Altered chromatin conformation and transcriptional regulation in watermelon following genome doubling.

Polyploidy has played a crucial role in plant evolution, development and function. Synthetic autopolyploid represents an ideal system to investigate the effects of polyploidization on transcriptional regulation. In this study, we deciphered the impact of genome duplication at phenotypic and molecular levels in watermelon. Overall, 88% of the genes in tetraploid watermelon followed a >1:1 dosage effect, and accordingly, differentially expressed genes were largely upregulated. In addition, a great number of hypomethylated regions (1688) were identified in an isogenic tetraploid watermelon. These differentially methylated regions were localized in promoters and intergenic regions and near transcriptional start sites of the identified upregulated genes, which enhances the importance of methylation in gene regulation. These changes were reflected in sophisticated higher-order chromatin structures. The genome doubling caused switching of 108 A and 626 B compartments that harbored genes associated with growth, development and stress responses.

Improvement of Postharvest Quality of Plum (Prunus domestica L.) Using Polysaccharide-Based Edible Coatings.

Polysaccharide-based edible coatings are served as an attractive preservation method for postharvest maintenance of most fruits. The current study examined the effect of carboxymethylcellulose (CMC)- and pectin (Pec)- based edible coatings on titratable acidity (TA), firmness; vitamin C (vit C); total soluble solids (TSS); pH; total phenolics; anthocyanin and flavonoid contents; total antioxidant capacity (based on 1,1-Diphenyl-2-picryl-hydrazyl hydrate (DPPH)); the activities of peroxidase (POD), polyphenol oxidase (PPO) and polygalacturonase (PG) enzymes; and weight loss during cold storage. The results showed that each coating and their combinations caused positive effects in all measured parameters except weight loss. The applied coatings preserved firmness and improved total phenols, anthocyanin and flavonoid contents, antioxidant capacity and POD activity. In addition, TSS decreased and pH values remained more or less stable with the coating application. The coatings delayed TA and vitamin C loss, and decreased enzymatic activities such as PPO and PG. It could be stated that CMC at 1% and Pec at 1.5% separately demonstrated the best results for most of the measured parameters; and 0.5% Pec + 1.5% CMC could be considered as the best combination. In conclusion, application of CMC, Pec, or their combinations would be considered as an interesting approach to improve postharvest quality characteristics of plum fruit.

Analysis of peanut leaf proteome.

Peanut (Arachis hypogaea) is one of the most important sources of plant protein. Current selection of genotypes requires molecular characterization of available populations. Peanut genome database has several EST cDNAs which can be used to analyze gene expression. Analysis of proteins is a direct approach to define function of their associated genes. Proteome analysis linked to genome sequence information is critical for functional genomics. However, the available protein expression data is extremely inadequate. Proteome analysis of peanut leaf was conducted using two-dimensional gel electrophoresis in combination with sequence identification using MALDI/TOF to determine their identity and function related to growth, development and responses to stresses. Peanut leaf proteins were resolved into 300 polypeptides with pI values between 3.5 and 8.0 and relative molecular masses from 12 to 100 kDa. A master leaf polypeptide profile was generated based on the consistently expressed protein pattern. Proteins present in 205 spots were identified using GPS software and Viridiplantae database (NCBI). Identity of some of these proteins included RuBisCO, glutamine synthetase, glyoxisomal malate dehydrogenase, oxygen evolving enhancer protein and tubulin. Bioinformatical analyses showed that there are 133 unique protein identities. They were categorized into 10 and 8 groups according to their cellular compartmentalization and biological functionality, respectively. Enzymes necessary for carbohydrate metabolism and photosynthesis dominated in the set of identified proteins. The reference map derived from a drought-tolerant cv.Vemana should serve as the basis for further investigations of peanut physiology such as detection of expressed changes due to biotic and abiotic stresses, plant development. Furthermore, the leaf proteome map will lead to development of protein markers for cultivar identification at seedling stage of the plant. Overall, this study will contribute to improve our understanding of plant genetics and metabolism, and overall assist in the selection and breeding programs geared toward crop improvement.

Characterization of unique and differentially expressed proteins in anthracnose-tolerant Florida hybrid bunch grapes.

Anthracnose is a major disease in Florida hybrid bunch grapes, caused by a fungus viz. Elsinoe ampelina. Florida hybrid bunch grapes are grown in southeastern USA for their superior wine characteristics. However, the effect of anthracnose on grape productivity and wine quality is a major concern to grape growers. Our research is aimed at determining biochemical basis of anthracnose tolerance in Florida hybrid bunch grape. Leaf samples were collected from the plants infected with E. ampelina at different periods and analyzed for differential protein expression using high throughput two-dimensional gel electrophoresis. Among the 32 differentially expressed leaf proteins, two were uniquely expressed in tolerant genotypes in response to E. ampelina infection. These proteins were identified as mitochondrial adenosine triphosphate synthase and glutamine synthetase, which are known to play a major role in carbohydrate metabolism and defense. Several proteins including ribulose 1-5 bisphosphate-carboxylase involved in photosynthesis were found to be suppressed in susceptible genotypes compared to tolerant genotypes following E. ampelina infection. The results indicate that the anthracnose-tolerant genotypes have the ability to up-regulate and induce new proteins upon infection to defend the invasion of the pathogen as well as maintain the normal regulatory processes.

Efficient protocol for isolation of functional RNA from different grape tissue rich in polyphenols and polysaccharides for gene expression studies

Extraction of RNA from plant tissue containing high levels of polyphenols and polysaccharides is tedious and difficult in grapes. Although several protocols have been published for plant RNA isolation, most have failed to yield high quality RNA in sufficient quantity from mature and diseased grape tissue. We describe a protocol for isolating intact and high quality RNA from various grape tissues as evident by high A260/A280 absorbance ratio (1.8 to 1.9) and electrophoretic profile on denaturing formaldehyde agarose gel. On an average, 205 µg RNA per g of fresh tissue were obtained using this modified protocol. RNA quality was further assessed through RT-PCR, differential display RT-PCR and subtractive hybridization, and found to be suitable for molecular studies.