Papers by Chris Maliepaard
Genetics, 2015
The creation of genetic linkage maps in polyploid species has been a long-standing problem for wh... more The creation of genetic linkage maps in polyploid species has been a long-standing problem for which various approaches have been proposed. In the case of autopolyploids, a commonly used simplification is that random bivalents form during meiosis. This leads to relatively straightforward estimation of recombination frequencies using maximum likelihood, from which a genetic map can be derived. However, autopolyploids such as tetraploid potato (Solanum tuberosum L.) may exhibit additional features, such as double reduction, not normally encountered in diploid or allopolyploid species. In this study, we produced a high-density linkage map of tetraploid potato and used it to identify regions of double reduction in a biparental mapping population. The frequency of multivalents required to produce this degree of double reduction was determined through simulation. We also determined the effect that multivalents or preferential pairing between homologous chromosomes has on linkage mapping. ...
Frontiers in Plant Science, 2015
In order to develop a versatile and large SNP array for rose, we set out to mine ESTs from divers... more In order to develop a versatile and large SNP array for rose, we set out to mine ESTs from diverse sets of rose germplasm. For this RNA-Seq libraries containing about 700 million reads were generated from tetraploid cut and garden roses using Illumina paired-end sequencing, and from diploid Rosa multiflora using 454 sequencing. Separate de novo assemblies were performed in order to identify single nucleotide polymorphisms (SNPs) within and between rose varieties. SNPs among tetraploid roses were selected for constructing a genotyping array that can be employed for genetic mapping and marker-trait association discovery in breeding programs based on tetraploid germplasm, both from cut roses and from garden roses. In total 68,893 SNPs were included on the WagRhSNP Axiom array. Next, an orthology-guided assembly was performed for the construction of a non-redundant rose transcriptome database. A total of 21,740 transcripts had significant hits with orthologous genes in the strawberry (Fragaria vesca L.) genome. Of these 13,390 appeared to contain the full-length coding regions. This newly established transcriptome resource adds considerably to the currently available sequence resources for the Rosaceae family in general and the genus Rosa in particular.
BMC Proceedings, 2010
Background: The simulation of the data for the QTLMAS 2009 Workshop is described. Objective was t... more Background: The simulation of the data for the QTLMAS 2009 Workshop is described. Objective was to simulate observations from a growth curve which was influenced by a number of QTL. Results: The data consisted of markers, phenotypes and pedigree. Genotypes of 453 markers, distributed over 5 chromosomes of 1 Morgan each, were simulated for 2,025 individuals. From those, 25 individuals were parents of the other 2,000 individuals. The 25 parents were genetically related. Phenotypes were simulated according to a logistic growth curve and were made available for 1,000 of the 2,000 offspring individuals. The logistic growth curve was specified by three parameters. Each parameter was influenced by six Quantitative Trait Loci (QTL), positioned at the five chromosomes. For each parameter, one QTL had a large effect and five QTL had small effects. Variance of large QTL was five times the variance of small QTL. Simulated data was made available at
The authors developed an analytic software package for the objective and reproducible assessment ... more The authors developed an analytic software package for the objective and reproducible assessment of a single leg separation (SLS) in the outlet strut of Björk-Shiley convexoconcave (BSCC) prosthetic heart valves. The radiographic cinefilm recordings of 18 phantom valves (12 intact and 6 SLS) and of 43 patient valves were acquired. After digitization of regions of interest in a cineframe, several processing steps were carried out to obtain a one-dimensional corrected and averaged density profile along the central axis of each strut leg. To characterize the degree of possible separation, two quantitative measures were introduced: the normalized pit depth (NPD) and the depth-sigma ratio (DSR). The group of 43 patient studies was divided into a learning set (25 patients) and a test set (18 patients). All phantom valves with an SLS were detected (sensitivity, 100%) at a specificity of 100%. The threshold values for the NPD and the DSR to decide whether a fracture was present or not were 3.6 and 2.5, respectively. On the basis of the visual interpretations of the 25 patient studies (learning set) by an expert panel, it was concluded that none of the patients had an SLS. To achieve a 100% specificity by quantitative analysis, the threshold values for the NPD and the DSR were set at 5.8 and 2.5, respectively, for the patient data. Based on these threshold values, the analysis of patient data from the test set resulted in one false-negative detection and three false-positive detections. An analytic software package for the detection of an SLS was developed. Phantom data showed excellent sensitivity (100%) and specificity (100%). Further research and software development is needed to increase the sensitivity and specificity for patient data.
... Papier sur la visualisation de phylogénies @InProceedings{AK02, author = {Nina Amenta and Jef... more ... Papier sur la visualisation de phylogénies @InProceedings{AK02, author = {Nina Amenta and Jeff Klingner}, title = {Case Study ... article{SZGBDDR96, author = "Doug Schaffer and Zhengping Zuo and Saul Greenberg and Lyn Bartram and John Dill and Shelli Dubs and Mark ...
Volume 3 • Issue 3 • 1000126 metabolites. Therefore, we considered potato tuber flesh colour as t... more Volume 3 • Issue 3 • 1000126 metabolites. Therefore, we considered potato tuber flesh colour as the phenotypic trait of interest, the response in our regression and a large metabolomics data set as the set of predictor variables. For tuber flesh colour, there is a well-established relationship to the carotenoid pathway, and especially to beta caroteen [10], therefore, compounds related to this pathway are expected to be observed in a top list or selected set of predictive variables.
