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Gramene (http://www.gramene.org) is an online, open source, curated resource for plant comparative genomics and pathway analysis designed to support researchers working in plant genomics, breeding, evolutionary biology, system biology, and metabolic engineering. It exploits phylogenetic relationships to enrich the annotation of genomic data and provides tools to perform powerful comparative analyses across a wide spectrum of plant species. It consists of an integrated portal for querying, visualizing and analyzing data for 44 plant reference genomes, genetic variation data sets for 12 species, expression data for 16 species, curated rice pathways and orthology-based pathway projections for 66 plant species including various crops. Here we briefly describe the functions and uses of the Gramene database.

A high-throughput screening system for Citrus lines were established with higher sugar and acid contents using Fourier transform infrared (FT-IR) spectroscopy in combination with multivariate analysis. FT-IR spectra confirmed typical spectral differences between the frequency regions of 950-1100 cm(-1), 1300-1500 cm(-1), and 1500-1700 cm(-1). Principal component analysis (PCA) and subsequent partial least square-discriminant analysis (PLS-DA) were able to discriminate five Citrus lines into three separate clusters corresponding to their taxonomic relationships. The quantitative predictive modeling of sugar and acid contents from Citrus fruits was established using partial least square regression algorithms from FT-IR spectra. The regression coefficients (R(2)) between predicted values and estimated sugar and acid content values were 0.99. These results demonstrate that by using FT-IR spectra and applying quantitative prediction modeling to Citrus sugar and acid contents, excellent Citrus lines can be early detected with greater accuracy.

Using cotyledonary explants excised from seedlings germinated in vitro, efficient plant regeneration via organogenesis was established for two winter squash (Cucurbita maxima Duch.) cultivars. To establish optimal conditions for adventitious shoot induction, a variety of explants were prepared from seedlings of different ages and these were cultured using media containing different concentrations of 6-benzylaminopurine (BA). For both cultivars, plant regeneration was optimal when the proximal parts of cotyledons from 4-day-old seedlings were cultured on induction medium composed of Murashige and Skoog (MS) medium with 1 mg/l BA. After 3 weeks of culture in induction medium, 82 and 92% of explants from the two cultivars regenerated shoots. Adventitious shoots were subcultured on elongation medium composed of MS medium with 0.1 mg/l BA and the elongated shoots were successfully rooted in MS medium without growth regulators for 2 weeks. Flow cytometric analysis revealed that most of the regenerated plants were diploid.