exhibited enrichment of transcripts involved in homogalacturonon degradation. Genes regulating auxin biosynthesis were induced during early seed development. We validated the stage-specificity of regulatory regions of three panicle-specific genes, OsAGO3, OsSub42, and RTS, and an early seed-specific gene, XYH, in transgenic rice. The data generated here provides a snapshot of the underlying complexity of the gene networks regulating rice reproductive development.