FruitGeneDB is a database that contains a HT (heat treatment)-responsive gene dataset (HTds) and four fruit gene expression datasets (FEds) from several species, cultivars and postharvest conditions, focused on the known benefits of HT to ameliorate fruit chilling injury (CI) disorders during cold storage (CS). FruitGeneDB serves gene functional studies, contributing to the identification of new HT, CS and CI molecular players for several species.
cisAnalyzer is a novel Perl and R based tool able to assess DNA/RNA or peptididc cis-elements presence, localization and enrichment on a set of target nucleotide or amino acid sequences. It reports both the classic results of motif searches and generates and illustrates downstream analyses that gather motif- or target sequences-centered information, fasting the biological interpretation of the predictions. Users can search known motifs from a curated plant cis-elements dataset (PASPds) on promoters, own motifs from any species or discover new motifs by selecting the enrichment lineal pattern discovery on their target sequence set.
Reference: Gismondi M et al. (2020) Generation of fruit postharvest gene datasets and a novel motif analysis tool for functional studies: uncovering links between peach fruit heat treatment and cold storage responses. Planta. 251(2):53. DOI: https://doi.org/10.1007/s00425-020-03340-2
The success of plant breeding programs is reflected in their ability to select genotypes with good adaptation and stability at the cultivated area. In advanced stages of these programs, multi-environment trials (MET) are one of the most common experiments carried out. These trials are essential due to the prevalence of genotype-environment (GE) interactions, which represent one of the main problems for plant breeders. Key concepts such as mega-environments, specific adaptation, and stability can be analyzed out of the GE interaction.
Geneticae Shiny Web APP is an application that provides a graphical user interface for MET data analyses, so that it can be used by breeders and analysts with no previous experience in programming. It is an interactive, non-commercial and open source software, offering a free alternative to available commercial software. It is based on geneticae R package, created to gather in one place the most useful functions for GE interaction analysis. It also implements new methodology recently found in literature.
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