Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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    An open simulation strategy for rapid control design in aerial and maritime drone teams : A comprehensive tutorial
    Velasco, Omar ; Valente, João ; Alhama Blanco, Pablo J. ; Abderrahim, Mohammed - \ 2020
    Drones 4 (2020)3. - ISSN 2504-446X - p. 1 - 20.
    Limnology - Multi-robot system - Open source - Robotic simulation - Unmanned aerial vehicle - Unmanned surface vehicle - Water drone

    The deployment of robot controllers into the real robotic platform is cumbersome and time consuming, especially when testing scenarios involve several robots or are sites not easily accessible. Besides this, most of the time, testing on the real platforms or real conditions provides little value in the early stages of controller design and prototype, phases where debugging and suitability of the controller are the main objectives. This paper proposes a simulation strategy for developing and testing controllers for Unmanned Aerial and Surface Vehicle coordination and interaction with the environment. The simulation strategy is based on V-REP and Matlab/Simulink which provide a large set of features, modularity and compatibility across platforms. Results show that this approach significantly reduces development and delivery times by providing an off-the-shelf simulation environment and a step-by-step implementation guidelines. The source code to deploy the simulations is available in an open-source repository.

    Online drone education, a mapping review
    Velasco, Omar ; Valente, Joao - \ 2020
    In: Proceedings of the 2020 IEEE Global Engineering Education Conference, EDUCON 2020. - IEEE computer society (IEEE Global Engineering Education Conference, EDUCON ) - ISBN 9781728109312 - p. 1286 - 1289.
    Drones - M00C - Online Education - UAV

    As Unmanned Aerial Vehicles (UAV) increase in popularity, legislation, use and applications education becomes a paramount objective for safety reasons and correct usage of this technology. Online education is becoming one of the main sources of knowledge, especially thanks to the wider geographical and social reach. Online education regarding UAVs has become a crucial mean to transfer and spread this knowledge. This work presents a mapping review of the state of such education with the aim of finding knowledge gaps and areas of improvement.

    Scaling readiness : Concepts, practices, and implementation
    Sartas, Murat ; Schagen, Boudy van; Velasco, Claudio ; Thiele, Graham ; Proietti, Claudio ; Leeuwis, Cees - \ 2020
    Lima : International Potato Center (Working paper ) - ISBN 9789290605324 - 217
    Pseudo-chromosome-length genome assembly of a double haploid "Bartlett" pear (Pyrus communis L.)
    Linsmith, Gareth ; Rombauts, Stephane ; Montanari, Sara ; Deng, Cecilia H. ; Celton, Jean Marc ; Guérif, Philippe ; Liu, Chang ; Lohaus, Rolf ; Zurn, Jason D. ; Cestaro, Alessandro ; Bassil, Nahla V. ; Bakker, Linda V. ; Schijlen, Elio ; Gardiner, Susan E. ; Lespinasse, Yves ; Durel, Charles Eric ; Velasco, Riccardo ; Neale, David B. ; Chagné, David ; Peer, Yves Van de; Troggio, Michela ; Bianco, Luca - \ 2019
    GigaScience 8 (2019)12. - ISSN 2047-217X
    chromosome-scale assembly - Hi-C - Pac-Bio sequencing - Pyrus communis L

    BACKGROUND: We report an improved assembly and scaffolding of the European pear (Pyrus communis L.) genome (referred to as BartlettDHv2.0), obtained using a combination of Pacific Biosciences RSII long-read sequencing, Bionano optical mapping, chromatin interaction capture (Hi-C), and genetic mapping. The sample selected for sequencing is a double haploid derived from the same "Bartlett" reference pear that was previously sequenced. Sequencing of di-haploid plants makes assembly more tractable in highly heterozygous species such as P. communis. FINDINGS: A total of 496.9 Mb corresponding to 97% of the estimated genome size were assembled into 494 scaffolds. Hi-C data and a high-density genetic map allowed us to anchor and orient 87% of the sequence on the 17 pear chromosomes. Approximately 50% (247 Mb) of the genome consists of repetitive sequences. Gene annotation confirmed the presence of 37,445 protein-coding genes, which is 13% fewer than previously predicted. CONCLUSIONS: We showed that the use of a doubled-haploid plant is an effective solution to the problems presented by high levels of heterozygosity and duplication for the generation of high-quality genome assemblies. We present a high-quality chromosome-scale assembly of the European pear Pyrus communis and demostrate its high degree of synteny with the genomes of Malus x Domestica and Pyrus x bretschneideri.

