Genetic dissection of the dwarfing effect of the apple rootstock 'M.9' : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Plant Biology at Massey University, Palmerston North, New Zealand

The dwarfing phenomenon in apple is mainly characterized by the ability of a rootstock to reduce the vegetative growth and ultimate size of the scion grafted onto it. Many hypotheses have been proposed to explain the dwarfing effect of rootstocks, from the production and translocation of hormones to the altered anatomy of the graft union. However, despite the numerous studies undertaken, none of the studies support a single hypothesis. This study focussed on identifying genetic markers for genomic regions influencing the dwarfing effect of 'Malling 9' ('M.9'). Two rootstock populations derived from crosses between 'M.9' and the vigorous rootstock 'Robusta 5' ('R5') were propagated and phenotyped at the HortResearch Havelock North Research Centre (New Zealand). Bulked segregant analysis (BSA) and QTL analysis were performed using phenotypic data collected from scions grafted onto the rootstock populations. Several genomic regions in 'M.9' and 'R5' were found to have a significant influence on the dwarfing phenotype and other related traits. The percentage of variation explained by these QTLs ranged from 4.2% to 57.2%. A large number of traits had significant variation associated with the major dwarfing QTL DWJ (identified previously by BSA), confirming the influence of this gene on tree architecture. To identify the genes responsible for the dwarfing effect, a microarray analysis on RNA extracted from bark tissues was performed to detect genes differentially expressed among dwarfing and vigorous rootstocks derived from the 'M.9' x 'R5' family. Following the mapping of 16 markers developed from 12 candidate genes, their position was compared with those of the QTLs identified previously and co­ localisations among genes and QTLs were identified. Results to date indicate that none of these particular CGs co-segregate with DW1. In order to estimate the number of different genetic sources of dwarfing present in commercial rootstocks, two SSR markers mapping about 0.5 cM away from the dwarfing QTL DWJ were screened over 58 rootstock accessions. The majority of the dwarf and semi-dwarf accessions screened carried the locus DWl, indicating that there may be only a single genetic source of dwarfing in apple rootstocks. The identification of markers for dwarfing will have a major impact on apple rootstock breeding, which currently relies on laborious phenotyping of individuals in breeding populations that presently takes at least 5-7 years to adequately perform. The identification of the genetic function of DWJ would provide an opportunity to develop dwarfing rootstocks for other members of the Rosaceae family for which such rootstocks have not yet been developed

Espaço Público: Espetáculo, vigilância e controle

3º congresso – As múltiplas Faces da Arquitetura Contemporânea de 2016 – As múltiplas Faces da Arquitetura Contemporânea – foram apresentados pelos/as estudantes da disciplina de Crítica e História da Arquitetura e da Cidade IV sob orientação da professora Andreia Moassab, do curso de Arquitetura e Urbanismo da Universidade Federal da Integração Latino-americana – UNILA. O congresso é parte da avaliação final da disciplina, no qual os/as estudantes apresentam a sua versão e dialogam com autores/as e textos de referência sobre a arquitetura nas últimas décadasO espaço público tem como característica o coletivo, segundo a pesquisadora Diane Ghirardo. A autora demonstra como este espaço, após a segunda guerra mundial foi repensado. Se no período antecedente o espaço público constituía uma esfera otimista, voltado ao povo, a partir das décadas de 50 e 60, ele passa a ter uma concepção exclusivista, barrado às diferenças que compõem a sociedad

Genome-wide SNP identification by high-throughput sequencing and selective mapping allows sequence assembly positioning using a framework genetic linkage map

