Browsing by Author "Kakumanu, Akshay"
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- Effects of Drought on Gene Expression in Maize Reproductive and Leaf Meristem Tissues as Revealed by Deep SequencingKakumanu, Akshay (Virginia Tech, 2012-06-28)Drought is a major environmental stress factor that poses a serious threat to food security. The effects of drought on early reproductive tissue at 1-2 DAP (days after pollination) is irreversible in nature and leads to embryo abortion, directly affecting the grain yield production. We developed a working RNA-Seq pipeline to study maize (Zea mays) drought transcriptome sequenced by Illumina GSIIx technology to compare drought treated and well- watered fertilized ovary (1-2DAP) and basal leaf meristem tissue. The pipeline also identified novel splice junctions - splice variants of previously known gene models and potential novel transcription units. An attempt was also made to exploit the data to understand the drought mediated transcriptional events (e.g. alternative splicing). Gene Ontology (GO) enrichment analysis revealed massive down-regulation of cell division and cell cycle genes in the drought stressed ovary only. Among GO categories related to carbohydrate metabolism, changes in starch and sucrose metabolism-related genes occurred in the ovary, consistent with a decrease in starch levels, and in sucrose transporter function, with no comparable changes occurring in the leaf meristem. ABA-related processes responded positively, but only in the ovaries. GO enrichment analysis also suggested differential responses to drought between the two tissues in categories such as oxidative stress-related and cell cycle events. The data are discussed in the context of the susceptibility of maize kernel to drought stress leading to embryo abortion, and the relative robustness of actively dividing vegetative tissue taken at the same time from the same plant subjected to the same conditions. A hypothesis is formulated, proposing drought-mediated intersecting effects on the expression of invertase genes, glucose signaling (hexokinase 1-dependent and independent), ABA-dependent and independent signaling, antioxidant responses, PCD, phospholipase C effects, and cell cycle related processes. This work was supported by the National Science Foundation Plant Genome Research Pro- gram (grant no. DBI0922747), iPlant Collaborative (NSF DBI-0735191) and also NSF ABI1062472.
- Metabolic and Transcriptional Reprogramming in Developing Soybean (Glycine max) EmbryosCollakova, Eva; Aghamirzaie, Delasa; Fang, Yihui; Klumas, Curtis; Tabataba, Farzaneh; Kakumanu, Akshay; Myers, Elijah; Heath, Lenwood S.; Grene, Ruth (MDPI, 2013-05-14)Soybean (Glycine max) seeds are an important source of seed storage compounds, including protein, oil, and sugar used for food, feed, chemical, and biofuel production. We assessed detailed temporal transcriptional and metabolic changes in developing soybean embryos to gain a systems biology view of developmental and metabolic changes and to identify potential targets for metabolic engineering. Two major developmental and metabolic transitions were captured enabling identification of potential metabolic engineering targets specific to seed filling and to desiccation. The first transition involved a switch between different types of metabolism in dividing and elongating cells. The second transition involved the onset of maturation and desiccation tolerance during seed filling and a switch from photoheterotrophic to heterotrophic metabolism. Clustering analyses of metabolite and transcript data revealed clusters of functionally related metabolites and transcripts active in these different developmental and metabolic programs. The gene clusters provide a resource to generate predictions about the associations and interactions of unknown regulators with their targets based on guilt-by-association relationships. The inferred regulators also represent potential targets for future metabolic engineering of relevant pathways and steps in central carbon and nitrogen metabolism in soybean embryos and drought and desiccation tolerance in plants.