    Genome wide association studies and whole transcriptomic survey decipher the fruit texture regulation in apple towards the selection of novel superior accessions
    Guardo, M. Di; Tadiello, A. ; Farneti, B. ; Busatto, N. ; Delledonne, M. ; Guerra, W. ; Letschka, T. ; Lozano, L. ; Velasco, R. ; Weg, E. Van de; Bink, M. ; Costa, F. - \ 2019
    Acta Horticulturae 1242 (2019). - ISSN 0567-7572 - p. 441 - 446.
    Ethylene - Fruit quality - GWAS - Marker assisted selection - Pedigree based analysis - Texture

    Fruit quality is represented by a series of genetically controlled features that change throughout the entire ontogenic life. Among the several quality traits, texture plays a crucial role, impacting both consumers’ appreciation and postharvest performance. In order to decipher its regulation a multidisciplinary approach was employed. Initially, the texture performance was measured with a high resolution phenotyping device, represented by a texture analyzer equipped with an acoustic device. In the first attempt to dissect the fruit texture genetic control, two QTL mapping strategies were used. The first approach employed six bi-parental families linked by a common pedigree scheme, known as pedigree based analysis. The joint analysis of the phenotypic and genotypic data set through a Bayesian statistics identified a series of genomic regions related to both mechanical and acoustic signatures. These regions were further validated with a genome wide association study approach, which considered a much larger phenotypic and genotypic variation. To complement the genetic information, a whole transcriptome analysis was also carried out. To this end, two microarray platforms were designed and used to unravel the functional machinery ongoing during the fruit development and ripening phases, especially with regards to the plant hormone ethylene. In this study, the role of this hormone was dissected applying 1-MCP, a molecule competing with ethylene at receptor level. The combination of these resources provides a valuable source of information, essential to step forward in the comprehension of the genetic and physiological regulation of the fruit texture in apple. This knowledge would enable, in a close future, a more accurate and precise selection of the most favourable and valuable new apple accessions distinguished by a superior fruit quality.

    Experimental design of a mobile landing platform to Assist Aerial Surveys in fluvial environments
    Borreguero, David ; Velasco, Omar ; Valente, João - \ 2019
    Applied Sciences 9 (2019)1. - ISSN 2076-3417
    Field robotics - Fluvial environments - Mechatronics - Unmanned aerial vehicles - Unmanned surface vehicles

    Sampling aquatic ecosystems is a laborious and expensive task, especially when covering large areas. This can be improved using unmanned aerial vehicles (UAVs) equipped with various remote sensing sensors. However, the UAV performance and autonomy may vary due to external factors when it is operated outdoors. In some cases, an emergency landing maneuver is necessary to avoid an accident, since in fluvial environments, the UAV control landing becomes a difficult operation. Therefore, it is important to have a backup platform on the water to fix this problem. This paper presents the design and development of a custom-built unmanned surface vehicle using open-source tools and with two types of operation-remotely piloted and autonomous-to support remote sensing practices with UAVs in fluvial environments. Finally, part of the software developed within this project was released in an open-source repository.

    A Conceptual Framework for Identifying the Binding Constraints to Tourism-Driven Inclusive Growth
    Bakker, Martine - \ 2019
    Tourism Planning and Development 16 (2019)5. - ISSN 2156-8316 - p. 575 - 590.
    constraints - diagnostic - Inclusive growth - inequality - tourism and development

    Continued discussions concerning the adverse effects of high levels of inequality require a better understanding of tourism’s contribution to inclusive growth. If tourism is to be supportive of inclusive growth, it must create productive employment opportunities, while also ensuring equal access to these opportunities. This paper aims to analyse the constraints that prohibit the tourism sector from being a catalyst for inclusive growth, by developing a Tourism-Driven Inclusive Growth Diagnostic (T-DIGD) framework. This conceptual framework is adapted from the Hausmann, Rodrik, and Velasco growth diagnostic to the specific needs of the tourism sector and can support practitioners through a structured knowledge building process, in the design of policies and interventions that can promote inclusive growth. The TIGDF departs from conventional and mainly quantitative approaches of the drivers of tourism growth and focuses on the “deep determinants” of tourism-driven inclusive growth.

