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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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.
Preference mapping of apple varieties in Europe
Bonany, J. ; Buehler, A. ; Carbó, J. ; Codarin, C. ; Donati, F. ; Echeverria, G. ; Egger, S. ; Guerra, W. ; Hilaire, C. ; Höller, I. ; Iglesias, I. ; Jesionkowska, K. ; Konopacka, D. ; Kruczynska, D. ; Martinelli, A. ; PItiot, C. ; Sansavini, S. ; Stehr, R. ; Schoorl, F.W. - \ 2014
Food Quality and Preference 32 (2014)c. - ISSN 0950-3293 - p. 317 - 329.
vegetable consumption - fruit - population - acceptance - consumers - barriers - industry - quality
A consumer test carried out in 7 different European countries compared 3 standard apple varieties to 8 new ones. A total of 4290 consumers took part in the test. Data from this test was used to develop a preference map for apple. The preference map was constructed with 3 main dimensions (1 – sweetness, fruitiness, flowery attributes, 2 – acidity, firmness, 3 – juiciness and crispness). Consumers were segmented in 6 clusters according to their preferences. The 6 clusters were grouped into two main mega clusters A (68% of consumers) and B (32% of consumers). Megacluster A (Clusters 1, 2, 5 and 6) was characterized by preferring sweet apples. Clusters 2 and 5 (41% of consumers) liked sweet apples independently of their acidity and firmness and moderate positive values on dimension of juiciness and crispness. Cluster 1 (21% of consumers) had an optimal point in positive values of the sweetness dimension, moderate negative value for acidity and firmness and moderate positive value for juiciness and crispness. Cluster 6 (6% of consumers) besides preferring sweet varieties disliked acid-firm varieties. As to regard to megacluster B (Clusters 3 and 4) (32% of consumers), they preferred varieties that were acidic-firm and juiciy and crisp with values in the mid range of the sweetness dimension. In spite of the difficulties in translating preference dimensions into standard practical values for fruit quality and the fact of being a punctual measurement of consumer behaviour, this preference map could be of practical use of different actors on the fruit value chain like marketers and breeders.
Consumer eating quality acceptance of new apple varieties in different European countries
Bonany, J. ; Buehler, A. ; Carbo, J. ; Codarin, C. ; Donati, F. ; Echeverria, G. ; Egger, S. ; Guerra, W. ; Hilaire, C. ; Hoeller, I. ; Iglesias, I. ; Jesionkowska, K. ; Konopacka, D. ; Kruczynska, D. ; Martinelli, A. ; PItiot, C. ; Sansavini, S. ; Stehr, R. ; Schoorl, F.W. - \ 2013
Food Quality and Preference 30 (2013)2. - ISSN 0950-3293 - p. 250 - 259.
fruit color development - anthocyanin content - scab-resistant - strains - acceptability - preferences - gala - cultivars - firmness
During January and February 2007 a European consumer test of eight new apple varieties and three standard ones was carried out in different European countries. The most common apple varieties were compared to new ones, focusing on consumer acceptance and the potential for increasing apple consumption. We sought to test the hypothesis that the introduction of new improved varieties would help to increase fruit consumption. Data from a sensory test involving 4290 consumers in seven different countries were analysed for the effects of variety and test country, age, gender and apple consumption habit of the consumer on eating quality acceptance. The results obtained showed a strong interaction between country and variety, although a group of four varieties (‘Gold Pink’, ‘CIVni’, ‘Cripps Pink’ and ‘Fuji’) formed part of a group of the varieties that were most accepted in all of the countries except Germany. Significant interactions between variety and age and variety and gender were observed, but their magnitudes were not considered to be of any practical significance. No statistically significant interaction was found between variety and apple consumption habit on eating quality acceptance.
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.
Role of the genes Md-ACO1 and Md-ACS1 in ethylene production and shelf life of apple (Malus domestica Borkh)
Costa, F. ; Stella, S. ; Weg, W.E. van de; Guerra, W. ; Cecchinel, M. ; Dallavia, J. ; Koller, B. ; Sansavini, S. - \ 2005
Euphytica 141 (2005)1-2. - ISSN 0014-2336 - p. 181 - 190.
1-aminocyclopropane-1-carboxylate synthase - pumila mill. - fruit - expression - biosynthesis - tomato - oxidase - allele - plants
Shelf life determines the economic life time of mature apples, which can be either freshly harvested or stored. Good shelf life is highly associated with a slow decrease of fruit firmness at room temperature. Apple is a climacteric fruit, in which loss of firmness seems to be physiologically related to ethylene. Ethylenes biosynthetic pathway is controlled by two large gene families coding for 1-aminocyclopropane-1-carboxylate synthase (ACS) and 1-aminocyclopropane-1-carboxylate oxydase (ACO). In this study, one ACS and one ACO gene were examined for their effect on ethylene production and shelf life in apple using gene specific molecular marker, and have also been positioned on a molecular marker linkage map. The ACO marker was developed in this research and mapped on linkage group (LG) 10 of the crosses Prima × Fiesta and Fuji × Mondial Gala, within the 5% border of a previously identified fruit firmness QTL [Theor Appl Genet 100 (2000) 1074]. We denoted this locus as Md-ACO1. In addition, we mapped the previously developed Md-ACS1 marker [Theor Appl Genet 101 (2000) 742] on LG15. Studies on the cross Fuji × Braeburn revealed that Md-ACS1 and Md-ACO1 independently affect the internal ethylene concentration (IEC) as well as shelf life of apple, Md-ACS1 having the strongest effect. Descendants homozygous for Md-ACS1-2 and Md-ACO1-1 showed to have the lowest ethylene production as well as superior shelf-life. These two genes are candidates to be included in marker assisted breeding
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