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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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.
Bayesian QTL analyses using pedigreed families of an outcrossing specis, with application to fruit firmness in apple
Bink, M.C.A.M. ; Jansen, J. ; Madduri, M. ; Voorrips, R.E. ; Durel, C.E. ; Kouassi, A.B. ; Laurens, F. ; Mathis, F. ; Gessler, C. ; Gobbin, D. ; Rezzonico, F. ; Patocchi, A. ; Kellerhals, M. ; Boudichevskaia, A. ; Dunemann, F. ; Peil, A. ; Nowicka, A. ; Lata, B. ; Stankiewicz-Kosyl, M. ; Jeziorek, K. ; Pitera, E. ; Soska, A. ; Tomala, K. ; Evans, K.M. ; Fernández-Fernández, F. ; Guerra, W. ; Korbin, M. ; Keller, S. ; Lewandowski, M. ; Plocharski, W. ; Rutkowski, K. ; Zurawicz, E. ; Costa, F. ; Sansavini, S. ; Tartarini, S. ; Komjanc, M. ; Mott, D. ; Antofie, A. ; Lateur, M. ; Rondia, A. ; Gianfranceschi, L. ; Weg, W.E. van de - \ 2014
Theoretical and Applied Genetics 127 (2014)5. - ISSN 0040-5752 - p. 1073 - 1090.
quantitative trait loci - x domestica borkh. - quality traits - plant-populations - phenotypic data - genome - relatedness - prediction - cultivars - selection
Key message - Proof of concept of Bayesian integrated QTL analyses across pedigree-related families from breeding programs of an outbreeding species. Results include QTL confidence intervals, individuals’ genotype probabilities and genomic breeding values. Abstract - Bayesian QTL linkage mapping approaches offer the flexibility to study multiple full sib families with known pedigrees simultaneously. Such a joint analysis increases the probability of detecting these quantitative trait loci (QTL) and provide insight of the magnitude of QTL across different genetic backgrounds. Here, we present an improved Bayesian multi-QTL pedigree-based approach on an outcrossing species using progenies with different (complex) genetic relationships. Different modeling assumptions were studied in the QTL analyses, i.e., the a priori expected number of QTL varied and polygenic effects were considered. The inferences include number of QTL, additive QTL effect sizes and supporting credible intervals, posterior probabilities of QTL genotypes for all individuals in the dataset, and QTL-based as well as genome-wide breeding values. All these features have been implemented in the FlexQTL™ software. We analyzed fruit firmness in a large apple dataset that comprised 1,347 individuals forming 27 full sib families and their known ancestral pedigrees, with genotypes for 87 SSR markers on 17 chromosomes. We report strong or positive evidence for 14 QTL for fruit firmness on eight chromosomes, validating our approach as several of these QTL were reported previously, though dispersed over a series of studies based on single mapping populations. Interpretation of linked QTL was possible via individuals’ QTL genotypes. The correlation between the genomic breeding values and phenotypes was on average 90 %, but varied with the number of detected QTL in a family. The detailed posterior knowledge on QTL of potential parents is critical for the efficiency of marker-assisted breeding.
A qRT-PCR assay for the expression of all Mal d 1 isoallergen genes
Pagliarani, G. ; Paris, R. ; Arens, P. ; Tartarini, S. ; Ricci, G. ; Smulders, M.J.M. ; Weg, W.E. van de - \ 2013
BMC Plant Biology 13 (2013). - ISSN 1471-2229 - 25 p.
apple malus-domestica - bet v 1 - major allergen mal-d-1 - ige-binding epitopes - birch pollen - l. borkh - in-vivo - fruit - cultivars - food
Background - A considerable number of individuals suffer from oral allergy syndrome (OAS) to apple, resulting in the avoidance of apple consumption. Apple cultivars differ greatly in their allergenic properties, but knowledge of the causes for such differences is incomplete. Mal d 1 is considered the major apple allergen. For Mal d 1, a wide range of isoallergens and variants exist, and they are encoded by a large gene family. To identify the specific proteins/genes that are potentially involved in the allergy, we developed a PCR assay to monitor the expression of each individual Mal d 1 gene. Gene-specific primer pairs were designed for the exploitation of sequence differences among Mal d 1 genes. The specificity of these primers was validated using both in silico and in vitro techniques. Subsequently, this assay was applied to the peel and flesh of fruits from the two cultivars 'Florina' and 'Gala'. Results - We successfully developed gene-specific primer pairs for each of the 31 Mal d 1 genes and incorporated them into a qRT-PCR assay. The results from the application of the assay showed that 11 genes were not expressed in fruit. In addition, differential expression was observed among the Mal d 1 genes that were expressed in the fruit. Moreover, the expression levels were tissue and cultivar dependent. Conclusion - The assay developed in this study facilitated the first characterisation of the expression levels of all known Mal d 1 genes in a gene-specific manner. Using this assay on different fruit tissues and cultivars, we obtained knowledge concerning gene relevance in allergenicity. This study provides new perspectives for research on both plant breeding and immunotherapy.