    Innovation platforms in agricultural research development : Ex-ante Appraisal of the Purposes and Conditions Under Which Innovation Platforms can Contribute to Agricultural Development Outcomes
    Schut, Marc ; Kamanda, Josey ; Gramzow, Andreas ; Dubois, Thomas ; Stoian, Dietmar ; Andersson, Jens A. ; Dror, Iddo ; Sartas, Murat ; Mur, Remco ; Kassam, Shinan ; Brouwer, Herman ; Devaux, André ; Velasco, Claudio ; Flor, Rica Joy ; Gummert, Martin ; Buizer, Djuna ; Mcdougall, Cynthia ; Davis, Kristin ; Tui, Sabine Homann-Kee ; Lundy, Mark - \ 2019
    Experimental Agriculture 55 (2019)4. - ISSN 0014-4797 - p. 575 - 596.
    Innovation platforms are fast becoming part of the mantra of agricultural research for development projects and programmes. Their basic tenet is that stakeholders depend on one another to achieve agricultural development outcomes, and hence need a space where they can learn, negotiate and coordinate to overcome challenges and capture opportunities through a facilitated innovation process. Although much has been written on how to implement and facilitate innovation platforms efficiently, few studies support ex-ante appraisal of when and for what purpose innovation platforms provide an appropriate mechanism for achieving development outcomes, and what kinds of human and financial resource investments and enabling environments are required. Without these insights, innovation platforms run the risk of being promoted as a panacea for all problems in the agricultural sector. This study makes clear that not all constraints will require innovation platforms and, if there is a simpler and cheaper alternative, that should be considered first. Based on the review of critical design principles and plausible outcomes of innovation platforms, this study provides a decision support tool for research, development and funding agencies that can enhance more critical thinking about the purposes and conditions under which innovation platforms can contribute to achieving agricultural development outcomes.
    Intensification of rice-based farming systems in Central Luzon, Philippines : Constraints at field, farm and regional levels
    Silva, João Vasco ; Reidsma, Pytrik ; Lourdes Velasco, Ma ; Laborte, Alice G. ; Ittersum, Martin K. van - \ 2018
    Agricultural Systems 165 (2018). - ISSN 0308-521X - p. 55 - 70.
    Crop management - Farm structural change - Farmers’ objectives - Integrated assessment - Sustainable intensification - Yield gap

    Understanding the opportunities for sustainable intensification requires an integrated assessment at field, farm and regional levels of past developments. Two hypotheses regarding current rice production in Central Luzon (Philippines) were developed for this purpose. First, we hypothesize that there are trade-offs between rice yields, labour productivity, gross margin and N use efficiency and, second, that farm(er) characteristics and socio-economic conditions at farm and regional level affect the management practices used by farmers. These hypotheses were tested using two household surveys characterizing rice-based farming systems in Central Luzon in terms of changes over time (1966–2012) and spatial variability. Over the past half-century there was an increase in the proportion of irrigated fields and adoption of improved varieties, which allowed the cultivation of a dry season rice crop in Central Luzon. Moreover, transplanting has been replaced by direct-seeding and herbicides substituted hand-weeding. These resulted in greater rice yields and labour productivity, and contributed to gradual transition from subsistence to commercial farming systems, as observed in the increasing proportion of hired labour and rice sold. Our results indicate the existence of a trade-off between rice yields, labour productivity and N use efficiency as yield levels maximising labour productivity and N use efficiency were ca. 25% and 35% lower than climatic potential yield in the wet and dry season, respectively. At field level, this can be explained by 1) the use of transplanting as crop establishment method, which resulted into higher yields but lower labour productivity as compared to direct-seeding, and 2) the high N application levels, which led to higher yields but lower N use efficiency. In contrast, yield levels which maximised gross margin were ca. 80% of the climatic potential in both wet and dry seasons, so there was little trade-off between rice yields and economic performance. Regarding the second hypothesis results were not always conclusive. As an example, N application per ha was negatively associated with farm size and the timing of the first fertiliser application positively associated with household size and with the number of parcels. More intensive practices, and better farm performance, were recorded in the province at the heart of the irrigation system. We thus conclude that closing rice yield gaps in the production systems of Central Luzon incurs trade-offs with environmental and social objectives at field and farm levels but less with economic objectives. However, we could not clearly show whether, and to what extent, management practices used by farmers are influenced by farm or regional level constraints.

