Comparative transcriptome analyses between cultivated and wild grapes reveal conservation of expressed genes but extensive rewiring of co-expression networks.

Key message The transcriptomes of wild and cultivated grapes consists of similar expressed genes but distinct wiring of co-expressed modules associated with environmental conditions. Abstract Grapevine is an important fruit crop worldwide, with high economic value and widespread distribution. Commercial production is based on Vitis vinifera, and, to a lesser extent, on hybrids with American grapes, such as V. labrusca. Wild grape relatives are important sources of resistance against biotic and abiotic factors; however, their global gene expression patterns remain poorly characterized. We associated genome-wide transcript profling to phenotypic analyses to investigate the responses of cultivated and wild vines to vineyard conditions. The expressed genes in the Vitis reference transcriptome are largely shared by wild grapes, V. labrusca hybrids and vinifera cultivars. In contrast, signifcant diferential regulation between wild and vinifera genotypes represents 80% of gene expression variation, regardless of the environment. In wild grapes, genes associated to regulatory processes are downregulated, whereas those involved in metabolic pathways are upregulated, in comparison to vinifera. Photosynthesis-related ontologies are overrepresented in the induced genes, in agreement with higher contents of chlorophyll in wild grapes. Co-regulated gene network analyses provide evidence of more complex transcriptome organization in vinifera. In wild grapes, genes involved in signaling pathways of stress-related hormones are overrepresented in modules associated with the environment. Consensus network analyses revealed high preservation within co-regulated gene modules between cultivated and wild grapes, but divergent relationships among the expression clusters. In conclusion, the distinct phenotypes of wild and cultivated grapes are underlain by diferences in gene expression, but also by distinct higher-order organization of the transcriptome and contrasting association of co-expressed gene clusters with the environment

Genetic diversity in soybean germplasm identified by SSR and EST-SSR markers.

Os objetivos deste trabalho foram avaliar a diversidade genética de 79 acessos de soja de diferentes regiões do mundo, agrupá-los de acordo com a similaridade e testar a correlação entre os dois tipos de marcadores utilizados. Foram utilizados marcadores microssatélites genômicos (SSR) e funcionais (EST-SSR). Trinta pares de primers SSR foram selecionados (20 genômicos e 10 EST-SSR) de acordo com sua distribuição nos 20 grupos de ligação da soja, com sua unidade de repetição trinucleotídica e com seu conteúdo de informação polimórfica. Todos os lócus analisados foram polimórficos, e 259 alelos foram encontrados. O número de alelos por lócus variou entre 2?21, com média de 8,63. Os acessos possuem uma quantidade significativa de alelos raros, sendo os acessos 19, 35, 63 e 65 os que apresentaram maior número de alelos exclusivos. Os acessos 75 e 79 são os mais similares e os acessos 31 e 35, e 40 e 78 são os mais divergentes. Foi observada baixa correlação entre resultados de SSR e EST-SSR. Portanto, uma análise adequada de diversidade em soja deve ser feita utilizando-se tanto marcadores microssatélites genômicos como funcionais. A diversidade genética dos acessos selecionados é alta, tendo sido encontrados cinco grupos e vários subgrupos. Observou-se moderada relação entre divergência genética e origem geográfica dos acessos

Identification of a novel a-L-arabinofuranosidase gene associated with mealiness in apple.

In order to investigate the genetic bases of the physiological syndrome mealiness that causes abnormal fruit softening and juice loss in apples, an integrative approach was devised, consisting of sensory, instrumental, biochemical, genetic, and genomic methods. High levels of activity of a-L-arabinofuranosidase (a-AFase), a hydrolase acting on the pectic component of the cell walls, were found in individuals exhibiting the mealiness phenotype in a segregating population. The expression levels of the previously uncharacterized apple AF gene MdAF3 are higher in fruits from plants consistently showing mealiness symptons and high a-AFase activity. The transcription of MdAF3 is differentially regulated in distinct genomic contexts and appears to be independent of ethylene. Thus, it is likely to be controlled by endogenous developmental mechanisms associated with fruit ripening. The use of integrative approaches has allowed the identification of a novel contributor to the mealiness phenotype in apple and it has been possible to overcome the problems posed by the unavailability of near-isogenic lines to dissect the genetic bases of a complex physiological trait in woody perennial species

Genome-wide analysis of the AP2/ERF superfamily in apple and transcriptional evidence of ERF involvement in scab pathogenesis.