Genomic organisation of the Mal d 1 gene cluster on linkage group 16 in apple
Pagliarani, G. ; Paris, R. ; Iorio, A.R. ; Tartarini, S. ; Ducra, S. ; Arens, P. ; Peters, S. ; Weg, W.E. van de - \ 2012
Molecular Breeding 29 (2012)3. - ISSN 1380-3743 - p. 759 - 778.
bet v 1 - birch pollen allergen - x-domestica borkh. - major allergen - duplicate genes - resistance locus - scab resistance - arabidopsis - expression - cloning
European populations exhibit progressive sensitisation to food allergens, and apples are one of the foods for which sensitisation is observed most frequently. Apple cultivars vary greatly in their allergenic characteristics, and a better understanding of the genetic basis of low allergenicity may therefore allow allergic individuals to increase their fruit intake. Mal d 1 is considered to be a major apple allergen, and this protein is encoded by the most complex allergen gene family. Not all Mal d 1 members are likely to be involved in allergenicity. Therefore, additional knowledge about the existence and characteristics of the different Mal d 1 genes is required. In the present study, we investigated the genomic organisation of the Mal d 1 gene cluster in linkage group 16 of apple through the sequencing of two bacterial artificial chromosome clones. The results provided new information on the composition of this family with respect to the number and orientation of functional and pseudogenes and their physical distances. The results were compared with the apple and peach genome sequences that have recently been made available. A broad analysis of the whole apple genome revealed the presence of new genes in this family, and a complete list of the observed Mal d 1 genes is supplied. Thus, this study provides an important contribution towards a better understanding of the genetics of the Mal d 1 family and establishes the basis for further research on allelic diversity among cultivars in relation to variation in allergenicity
Estimation of genetic parameters and prediction of breeding values for apple fruit-quality traits using pedigreed plant material in Europe
Kouassi, A.B. ; Durel, C.E. ; Costa, F. ; Tartarini, S. ; Weg, W.E. van de; Evans, K. ; Fernandez-Fernandez, F. ; Govan, C. ; Boudichevskaja, A. ; Dunemann, F. ; Antofie, A. ; Lateur, M. ; Stankiewicz-Kosyl, M. ; Soska, A. ; Tomala, K. ; Lewandowski, M. ; Rutkovski, K. ; Zurawicz, E. ; Guerra, W. ; Laurens, F. - \ 2009
Tree Genetics and Genomes 5 (2009)4. - ISSN 1614-2942 - p. 659 - 672.
sensory interpretation - variance-components - information
Genetic parameters for apple (Malus x domestica) fruit external traits (fruit size, ground colour, proportion of over colour and attractiveness) and sensory traits (firmness, crispness, texture, juiciness, flavour, sugar, acidity and global taste) were estimated using 2,207 pedigreed genotypes from breeding programmes in six European countries. Data were scored for 3 years and four periods during storage. Analyses were performed with a restricted maximum likelihood method using VCE 5.1.2 software. Heritability estimates ranged from medium to high for instrumental traits. Genetic correlations between firmness and sugar were medium and low between firmness and acidity. Sensory traits showed low to high heritability, acidity and flavour being, respectively, the most and the less heritable. Global taste was strongly correlated with texture, juiciness, and flavour and relatively less correlated with crispness and acidity. Sensory sugar and acidity showed highly negative correlations whereas their instrumental measurements showed low and increasing positive correlations from harvest to 4 months post-harvest. Sugar exhibited a higher sensory/instrumental divergence. Conversely, instrumental and sensory firmness were highly correlated. Fruit external characteristics had medium heritability. Fruit attractiveness had highest and lowest correlations with fruit size and ground colour, respectively. Best linear unbiased predictors of breeding values were computed for all genotypes with the software PEST. The results were analysed with regard to the dynamic and the reliability of genetic parameters according to the scoring dates. Original issues of the study and the importance of the obtained results for efficient designs of further apple fruit quality breeding programmes were discussed.