    An integrated approach for increasing breeding efficiency in apple and peach in Europe
    Laurens, Francois ; Aranzana, Maria José ; Arus, Pere ; Bassi, Daniele ; Bink, Marco ; Bonany, Joan ; Caprera, Andrea ; Corelli-Grappadelli, Luca ; Costes, Evelyne ; Durel, Charles Eric ; Mauroux, Jehan Baptiste ; Muranty, Hélène ; Nazzicari, Nelson ; Pascal, Thierry ; Patocchi, Andrea ; Peil, Andreas ; Quilot-Turion, Bénédicte ; Rossini, Laura ; Stella, Alessandra ; Troggio, Michela ; Velasco, Riccardo ; De Weg, Eric Van - \ 2018
    Horticulture Research 5 (2018)1. - ISSN 2052-7276
    Despite the availability of whole genome sequences of apple and peach, there has been a considerable gap between genomics and breeding. To bridge the gap, the European Union funded the FruitBreedomics project (March 2011 to August 2015) involving 28 research institutes and private companies. Three complementary approaches were pursued: (i) tool and software development, (ii) deciphering genetic control of main horticultural traits taking into account allelic diversity and (iii) developing plant materials, tools and methodologies for breeders. Decisive breakthroughs were made including the making available of ready-to-go DNA diagnostic tests for Marker Assisted Breeding, development of new, dense SNP arrays in apple and peach, new phenotypic methods for some complex traits, software for gene/QTL discovery on breeding germplasm via Pedigree Based Analysis (PBA). This resulted in the discovery of highly predictive molecular markers for traits of horticultural interest via PBA and via Genome Wide Association Studies (GWAS) on several European genebank collections. FruitBreedomics also developed pre-breeding plant materials in which multiple sources of resistance were pyramided and software that can support breeders in their selection activities. Through FruitBreedomics, significant progresses were made in the field of apple and peach breeding, genetics, genomics and bioinformatics of which advantage will be made by breeders, germplasm curators and scientists. A major part of the data collected during the project has been stored in the FruitBreedomics database and has been made available to the public. This review covers the scientific discoveries made in this major endeavour, and perspective in the apple and peach breeding and genomics in Europe and beyond.
    Genome-wide association mapping of flowering and ripening periods in apple
    Urrestarazu, Jorge ; Muranty, Hélène ; Denancé, Caroline ; Leforestier, Diane ; Ravon, Elisa ; Guyader, Arnaud ; Guisnel, Rémi ; Feugey, Laurence ; Aubourg, Sébastien ; Celton, Jean Marc ; Daccord, Nicolas ; Dondini, Luca ; Gregori, Roberto ; Lateur, Marc ; Houben, Patrick ; Ordidge, Matthew ; Paprstein, Frantisek ; Sedlak, Jiri ; Nybom, Hilde ; Garkava-Gustavsson, Larisa ; Troggio, Michela ; Bianco, Luca ; Velasco, Riccardo ; Poncet, Charles ; Théron, Anthony ; Moriya, Shigeki ; Bink, Marco C.A.M. ; Laurens, François ; Tartarini, Stefano ; Durel, Charles Eric - \ 2017
    Frontiers in Plant Science 8 (2017). - ISSN 1664-462X
    Adaptive traits - Association genetics - Germplasm collection - GWAS - Malus × domestica Borkh - Microsynteny - Quantitative trait loci - SNP
    Deciphering the genetic control of flowering and ripening periods in apple is essential for breeding cultivars adapted to their growing environments. We implemented a large Genome-Wide Association Study (GWAS) at the European level using an association panel of 1,168 different apple genotypes distributed over six locations and phenotyped for these phenological traits. The panel was genotyped at a high-density of SNPs using the Axiom®Apple 480 K SNP array. We ran GWAS with a multi-locus mixed model (MLMM), which handles the putatively confounding effect of significant SNPs elsewhere on the genome. Genomic regions were further investigated to reveal candidate genes responsible for the phenotypic variation. At the whole population level, GWAS retained two SNPs as cofactors on chromosome 9 for flowering period, and six for ripening period (four on chromosome 3, one on chromosome 10 and one on chromosome 16) which, together accounted for 8.9 and 17.2% of the phenotypic variance, respectively. For both traits, SNPs in weak linkage disequilibrium were detected nearby, thus suggesting the existence of allelic heterogeneity. The geographic origins and relationships of apple cultivars accounted for large parts of the phenotypic