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.
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.
A new versatile database created for geneticists and breeders to link molecular and phenotypic data in perennial crops: the AppleBreed DataBase
Antofie, A. ; Lateur, M. ; Oger, R. ; Patocchi, A. ; Durel, C.E. ; Weg, W.E. van de - \ 2007
Bioinformatics 23 (2007)7. - ISSN 1367-4803 - p. 882 - 891.
genome database - plant genome - zmdb
Objective: AppleBreed DataBase (DB) aims to store genotypic and phenotypic data from multiple pedigree verified plant populations (crosses, breeding selections and commercial cultivars) so that they are easily accessible for geneticists and breeders. It will help in elucidating the genetics of economically important traits, in identifying molecular markers associated with agronomic traits, in allele mining and in choosing the best parental cultivars for breeding. It also provides high traceability of data over generations, years and localities. AppleBreed DB could serve as a generic database design for other perennial crops with long economic lifespans, long juvenile periods and clonal propagation. Results: AppleBreed DB is organized as a relational database. The core element is the GENOTYPE entity, which has two sub-classes at the physical level: TREE and DNA-SAMPLE. This approach facilitates all links between plant material, phenotypic and molecular data. The entities TREE, DNA-SAMPLE, PHENOTYPE and MOLECULAR DATA allow multi-annual observations to be stored as individual samples of individual trees, even if the nature of these observations differs greatly (e.g. molecular data on parts of the apple genome, physico-chemical measurements of fruit quality traits, and evaluation of disease resistance). AppleBreed DB also includes synonyms for cultivars and pedigrees. Finally, it can be loaded and explored through the web, and comes with tools to present basic statistical overviews and with validation procedures for phenotypic and marker data to certify data quality. AppleBreed DB was developed initially as a tool for scientists involved in apple genetics within the framework of the European project, `High-quality Disease Resistance in Apples for Sustainable Agriculture¿ (HiDRAS), but it is also applicable to many other perennial crops.
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