Song Joong Yun

Resveratrol accumulation and resveratrol synthase gene expression in response to abiotic stresses and hormones in peanut plants

Abstract The peanut is one of the limited number of plant species that synthesize resveratrol, which is both a phytoalexin with antifungal activity and a phytochemical associated with reduced cancer risk and reduced cardiovascular disease. We investigated resveratrol content and resveratrol synthase gene expression in response to various stresses and hormones in order to understand the mode of resveratrol synthesis in peanut plants. Resveratrol was present in substantial amounts (1.2–2.6 μg/g FW) in leaves, roots and shells, but very little (0.05–0.06 μg/g FW) was found in developing seeds and seed coats of field-grown peanuts. Accumulation of resveratrol in leaves increased over 200-fold in response to UV light, over 20-fold in response to paraquat, and between two- and ninefold in response to wounding, H2O2, salicylic acid (SA), jasmonic acid and ethephon, 24 h after treatment. No accumulation of resveratrol was induced by abscisic acid. Changes in resveratrol content were correlated with levels of RS mRNA, indicating a transcriptional control of resveratrol synthase activity. The results suggest that resveratrol synthesis is induced by biotic and abiotic factors through the regulation of RS transcription, and that stress hormones such as SA and ethylene are involved in the RS gene expression in peanut.

Transcriptome profiling characterizes phosphate deficiency effects on carbohydrate metabolism in rice leaves

Phosphorus (P) is a structural component of nucleic acids and phospholipids and plays important roles in plant growth and development. P accumulation was significantly reduced (about 35%) in rice leaves from plants grown under low (32 μM) P compared to 320 μM P grown plants. Genome response to low P was examined using the rice 60K oligonucleotide DNA microarrays. At the threshold significance of |log₂| fold>2.0, 21,033 genes (about 33.7% of all genes on the microarray) were affected by P deficiency. Among all genes on the microarray, 4271 genes were sorted into 51 metabolic pathways. Low P affected 1494 (35.0%) genes and the largest category of genes was related to sucrose degradation to ethanol and lactate pathway. To survey the role of P in rice, 25 pathways were selected based on number of affected genes. Among these pathways, cytosolic glycolysis contained the least number of upregulated but most down-regulated genes. Low P decreased glucose, pyruvate and chlorophyll, and genes related to carbon metabolism and chlorophyllide a biosynthesis. However, sucrose and starch levels increased. These results indicate that P nutrition affects diverse metabolic pathways mostly related to glucose, pyruvate, sucrose, starch, and chlorophyll a.

Inverse relationship between boron toxicity tolerance and boron contents of barley seed and root

ABSTRACT A filter-paper bioassay method was used to investigate the differential response of 23 barley (Hordeum vulgare L.) genotypes to boron (B) toxicity. Two-day-old seedlings with equal radicles were treated with 10 (B10) or 100 (B100) ppm B for 10 d. Root and shoot growth was not affected by B10, but root growth was significantly reduced by B100. The shoot growth at B100 was either unaffected or affected to a smaller extent than the root. A significant inverse correlation was found between B content of seed and seed germination, and between root growth and B contents of root and shoot under B100. The barley genotypes with lower B contents in seeds had a higher germination, longer root length, and accumulated less B in roots and shoots when treated with B100. The B-tolerant genotypes with longer roots had lower B contents in their seed, root, and shoot and vice versa. These results suggest that a great variation exists among barley genotypes in response to high B application. There was no difference between naked (uncovered) and covered varieties in response to B100. The B tolerance could be attributed to the lower B content of seed and lower uptake or accumulation of B in the root and shoot.