variation. Variation in genotypic frequency of the SNPs associated with the two traits was connected to the geographic origin of the genotypes (grouped as North+East, West and South Europe), and indicated differential selection in different growing environments. Genes encoding transcription factors containing either NAC or MADS domains were identified as major candidates within the small confidence intervals computed for the associated genomic regions. A strong microsynteny between apple and peach was revealed in all the four confidence interval regions. This study shows how association genetics can unravel the genetic control of important horticultural traits in apple, as well as reduce the confidence intervals of the associated regions identified by linkage mapping approaches. Our findings can be used for the improvement of apple through marker-assisted breeding strategies that take advantage of the accumulating additive effects of the identified SNPs.
    Genome wide association study of two phenology traits (flowering time and maturity date) in apple
    Muranty, Hélène ; Urrestarazu, J. ; Denancé, C. ; Leforestier, D. ; Ravon, E. ; Guyader, A. ; Guisnel, R. ; Feugey, L. ; Tartarini, S. ; Dondini, L. ; Gregori, R. ; Lateur, M. ; Houben, E.H.P. ; Sedlak, J. ; Paprstein, F. ; Ordidge, M. ; Nybom, H. ; Garkava-Gustavsson, L. ; Troggio, M. ; Bianco, L. ; Velasco, R. ; Poncet, C. ; Théron, Anthony ; Bink, M.C.A.M. ; Laurens, F. ; Durel, C.E. - \ 2017
    In: 14th EUCARPIA Symposium on Fruit Breeding and Genetics International Society for Horticultural Science (Acta Horticulturae ) - ISBN 9789462611689 - p. 411 - 417.
    Germplasm collections - Malus × domestica - Marker-assisted selection
    The aim of Genome Wide Association Studies (GWAS) is to identify markers in tight linkage disequilibrium with loci controlling quantitative trait variation. These markers can then be used in marker-assisted selection (MAS) in fruit crops such as apple. The GWAS approach involves both phenotyping of a large population of mostly unrelated individuals for the traits of interest, and genotyping at high marker density. In the EU-FP7 project FruitBreedomics, almost 1,200 European diploid dessert apple accessions (old and/or local cultivars) from six germplasm collections were genotyped with the Affymetrix Axiom-Apple480K array (487,000 SNPs). Phenotypic data on a large number of traits have been gathered during the project. Here we focus on flowering period and harvesting date. Knowledge of the genetic control of these traits is necessary to develop cultivars that can face the challenges imposed by global climate change and to target cultivar development as a function of a prolonged vegetation period in the production regions. Different models were tested, including control for effects of population structure and relatedness between cultivars. The full model, controlling for both structure and relatedness, was shown to be the most appropriate to avoid spurious marker-trait associations. When analyzing data over all collections, one significant marker-trait association was obtained for each trait, on chromosomes 9 and 3, for flowering period and harvesting date, respectively. Thereby, genomic locations previously identified in bi-parental populations could now be confirmed for a genetically diverse germplasm.
    Guidelines for Innovation Platforms in Agricultural Research for Development : Decision support for research, development and funding agencies on how to design, budget and implement impactful Innovation Platforms
    Schut, M. ; Andersson, J.A. ; Dror, I. ; Kamanda, J. ; Sartas, M. ; Mur, R. ; Kassam, S. ; Brouwer, J.H. ; Stoian, D. ; Devaux, A. ; Velasco, C. ; Gramzow, A. ; Dubois, T. ; Flor, R.J. ; Gummert, M. ; Buizer, Djuna ; McDougall, C. ; Davis, K. ; Homann-Kee Tui, S. ; Lundy, M. - \ 2017
    International Institute of Tropical Agriculture - 88 p.
    Innovation Platforms are fast becoming part of the mantra of agricultural research for development projects and programmes. Their basic tenet is that stakeholders depend on one another to achieve agricultural development outcomes, and hence need a space where they can learn, negotiate, and coordinate to overcome challenges and capture opportunities through a facilitated innovation process. This important publication provides a critical analysis of Innovation Platforms, their defining features, key functions, and what they can and – as importantly – cannot do.

