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Identification of functional, noncoding elements that regulate transcription in the context of complex genomes is a major goal of modern biology. Localization of functionality to specific sequences is a requirement for genetic and computational studies. Here, we describe a generic approach, quantitative chromatin profiling, that uses quantitative analysis(More)
Present and future food security is a critical issue compounded by the consequences of climate change on agriculture. Stress perception and signal transduction in plants causes changes in gene or protein expression which lead to metabolic and physiological responses. Phytohormones play a central role in the integration of different upstream signals into(More)
The highly coordinated, dynamic nature of growth requires plants to perceive and react to various environmental signals in an interactive manner. Elaborate signaling networks mediate this plasticity in growth and the ability to adapt to changing environmental conditions. The fluctuations of stress-responsive hormones help alter the cellular dynamics and(More)
Selection for drought-tolerant cereal varieties has successfully moved to screening for grain yield under stress. Grain yield is the culmination of the process of grain filling, which in turn is closely linked to flag leaf functionalities. For grain filling to occur under drought, either a relatively uncompromised or a favorably reprogrammed functioning of(More)
Green Revolution (GR) rice varieties are high yielding but typically drought sensitive. This is partly due to the tight linkage between the loci governing plant height and drought tolerance. This linkage is illustrated here through characterization of qDTY1.1, a QTL for grain yield under drought that co-segregates with the GR gene sd1 for semi-dwarf plant(More)
Sub-QTLs and multiple intra-QTL genes are hypothesized to underpin large-effect QTLs. Known QTLs over gene families, biosynthetic pathways or certain traits represent functional gene-clusters of genes of the same gene ontology (GO). Gene-clusters containing genes of different GO have not been elaborated, except in silico as coexpressed genes within QTLs.(More)
There is a widespread consensus that drought will mostly affect present and future agriculture negatively. Generating drought-tolerant crops is thus a high priority. However complicated the underlying genetic and regulatory networks for differences in plant performance under stress are, they would be reflected in straightforward differences in primary(More)
Smallholder rice cultivation productivity is directly related to alleviating hunger and poverty. Biotic and abiotic stresses increasingly subvert the process, and drought is the most common stress. A mechanistic understanding of plant response to drought could lead to the use of gene-based markers to generate drought-tolerant rice. Such an understanding is(More)
Plants respond to stress conditions through early stress-response factors (ESRF), which serve the function of stress sensing and/or signal transduction. These mainly comprise qualitative and/or quantitative flux in the redox molecules, calcium ions (Ca2+), phosphatidic acid, hexose sugars and phytohormones. The role of resident proteins such as phytohormone(More)