Cis-regulatory signatures of orthologous stress-associated bZIP transcription factors from rice, sorghum and Arabidopsis based on phylogenetic footprints

BackgroundThe potential contribution of upstream sequence variation to the unique features of orthologous genes is just beginning to be unraveled. A core subset of stress-associated bZIP transcription factors from rice (Oryza sativa) formed ten clusters of orthologous groups (COG) with genes from the monocot sorghum (Sorghum bicolor) and dicot Arabidopsis (Arabidopsis thaliana). The total cis-regulatory information content of each stress-associated COG was examined by phylogenetic footprinting to reveal ortholog-specific, lineage-specific and species-specific conservation patterns.ResultsThe most apparent pattern observed was the occurrence of spatially conserved ‘core modules’ among the COGs but not among paralogs. These core modules are comprised of various combinations of two to four putative transcription factor binding site (TFBS) classes associated with either developmental or stress-related functions. Outside the core modules are specific stress (ABA, oxidative, abiotic, biotic) or organ-associated signals, which may be functioning as ‘regulatory fine-tuners’ and further define lineage-specific and species-specific cis-regulatory signatures. Orthologous monocot and dicot promoters have distinct TFBS classes involved in disease and oxidative-regulated expression, while the orthologous rice and sorghum promoters have distinct combinations of root-specific signals, a pattern that is not particularly conserved in Arabidopsis.ConclusionsPatterns of cis-regulatory conservation imply that each ortholog has distinct signatures, further suggesting that they are potentially unique in a regulatory context despite the presumed conservation of broad biological function during speciation. Based on the observed patterns of conservation, we postulate that core modules are likely primary determinants of basal developmental programming, which may be integrated with and further elaborated by additional intrinsic or extrinsic signals in conjunction with lineage-specific or species-specific regulatory fine-tuners. This synergy may be critical for finer-scale spatio-temporal regulation, hence unique expression profiles of homologous transcription factors from different species with distinct zones of ecological adaptation such as rice, sorghum and Arabidopsis. The patterns revealed from these comparisons set the stage for further empirical validation by functional genomics.

Phenotypic, Physiological, and Molecular Evaluation of Rice Chilling Stress Response at the Vegetative Stage

Rice is a chilling-sensitive plant that is particularly prone to injury during the early stages of seedling development and during flowering. Significant variation exists between subspecies with japonica cultivars generally being less sensitive than most indica cultivars. In most temperate and subtropical countries where rice is grown, crop damage often occurs during the early stages of seedling development due to occasional cold snaps coinciding with the first few weeks after direct seeding in late spring to early summer. Irreversible injuries often result in seedling mortality or if the crop survives a stress episode, plant vigor and resistance to pests and diseases are severely compromised. Recent physiological and molecular studies have shown that oxidative stress is the primary cause of early chilling injuries in rice and the differential responses of indica and japonica cultivars are defined to a large extent by gene expression related to oxidative signaling and defenses. In this chapter, we summarize basic phenotypic, physiological, and molecular procedures that can be adopted for routine evaluation of differential responses between cultivars as well as for functional genomics studies.

Upstream regulatory architecture of rice genes: summarizing the baseline towards genus-wide comparative analysis of regulatory networks and allele mining

Dissecting the upstream regulatory architecture of rice genes and their cognate regulator proteins is at the core of network biology and its applications to comparative functional genomics. With the rapidly advancing comparative genomics resources in the genus Oryza, a reference genome annotation that defines the various cis-elements and trans-acting factors that interface each gene locus with various intrinsic and extrinsic signals for growth, development, reproduction and adaptation must be established to facilitate the understanding of phenotypic variation in the context of regulatory networks. Such information is also important to establish the foundation for mining non-coding sequence variation that defines novel alleles and epialleles across the enormous phenotypic diversity represented in rice germplasm. This review presents a synthesis of the state of knowledge and consensus trends regarding the various cis-acting and trans-acting components that define spatio-temporal regulation of rice genes based on representative examples from both foundational studies in other model and non-model plants, and more recent studies in rice. The goal is to summarize the baseline for systematic upstream sequence annotation of the rapidly advancing genome sequence resources in Oryza in preparation for genus-wide functional genomics. Perspectives on the potential applications of such information for gene discovery, network engineering and genomics-enabled rice breeding are also discussed.