    It will be invaluable reading both for those who fund development projects and
    programmes and would like to understand when Innovation Platforms are the approach of choice, and for those practitioners who implement and facilitate Innovation Platforms and would like to understand better their design principles and practical implementation issues.

    Because Innovation Platforms have been successful in addressing agricultural challenges, there is a risk that they will be promoted as a panacea for all problems in the agricultural sector. As the authors make clear, however, not all constraints will require Innovation Platforms and, if there is a simpler and cheaper alternative, that should be the first choice. It is essential to think more critically about when, how, and in what form Innovation Platforms can contribute meaningfully to Agricultural development impacts.

    The document was developed through a learning collaboration between CGIAR
    research centres and other academic and more applied research centres. Eleven
    of the 15 CGIAR centres participated and contributed their expertise and experiences across multiple agricultural systems, geographies, and types of complex constraint. The booklet provides information grounded in a rich practical experience of key design and implementation principles, and the financial and human resources that need to be made available, and it makes suggestions for more effective monitoring, evaluation, and learning. It also lists reference materials, answers frequently asked questions, and provides a decision support tool for research, development, and funding agencies.

    All in all, this publication offers a lot for those who aspire to make sensible use of
    Innovation Platforms in pursuing agricultural development!
    Genome-wide association study unravels the genetic control of the apple volatilome and its interplay with fruit texture
    Farneti, Brian ; Guardo, Mario Di; Khomenko, Iuliia ; Cappellin, Luca ; Biasioli, Franco ; Velasco, Riccardo ; Costa, Fabrizio - \ 2017
    Journal of Experimental Botany 68 (2017)7. - ISSN 0022-0957 - p. 1467 - 1478.
    Ester - Fruit texture - Functional principal component analysis - GWAS - Multiple factor analysis - Phenylpropene - PTR-ToF-MS - SNP - VOCs - Volatilome

    Fruit quality represents a fundamental factor guiding consumers' preferences. Among apple quality traits, volatile organic compounds and texture features play a major role. Proton Transfer Reaction-Time of Flight-Mass Spectrometry (PTR-ToF-MS), coupled with an artificial chewing device, was used to profile the entire apple volatilome of 162 apple accessions, while the fruit texture was dissected with a TAXT-AED texture analyzer. The array of volatile compounds was classed into seven major groups and used in a genome-wide association analysis carried out with 9142 single nucleotide polymorphisms (SNPs). Marker-trait associations were identified on seven chromosomes co-locating with important candidate genes for aroma, such as MdAAT1 and MdIGS. The integration of volatilome and fruit texture data conducted with a multiple factor analysis unraveled contrasting behavior, underlying opposite regulation of the two fruit quality aspects. The association analysis using the first two principal components identified two QTLs located on chromosomes 10 and 2, respectively. The distinction of the apple accessions on the basis of the allelic configuration of two functional markers, MdPG1 and MdACO1, shed light on the type of interplay existing between fruit texture and the production of volatile organic compounds. c The Author 2017.