<p>Abstract</p> <p>Background</p> <p>Determining the position and order of contigs and scaffolds from a genome assembly within an organism's genome remains a technical challenge in a majority of sequencing projects. In order to exploit contemporary technologies for DNA sequencing, we developed a strategy for whole genome single nucleotide polymorphism sequencing allowing the positioning of sequence contigs onto a linkage map using the bin mapping method.</p> <p>Results</p> <p>The strategy was tested on a draft genome of the fungal pathogen <it>Venturia inaequalis</it>, the causal agent of apple scab, and further validated using sequence contigs derived from the diploid plant genome <it>Fragaria vesca</it>. Using our novel method we were able to anchor 70% and 92% of sequences assemblies for <it>V. inaequalis </it>and <it>F. vesca</it>, respectively, to genetic linkage maps.</p> <p>Conclusions</p> <p>We demonstrated the utility of this approach by accurately determining the bin map positions of the majority of the large sequence contigs from each genome sequence and validated our method by mapping single sequence repeat markers derived from sequence contigs on a full mapping population.</p

Widespread anti-sense transcription in apple is correlated with siRNA production and indicates a large potential for transcriptional and/or post-transcriptional control

Characterizing the transcriptome of eukaryotic organisms is essential for studying gene regulation and its impact on phenotype. The realization that anti-sense (AS) and noncoding RNA transcription is pervasive in many genomes has emphasized our limited understanding of gene transcription and post-transcriptional regulation. Numerous mechanisms including convergent transcription, anti-correlated expression of sense and AS transcripts, and RNAi remain ill-defined.Here, we have combined microarray analysis and high-throughput sequencing of small RNAs (sRNAs) to unravel the complexity of transcriptional and potential post-transcriptional regulation in eight organs of apple (Malus × domestica). The percentage of AS transcript expression is higher than that identified in annual plants such as rice and Arabidopsis thaliana. Furthermore, we show that a majority of AS transcripts are transcribed beyond 3′UTR regions, and may cover a significant portion of the predicted sense transcripts. Finally we demonstrate at a genome-wide scale that anti-sense transcript expression is correlated with the presence of both short (21–23 nt) and long (&gt; 30 nt) siRNAs, and that the sRNA coverage depth varies with the level of AS transcript expression. Our study provides a new insight on the functional role of anti-sense transcripts at the genome-wide level, and a new basis for the understanding of sRNA biogenesis in plants

Ethylene receptors and related proteins in climacteric and non-climacteric fruits

Fruits have been traditionally classified into two categories based on their capacity to produce and respond to ethylene during ripening. Fruits whose ripening is associated to a peak of ethylene production and a respiration burst are referred to as climacteric, while those that are not are referred to as non-climacteric. However, an increasing body of literature supports an important role for ethylene in the ripening of both climacteric and non-climacteric fruits. Genome and transcriptomic data have become available across a variety of fruits and we leverage these data to compare the structure and transcriptional regulation of the ethylene receptors and related proteins. Through the analysis of four economically important fruits, two climacteric (tomato and apple), and two non-climacteric (grape and citrus), this review compares the structure and transcriptional regulation of the ethylene receptors and related proteins in both types of fruit, establishing a basis for the annotation of ethylene-related genes. This analysis reveals two interesting differences between climacteric and non-climacteric fruit: i) a higher number of ETR genes are found in climacteric fruits, and ii) non-climacteric fruits are characterized by an earlier ETR expression peak relative to sugar accumulation

Ecological, modelling and genetic researches on bud phenology in apple to adapt the flowering phase facing temperature increases in occidental Europe

International audienceFruit tree industry shows many vulnerabilities to adapt to climate change due to perennialand complex cropping systems, considerable irrigation needs and multiple effects oftemperature. Moreover, clear increases in temperature have been recorded in all fruit treeareas of western Europe since the end of the 1980s. The annual mean temperaturesincreased by about 1°C, although the increase of monthly temperatures differeddepending on the regions and was greater in winter than in autumn at all studied locations(Figures 1 and 2). The present context of global warming renews the interest in budphenology which was the main agronomic trait obviously changed in recent past in Europe(Guédon and Legave, 2008, Legave, 2009). In what follows, we summarise results thathave been recently obtained on apple trees in France on phenological adaptation byecological, modelling and genetic approaches. Firstly, phenological data have beencollected for main cultivars and analysed through modelling to understand the observedchanges in climate contrasting regions (Figure 2). Following this analysis, genetic studieshave been carried out on apple progenies to provide efficient tools for programs aimed atbreeding better adapted varieties for future environmental conditions