Construction of an integrated consensus map of the Apple genome based on four mapping populations
N'Diaye, A. ; Weg, W.E. van de; Kodde, L.P. ; Koller, B. ; Dunemann, F. ; Thiermann, M. ; Tartarini, S. ; Gennari, F. ; Durel, C.E. - \ 2008
Tree Genetics and Genomes 4 (2008)4. - ISSN 1614-2942 - p. 727 - 743.
quantitative trait loci - genetic-linkage map - x-domestica borkh. - malus-pumila mill. - zea-mays l - scab resistance - venturia-inaequalis - rapd markers - qtl analysis - microsatellite markers
An integrated consensus genetic map for apple was constructed on the basis of segregation data from four genetically connected crosses (C1¿=¿Discovery × TN10-8, C2¿=¿Fiesta × Discovery, C3¿=¿Discovery × Prima, C4¿=¿Durello di Forli × Fiesta) with a total of 676 individuals using CarthaGene® software. First, integrated female¿male maps were built for each population using common female¿male simple sequence repeat markers (SSRs). Then, common SSRs over populations were used for the consensus map integration. The integrated consensus map consists of 1,046 markers, of which 159 are SSR markers, distributed over 17 linkage groups reflecting the basic chromosome number of apple. The total length of the integrated consensus map was 1,032 cM with a mean distance between adjacent loci of 1.1 cM. Markers were proportionally distributed over the 17 linkage groups (¿ 2¿=¿16.53, df¿=¿16, p¿=¿0.41). A non-uniform marker distribution was observed within all of the linkage groups (LGs). Clustering of markers at the same position (within a 1-cM window) was observed throughout LGs and consisted predominantly of only two to three linked markers. The four integrated female¿male maps showed a very good colinearity in marker order for their common markers, except for only two (CH01h01, CH05g03) and three (CH05a02z, NZ02b01, Lap-1) markers on LG17 and LG15, respectively. This integrated consensus map provides a framework for performing quantitative trait locus (QTL) detection in a multi-population design and evaluating the genetic background effect on QTL expression.
Local European cultivars as sources of durable scab resistance in apple
Laurens, F.N.D. ; Chevalier, M. ; Dolega, E. ; Gennari, F. ; Goerre, M. ; Fischer, C. ; Kellerhals, M. ; Lateur, M. ; Lefrancq, B. ; Parisi, L. ; Schouten, H.J. ; Tartarini, S. - \ 2004
Acta Horticulturae 663 (2004). - ISSN 0567-7572 - p. 115 - 121.
The Vf resistance gene has been widely used in apple breeding programmes to control Venturia inaequalis, the causal agent of scab, the major apple disease. Since the appearance of new strains that are able to overcome this major gene, research in Europe has been focused on durable resistance. The objective of one task of the European DARE project was to find cultivars which show a broad spectrum of resistance to the different scab races. This collaborative work involved 6 partners who tested 36 cultivars with various local scab inocula collected in the participating countries and with 8 monoconidial strains belonging to known races or isolated and characterized in the frame of the DARE project. Tests were performed each year from 1998 to 2001. Symptoms were assessed using macroscopic scoring scales. Some microscopic observations were performed; these resulted in a better knowledge of the host/pathogen interaction. Very diverse and complex resistance behaviours were found: the cultivars which showed the widest range of resistance were mostly local cultivars and some newly selected hybrids combining major genes and partial resistance. It would be worthwhile to include these individuals as parents in apple breeding programmes to improve the durability of scab resistance. Some methodologies and strategies to reach this goal will be proposed.
An overview of the position and robustness of scab resistance QTLs and major genes by aligning of genetic maps in five apple progenies
Durel, C.E. ; Calenge, F. ; Parisi, L. ; Weg, W.E. van de; Kodde, L.P. ; Liebhard, R. ; Gessler, C. ; Thiermann, M. ; Dunemann, F. ; Gennari, F. ; Tartarini, S. ; Lespinasse, Y. - \ 2004
Acta Horticulturae 663 (2004). - ISSN 0567-7572 - p. 135 - 140.
In the frame of the D.A.R.E. project, five mapping populations have been studied for partial scab resistance against several races of Venturia inaequalis. A main objective was to identify QTLs (quantitative traits loci) with broad spectrum of resistance towards a wide range of strains of the fungus. Genetic markers (mainly SSR and AFLP) were tested on each population and genetic maps were constructed for both parents of each population. Meanwhile, pathological tests with several isolates of different races of V. inaequalis were performed. Four major genomic regions appear to be involved in scab resistance: they are located on linkage groups (LG) LG-1, LG-2, LG-11, and LG-17. Some other linkage groups carry either QTLs or major resistance genes that are isolate specific: a QTL on LG-5, Vd on LG-10, and Vg on LG-12. The QTL region located on LG-17 clearly exhibited the widest spectrum of resistance
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