    High-quality de novo assembly of the apple genome and methylome dynamics of early fruit development
    Daccord, Nicolas ; Celton, Jean-Marc ; Linsmith, Gareth ; Becker, Claude ; Choisne, Nathalie ; Schijlen, Elio ; Geest, Henri van de; Bianco, Luca ; Micheletti, Diego ; Velasco, Riccardo ; Pierro, Erica Adele Di; Gouzy, Jérôme ; Rees, D.J.G. ; Guérif, Philippe ; Muranty, Hélène ; Durel, Charles Eric ; Laurens, François ; Lespinasse, Yves ; Gaillard, Sylvain ; Aubourg, Sébastien ; Quesneville, Hadi ; Weigel, Detlef ; Weg, Eric van de; Troggio, Michela ; Bucher, Etienne - \ 2017
    Nature Genetics 49 (2017)7. - ISSN 1061-4036 - p. 1099 - 1106.
    Using the latest sequencing and optical mapping technologies, we have produced a high-quality de novo assembly of the apple (Malus domestica Borkh.) genome. Repeat sequences, which represented over half of the assembly, provided an unprecedented opportunity to investigate the uncharacterized regions of a tree genome; we identified a new hyper-repetitive retrotransposon sequence that was over-represented in heterochromatic regions and estimated that a major burst of different transposable elements (TEs) occurred 21 million years ago. Notably, the timing of this TE burst coincided with the uplift of the Tian Shan mountains, which is thought to be the center of the location where the apple originated, suggesting that TEs and associated processes may have contributed to the diversification of the apple ancestor and possibly to its divergence from pear. Finally, genome-wide DNA methylation data suggest that epigenetic marks may contribute to agronomically relevant aspects, such as apple fruit development.
    Frequency of a natural truncated allele of MdMLO19 in the germplasm of Malus domestica
    Pessina, Stefano ; Palmieri, Luisa ; Bianco, Luca ; Gassmann, Jennifer ; De Weg, Eric Van; Visser, Richard G.F. ; Magnago, Pierluigi ; Schouten, Henk J. ; Bai, Yuling ; Riccardo Velasco, R. ; Malnoy, Mickael - \ 2017
    Molecular Breeding 37 (2017)1. - ISSN 1380-3743
    Podosphaera leucotricha is the causal agent of powdery mildew (PM) in apple. To reduce the amount of fungicides required to control this pathogen, the development of resistant apple cultivars should become a priority. Resistance to PM was achieved in various crops by knocking out specific members of the MLO gene family that are responsible for PM susceptibility (S-genes). In apple, the knockdown of MdMLO19 resulted in PM resistance. However, since gene silencing technologies such as RNAi are perceived unfavorably in Europe, a different approach that exploits this type of resistance is needed. This work evaluates the presence of non-functional naturally occurring alleles of MdMLO19 in apple germplasm. The screening of the re-sequencing data of 63 apple individuals led to the identification of 627 single nucleotide polymorphisms (SNPs) in five MLO genes (MdMLO5, MdMLO7, MdMLO11, MdMLO18, and MdMLO19), 127 of which were located in exons. The T-1201 insertion of a single nucleotide in MdMLO19 caused the formation of an early stop codon, resulting in a truncated protein lacking 185 amino acids, including the calmodulin-binding domain. The presence of the insertion was evaluated in 115 individuals. It was heterozygous in 64 and homozygous in 25. Twelve of the 25 individuals carrying the insertion in homozygosity were susceptible to PM. After barley, pea, cucumber, and tomato, apple would be the fifth species for which a natural non-functional mlo allele has been found
    Knockdown of MLO genes reduces susceptibility to powdery mildew in grapevine
    Pessina, Stefano ; Lenzi, Luisa ; Perazzolli, Michele ; Campa, Manuela ; Costa, Lorenza Dalla; Urso, Simona ; Valè, Giampiero ; Salamini, Francesco ; Velasco, Riccardo ; Malnoy, Mickael - \ 2016
    Horticulture Research 3 (2016). - ISSN 2052-7276
    Erysiphe necator is the causal agent of powdery mildew (PM), one of the most destructive diseases of grapevine. PM is controlled by sulfur-based and synthetic fungicides, which every year are dispersed into the environment. This is why PM-resistant varieties should become a priority for sustainable grapevine and wine production. PM resistance can be achieved in other crops by knocking out susceptibility S-genes, such as those residing at genetic loci known as MLO (Mildew Locus O). All MLO S-genes of dicots belong to the phylogenetic clade V, including grapevine genes VvMLO7, 11 and 13, which are upregulated during PM infection, and VvMLO6, which is not upregulated. Before adopting a gene-editing approach to knockout candidate S-genes, the evidence that loss of function of MLO genes can reduce PM susceptibility is necessary. This paper reports the knockdown through RNA interference of VvMLO6, 7, 11 and 13. The knockdown of VvMLO6, 11 and 13 did not decrease PM severity, whereas the knockdown of VvMLO7 in combination with VvMLO6 and VvMLO11 reduced PM severity up to 77%. The knockdown of VvMLO7 and VvMLO6 seemed to be important for PM resistance, whereas a role for VvMLO11 does not seem likely. Cell wall appositions (papillae) were present in both resistant and susceptible lines in response to PM attack. Thirteen genes involved in defense were less upregulated in infected mlo plants, highlighting the early mlo-dependent disruption of PM invasion.
    The knock-down of the expression of MdMLO19 reduces susceptibility to powdery mildew (Podosphaera leucotricha) in apple (Malus domestica)
    Pessina, Stefano ; Angeli, Dario ; Martens, Stefan ; Visser, Richard G.F. ; Bai, Yuling ; Salamini, Francesco ; Velasco, Riccardo ; Schouten, Henk J. ; Malnoy, Mickael - \ 2016
    Plant Biotechnology Journal 14 (2016)10. - ISSN 1467-7644 - p. 2033 - 2044.
    Arabidopsis thaliana - Malus domestica - MLO - Powdery mildew - RNA interference

