BackgroundIron toxicity is a root related abiotic stress, occurring frequently in flooded soils. It can affect the yield of rice in lowland production systems. This toxicity is associated with high concentrations of reduced iron (Fe2+) in the soil solution. Although the first interface of the element is in the roots, the consequences of an excessive uptake can be observed in several rice tissues. In an original attempt to find both genes and transposable elements involved in the response to an iron toxicity stress, we used a microarray approach to study the transcriptional responses of rice leaves of cv. Nipponbare (Oryza sativa L. ssp. japonica) to iron excess in nutrient solution.ResultsA large number of genes were significantly up- or down-regulated in leaves under the treatment. We analyzed the gene ontology and metabolic pathways of genes involved in the response to this stress and the cis-regulatory elements (CREs) present in the promoter region of up-regulated genes. The majority of genes act in the pathways of lipid metabolic process, carbohydrate metabolism, biosynthesis of secondary metabolites and plant hormones. We also found genes involved in iron acquisition and mobilization, transport of cations and regulatory mechanisms for iron responses, and in oxidative stress and reactive oxygen species detoxification. Promoter regions of 27% of genes up-regulated present at least one significant occurrence of an ABA-responsive CRE. Furthermore, and for the first time, we were able to show that iron stress triggers the up-regulation of many LTR-retrotransposons. We have established a complete inventory of transposable elements transcriptionally activated under iron excess and the CREs which are present in their LTRs.ConclusionThe short-term response of Nipponbare seedlings to iron excess, includes activation of genes involved in iron homeostasis, in particular transporters, transcription factors and ROS detoxification in the leaves, but also many transposable elements. Our data led to the identification of CREs which are associated with both genes and LTR-retrotransposons up-regulated under iron excess. Our results strengthen the idea that LTR-retrotransposons participate in the transcriptional response to stress and could thus confer an adaptive advantage for the plant.Electronic supplementary materialThe online version of this article (doi:10.1186/s12284-015-0045-6) contains supplementary material, which is available to authorized users.

Rice is a model genome for cereal research, providing important information about genome structure and evolution. Retrotransposons are common components of grass genomes, showing activity at transcription, translation and integration levels. Their abundance and ability to transpose make them good potential markers. In this study, we used 2 multilocus PCR-based techniques that detect retrotransposon integration events in the genome: IRAP (inter-retrotransposon amplified polymorphism) and REMAP (retrotransposon-microsatellite amplified polymorphism). Markers derived from Tos17, a copia-like endogenous retrotransposon of rice, were used to identify genetic similarity among 51 rice cultivars (Oryza sativa L.). Genetic similarity analysis was performed by means of the Dice coefficient, and dendrograms were developed by using the average linkage distance method. A cophenetic correlation coefficient was also calculated. The clustering techniques revealed a good adjustment between matrices, with correlation coefficients of 0.74 and 0.80, or lower (0.21) but still significant, between IRAP and REMAP-based techniques. Consistent clusters were found for Japanese genotypes, while a subgroup clustered the irrigated Brazilian genotypes.

The objective of this work was to evaluate the genetic variability for the synthesis of bioactive compounds and minerals in pumpkin (Cucurbita moschata) landraces. Total phenolic compounds, carotenoids, antioxidant activity and minerals were evaluated in 10 accessions of Cucurbita moschata landraces from the Genebank of Embrapa Temperate Agriculture (Pelotas -RS, Brazil). Twenty plants of each accession were cultivated in the field during the spring/summer of 2013/2014. After harvesting of mature fruits, the seeds were discarded and opposite longitudinal portions of the pulp were manually prepared for analysis of the bioactive compounds. For the determination of minerals, pumpkin samples were frozen in plastic bags, and after freeze-dried and milled. All analysis were performed in triplicate. The data obtained showed high genetic variability for the synthesis of phenolic compounds, carotenoids, antioxidant activity and minerals. The accessions C52, C81, C267 e C389 showed high levels of antioxidants and minerals, being recommended for use in pumpkin breeding programs. The accessions C52 and C389 are promising, especially because they present the highest levels of total carotenoids.Keywords: pumpkin; cucurbitaceae; ex situ conservation; genetic resources; characterization.Practical Application: Pumpkins (Cucurbita moschata) are important to the human diet due to its functional properties and benefits for the human health. Identify genetic variability for the synthesis of bioactive compounds and minerals can be useful for breeding programs, to develop cultivars with improved benefits to the consumers.

RESUMO O objetivo deste trabalho foi caracterizar morfologicamente variedades crioulas de Cucurbita maxima do sul do Brasil. Nove variedades crioulas de C. maxima foram caracterizadas com sete descritores quantitativos e 13 descritores qualitativos. As sementes foram cultivadas em casa de vegetação, em sacos de poliestireno preto, preenchidos com substrato. Quando as plantas apresentavam no mínimo duas folhas definitivas, 20 mudas de cada variedade foram transplantadas para o campo experimental, em delineamento completamente casualizado. Os dados quantitativos foram submetidos à análise de variância e foi utilizado o teste de Tukey para a comparação de médias, com o programa SAS 9.2. Os dados de caracteres quantitativos foram submetidos à análise de componentes principais, com o programa R. Para os caracteres qualitativos, a caracterização foi expressa pela moda de cada acesso, para cada descritor. Os caracteres qualitativos foram analisados como variáveis multicategóricas. A matriz de similaridade foi gerada no programa computacional GENES e foi construído um dendrograma, pelo método UPGMA, com o programa NTSYS. Ficou evidenciada a variabilidade genética para os caracteres quantitativos e qualitativos avaliados. A análise de variância evidenciou diferenças significativas entre as médias. Peso, formato, cor do fruto, espessura da casca e número de sementes por fruto são caracteres relevantes para a indicação de variedades crioulas promissoras para o melhoramento genético, com potencial para uso como fontes de genes e desenvolvimento de cultivares.

Molecular characterization of landraces of peppers (Capsicum baccatum) with SSR markersCurrently, many landraces of C. baccatum are grown by farmers in Brazil. These populations are sources of genes for resistance or tolerance to abiotic and biotic stresses. However, most of these landraces are being lost due to genetic erosion caused by substitution of cultivars. In order to characterize and conserve landraces, since 2002 Embrapa Temperate Agriculture maintains an Active Germplasm Bank of Capsicum. This work has the objective to characterize landraces of C. baccatum using microsatellite markers. 20 accessions from the Active Germplasm Bank of Capsicum of Embrapa Temperate Agriculture were analyzed. DNA was extracted individually from young leaves collected from five plants of each accession. Eight microsatellite loci were analyzed. All loci were polymorphic. Molecular analysis of variance showed values of genetic diversity as 51.37% among accessions and 48.63% within the accessions. This fact showed the existence of segregation in many of these pepper landraces. The groups obtained by cluster analysis did not correlate with morphological fruit traits. Most of the genetic variability is found among different landraces, although there is also genetic variability within each accession.