In this study volatile and non-volatile compounds, as well as some breeding parameters, were meas... more In this study volatile and non-volatile compounds, as well as some breeding parameters, were measured in mature fruits of elite sweet pepper (Capsicum annuum) lines and hybrids from a commercial breeding program, several cultivated genotypes and one gene bank accession. In addition, all genotypes were evaluated for taste by a trained descriptive sensory expert panel. Metabolic contrasts between genotypes were caused by clusters of volatile and non-volatile compounds, which could be related to metabolic pathways and common biochemical precursors. Clusters of phenolic derivatives, higher alkanes, sesquiterpenes and lipid derived volatiles formed the major determinants of the genotypic differences. Flavour was described with the use of 14 taste attributes, of which the texture related attributes and the sweetsour contrast were the most discriminatory factors. The attributes juiciness, toughness, crunchiness, stickiness, sweetness, aroma, sourness and fruity/apple taste could be significantly predicted with combined volatile and non-volatile data. Fructose and (E)-2-hexen-1-ol were highly correlated with aroma, fruity/apple taste and sweetness. New relations were found for fruity/apple taste and sweetness with the compounds p-menth-1-en-9-al, (E)-b-ocimene, (Z)-2-penten-1-ol and (E)-geranylacetone. Based on the overall biochemical and sensory results, the perspectives for flavour improvement by breeding are discussed.
Wageningen UR publication. Title: MapQTL 4.0: Software for the calculation of QTL positions on ge... more Wageningen UR publication. Title: MapQTL 4.0: Software for the calculation of QTL positions on genetic maps (user manual ...
BMC Genetics, 2014
Background: Global trade has ensured that the ornamental horticulture continues to grow worldwide... more Background: Global trade has ensured that the ornamental horticulture continues to grow worldwide, with rose hybrids being the most economically important genus (Rosa x hybrida). Due to changes in global trade and an increase in energy costs the ornamental industry has seen a shift in the production and sale of flowers from the US and Europe alone to production in Africa and Latin America. As Kenya is a major exporter of roses to Europe we studied the genetic variation and heritability of specific morphological traits in a tetraploid population grown in the Netherlands and in Kenya. The aim was to estimate genotype by environment interaction (G × E) and to investigate the implications of (G × E) for rose breeding.
The electrophile-responsive element (EpRE) is a transcriptional enhancer involved in cancer-chemo... more The electrophile-responsive element (EpRE) is a transcriptional enhancer involved in cancer-chemoprotective gene expression effects of certain dietary compounds. In this study we measured the ability of extracts of glycosidase treated tomato fruits from 97 different accessions to induce EpRE-mediated luciferase expression using EpRE-LUX reporter cells and analyzed the same extracts using LC-MSbased untargeted metabolomics profiling. We were able to pinpoint those tomato compounds that were most correlated with EpRE-mediated luciferase induction, by combining reporter gene assay data with the metabolic profiles of the same extracts. Flavonoids were the compounds showing the strongest positive correlation with EpRE-LUX activity. These results were validated using a transgenic tomato line accumulating high levels of flavonoids. Results obtained corroborated that flavonoids are an important determinant of the ability of tomato fruit extracts to induce EpRE-mediated beneficial health effects. Overall, these results indicate that combining untargeted metabolomics with reporter gene assays provides a powerful tool for nutritionists, plant breeders and food chemists towards identification of potential health-beneficial constituents of tomato fruits, as well as of other crops and products derived thereof.
Journal of Bioinformatics and Computational Biology, 2005
Both cDNA microarray and spectroscopic data provide indirect information about the chemical compo... more Both cDNA microarray and spectroscopic data provide indirect information about the chemical compounds present in the biological tissue under consideration. In this paper simple univariate and bivariate measures are used to investigate correlations between both types of high dimensional analyses.
BMC proceedings, 2010
Five participants of the QTL-MAS 2009 workshop applied QTL analyses to the workshop common data s... more Five participants of the QTL-MAS 2009 workshop applied QTL analyses to the workshop common data set which contained a time-related trait: cumulative yield. Underlying the trait were 18 QTLs for three parameters of a logistic growth curve that was used for simulating the trait. Different statistical models and methods were employed to detect QTLs and estimate position and effect sizes of QTLs. Here we compare the results with respect to the numbers of QTLs detected, estimated positions and percentage explained variance. Furthermore, limiting factors in the QTL detection are evaluated. All QTLs for the asymptote and the scaling factor of the logistic curve were detected by at least one of the participants. Only one out of six of the QTLs for the inflection point was detected. None of the QTLs were detected by all participants. Dominant, epistatic and imprinted QTLs were reported while only additive QTLs were simulated. The power to map QTLs for the inflection point increased when more...
TAG Theoretical and Applied Genetics, 1998
... Aligning male and female linkage maps of apple (Malus pumila Mill.) ... Various types of mark... more ... Aligning male and female linkage maps of apple (Malus pumila Mill.) ... Various types of markers are being used in studying apple genetics. ...
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Papers by Chris Maliepaard