The APETALA2 (AP2)/ETHYLENE RESPONSE FACTOR (ERF) superfamily of transcriptional regulators is involved in several growth, development and stress responses processes in higher plants. Currently, the available information on the biological roles of AP2/ERF genes is derived from Arabidopsis thaliana. In the present work, we have investigated genomic and transcriptional aspects of AP2/ERF genes in the economically important perennial species, Malus × domestica. We have identified 259 sequences containing at least one ERF domain in apple genome. The vast majority of the putative proteins display predicted nuclear localization, compatible with a biological role in transcription regulation. The AP2 and ERF families are greatly expanded in apple. Wholegenome analyses in other plant species have identified a single genomic sequence with divergent ERF, whereas in apple seven soloists are present. In the apple genome, the most noteworthy expansion occurred in subgroups V, VIII and IX of the ERF family. Expression profiling analyses have revealed the association of ripeninginvolved ERF genes to scab (Venturia inequalis) pathogenesis in the susceptible Gala cultivar, indicating that gene expansion processes were accompanied by functional divergence. The presented analyses of AP2/ERF genes in apple provide evidences of shared ethylenemediated signaling pathways in ripening and disease responses

Marcadores moleculares para análise genética de germoplasma de pereira: uso na organização dos recursos genéticos e no melhoramento genético.

O objetivo deste estudo foi o de ajustar as metodologias científicas para a obtenção de marcadores microssatélites e RAPD para análise genética do germoplasma conservado em coleções de pera, visando à organização dos recursos genéticos da espécie do Brasil e ao apoio de atividades de melhoramento genético.bitstream/item/73908/1/Circular-Tecnica-93-online.pd

Contrasting transcriptional programs control postharvest development of apples (Malus x domestica Borkh.) submitted to cold storage and ethylene blockage.

Apple is commercially important worldwide. Favorable genomic contexts and postharvest technologies allow year-round availability. Although ripening is considered a unidirectional developmental process toward senescence, storage at low temperatures, alone or in combination with ethylene blockage, is effective in preserving apple properties. Quality traits and genome wide expression were integrated to investigate the mechanisms underlying postharvest changes. Development and conservation techniques were responsible for transcriptional reprogramming and distinct programs associated with quality traits. A large portion of the differentially regulated genes constitutes a program involved in ripening and senescence, whereas a smaller module consists of genes associated with reestablishment and maintenance of juvenile traits after harvest. Ethylene inhibition was associated with a reversal of ripening by transcriptional induction of anabolic pathways. Our results demonstrate that the blockage of ethylene perception and signaling leads to upregulation of genes in anabolic pathways. We also associated complex phenotypes to subsets of differentially regulated genes. KEYWORDS: 1-methylcyclopropene, firmness, fruit quality, gene expression, microarra

Resíduos de ácido 2,4-diclorofenoxiacético em vidrarias de cultura de tecidos: seus efeitos e um protocolo para descontaminação.

Resumo

Otimização de marcadores desenvolvidos para PCR convencional para uso em qPCR visando a diagnose de Xanthomonas campestris pv viticola em videira.

No Brasil, Xanthomonas campestris pv. viticola (Xcv), causadora do cancro bacteriano em videira, é uma praga quarentenária A2, com ocorrência no Semiárido Nordestino. A bactéria pode ser disseminada de plantas assintomáticas pela distribuição de material propagativo e ocorrências restritas da doença em outras regiões foram identificadas. Para diagnose confiável por PCR convencional, o DNA deve ser extraído de culturas de bactérias isoladas de tecido com sintomas suspeitos. Com a técnica, é possível detectar até 0,25 pg de DNA bacteriano total. Atualmente, métodos que empregam tecidos assintomáticos não estão disponíveis. O objetivo deste trabalho foi desenvolver um protocolo sensível à detecção de Xcv por qPCR, empregando iniciadores disponíveis da técnica convencional.(Embrapa Uva e Vinho. Documentos, 99