    Varieties resistant to powdery mildew (PM; caused by Podosphaera leucotricha) are a major component of sustainable apple production. Resistance can be achieved by knocking-out susceptibility S-genes to be singled out among members of the MLO (Mildew Locus O) gene family. Candidates are MLO S-genes of phylogenetic clade V up-regulated upon PM inoculation, such as MdMLO11 and 19 (clade V) and MdMLO18 (clade VII). We report the knock-down through RNA interference of MdMLO11 and 19, as well as the complementation of resistance with MdMLO18 in the Arabidopsis thaliana triple mlo mutant Atmlo2/6/12. The knock-down of MdMLO19 reduced PM disease severity by 75%, whereas the knock-down of MdMLO11, alone or in combination with MdMLO19, did not result in any reduction or additional reduction of susceptibility compared with MdMLO19 alone. The test in A. thaliana excluded a role for MdMLO18 in PM susceptibility. Cell wall appositions (papillae) were present in both PM-resistant and PM-susceptible plants, but were larger in resistant lines. No obvious negative phenotype was observed in plants with mlo genes knocked down. Apparently, MdMLO19 plays the pivotal role in apple PM susceptibility and its knock-down induces a very significant level of resistance.

    Development and validation of the Axiom®Apple480K SNP genotyping array
    Bianco, Luca ; Cestaro, Alessandro ; Linsmith, Gareth ; Muranty, Hélène ; Denancé, Caroline ; Théron, Anthony ; Poncet, Charles ; Micheletti, Diego ; Kerschbamer, Emanuela ; Pierro, Erica A. Di; Larger, Simone ; Pindo, Massimo ; De Weg, Eric Van; Davassi, Alessandro ; Laurens, François ; Velasco, Riccardo ; Durel, Charles Eric ; Troggio, Michela - \ 2016
    The Plant Journal 86 (2016)1. - ISSN 0960-7412 - p. 62 - 74.
    genome-wide association study - genotyping - linkage mapping - Malus × domestica Borkh. - SNP chip - validation

    Cultivated apple (Malus × domestica Borkh.) is one of the most important fruit crops in temperate regions, and has great economic and cultural value. The apple genome is highly heterozygous and has undergone a recent duplication which, combined with a rapid linkage disequilibrium decay, makes it difficult to perform genome-wide association (GWA) studies. Single nucleotide polymorphism arrays offer highly multiplexed assays at a relatively low cost per data point and can be a valid tool for the identification of the markers associated with traits of interest. Here, we describe the development and validation of a 487K SNP Affymetrix Axiom® genotyping array for apple and discuss its potential applications. The array has been built from the high-depth resequencing of 63 different cultivars covering most of the genetic diversity in cultivated apple. The SNPs were chosen by applying a focal points approach to enrich genic regions, but also to reach a uniform coverage of non-genic regions. A total of 1324 apple accessions, including the 92 progenies of two mapping populations, have been genotyped with the Axiom®Apple480K to assess the effectiveness of the array. A large majority of SNPs (359 994 or 74%) fell in the stringent class of poly high resolution polymorphisms. We also devised a filtering procedure to identify a subset of 275K very robust markers that can be safely used for germplasm surveys in apple. The Axiom®Apple480K has now been commercially released both for public and proprietary use and will likely be a reference tool for GWA studies in apple.

    A joint Laimburg - FEM molecular markers project for apple fruit quality traits using the Pedigree Based Analysis strategy
    Lozano, L. ; Guardo, M. Di; De Weg, W.E. Van; Bink, M.C.A.M. ; Velasco, R. ; Costa, F. ; Guerra, W. - \ 2015
    In: III International Symposium on Molecular Markers in Horticulture / Velasco, R., International Society for Horticultural Science (Acta Horticulturae ) - ISBN 9789462610989 - p. 91 - 94.
    Fruit quality - Malus ×domestica - Markerassisted selection - Pedigree Based Analysis - QTLs

    In apple breeding fruit quality is a crucial aspect to guarantee commercial success of new varieties. Among the several quality attributes, individual sugars and acid components, as well as texture, are considered important features due to their significant contribution to sensory quality and consumer's acceptance. In traditional breeding, however, selection for these particular traits is a time consuming process, due to the long unproductive juvenile phase of apple seedlings. This step can be assisted to date by the use of molecular markers, an important diagnostic tool useful to anticipate and assist the identification of novel apple varieties characterized by superior fruit quality behaviour. However, the routinely implementation of molecular markers in breeding programs is still limited. In this study a new approach named Pedigree Based Analysis will be used on six full-sib progenies and their pedigree (composed by 15 varieties, represented by founders and ancestors), to target the main set of quantitative trait loci (QTLs). This strategy will allow the identification of the most valuable alleles present in the breeding activities of both Italian institutes. The ultimate goal of the Laimburg - FEM joint project is the identification and validation of molecular markers as a suitable tool for Marker Assisted Breeding in the two on-going apple breeding programs.

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