Chris Maliepaard

dr.ir.

    19952020
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    Research Output 1995 2019

    2019

    Family-based haplotype estimation and allele dosage correction for polyploids using short sequence reads

    Motazedi, E., Maliepaard, C., Finkers, R., Visser, R. & De Ridder, D., 16 Apr 2019, In : Frontiers in Genetics. 10, MAR, 335.

    Research output: Contribution to journalArticleAcademicpeer-review

    Open Access
    Polyploidy
    Haplotypes
    Alleles
    Genotype
    Population

    FitTetra 2.0 - Improved genotype calling for tetraploids with multiple population and parental data support

    Zych, K., Gort, G., Maliepaard, C. A., Jansen, R. C. & Voorrips, R. E., 20 Mar 2019, In : BMC Bioinformatics. 20, 1, 148.

    Research output: Contribution to journalArticleAcademicpeer-review

    Open Access
    Tetraploidy
    Genotype
    Software
    Population
    Proportion
    Open Access
    Tetraploidy
    Quantitative Trait Loci
    Genome-Wide Association Study
    Solanum tuberosum
    tetraploidy
    1 Citation (Scopus)

    Multi-allelic QTL analysis of protein content in a bi-parental population of cultivated tetraploid potato

    Klaassen, M. T., Bourke, P. M., Maliepaard, C. & Trindade, L. M., 8 Jan 2019, In : Euphytica. 215, 2, 14.

    Research output: Contribution to journalArticleAcademicpeer-review

    Open Access
    Tetraploidy
    Quantitative Trait Loci
    Solanum tuberosum
    tetraploidy
    quantitative trait loci

    Quantifying the Power and Precision of QTL Analysis in Autopolyploids Under Bivalent and Multivalent Genetic Models

    Bourke, P. M., Hackett, C. A., Voorrips, R. E., Visser, R. G. F. & Maliepaard, C., 9 Jul 2019, In : G3 (Bethesda, Md.). 9, 7, p. 2107-2122 16 p.

    Research output: Contribution to journalArticleAcademicpeer-review

    Open Access
    Quantitative Trait Loci
    Genetic Models
    Meiosis
    Solanum tuberosum
    Polyploidy
    1 Citation (Scopus)

    Some thoughts on how to use markers in tetraploid rose breeding

    Smulders, M. J. M., van de Weg, W. E., Bourke, P. M., Voorrips, R. E., Arens, P. & Maliepaard, C., 1 Jan 2019, In : Acta Horticulturae. 1232, p. 1-6

    Research output: Contribution to journalArticleAcademicpeer-review

    tetraploidy
    Rosa
    alleles
    breeding
    genotyping
    1 Citation (Scopus)

    The effect of isolation methods of tomato pollen on the results of metabolic profiling

    Paupière, M. J., Tikunov, Y. M., Firon, N., de Vos, R. C. H., Maliepaard, C., Visser, R. G. F. & Bovy, A. G., 1 Jan 2019, In : Metabolomics. 15, 1, 11.

    Research output: Contribution to journalArticleAcademicpeer-review

    Open Access
    Lycopersicon esculentum
    Metabolites
    Pollen
    Metabolomics
    Contamination
    2018
    34 Citations (Scopus)

    A high-quality genome sequence of Rosa chinensis to elucidate ornamental traits

    Hibrand Saint-Oyant, L., Ruttink, T., Hamama, L., Kirov, I., Lakhwani, D., Zhou, N. N., Bourke, P. M., Daccord, N., Leus, L., Schulz, D., van de Geest, H., Hesselink, T., Van Laere, K., Debray, K., Balzergue, S., Thouroude, T., Chastellier, A., Jeauffre, J., Voisine, L., Gaillard, S. & 21 others, Borm, T. J. A., Arens, P., Voorrips, R. E., Maliepaard, C., Neu, E., Linde, M., Le Paslier, M. C., Bérard, A., Bounon, R., Clotault, J., Choisne, N., Quesneville, H., Kawamura, K., Aubourg, S., Sakr, S., Smulders, M. J. M., Schijlen, E., Bucher, E., Debener, T., De Riek, J. & Foucher, F., 2018, In : Nature Plants. 4, p. 473-484

    Research output: Contribution to journalArticleAcademicpeer-review

    Open Access
    Rosa chinensis
    Rosa
    genome
    plant spines
    doubled haploids

    Corrigendum: PolymapR - Linkage analysis and genetic map construction from F 1 populations of outcrossing polyploids

    Bourke, P. M., Van Geest, G., Voorrips, R. E., Jansen, J., Kranenburg, T., Shahin, A., Visser, R. G. F., Arens, P., Smulders, M. J. M. & Maliepaard, C., 15 Oct 2018, In : Bioinformatics. 35, 3, p. 540-540

    Research output: Contribution to journalComment/Letter to the editorAcademic

    Likelihood Functions
    Linkage Analysis
    Genetic Linkage
    Polyploidy
    Population
    12 Citations (Scopus)

    Exploiting next-generation sequencing to solve the haplotyping puzzle in polyploids: a simulation study

    Motazedi, E., Finkers, H. J., Maliepaard, C. A. & de Ridder, D., May 2018, In : Briefings in Bioinformatics. 19, 3, p. 387-403

    Research output: Contribution to journalArticleAcademicpeer-review

    Polyploidy
    Nucleotides
    Haplotypes
    Ploidies
    Polymorphism
    10 Citations (Scopus)

    Genetical genomics of quality related traits in potato tubers using proteomics

    Acharjee, A., Chibon, P. Y. F. R. P., Kloosterman, B. A., America, A. H. P., Renaut, J., Maliepaard, C. A. & Visser, R. G. F., 23 Jan 2018, In : BMC Plant Biology. 18, 20.

    Research output: Contribution to journalArticleAcademicpeer-review

    Open Access
    proteomics
    tubers
    potatoes
    genomics
    proteins
    8 Citations (Scopus)

    Multi-environment QTL analysis of plant and flower morphological traits in tetraploid rose

    Bourke, P. M., Gitonga, V. W., Voorrips, R. E., Visser, R. G. F., Krens, F. A. & Maliepaard, C., Oct 2018, In : Theoretical and Applied Genetics. 131, 10, p. 2055–2069

    Research output: Contribution to journalArticleAcademicpeer-review

    Open Access
    Tetraploidy
    Quantitative Trait Loci
    tetraploidy
    quantitative trait loci
    Rosa
    9 Citations (Scopus)

    PolymapR-linkage analysis and genetic map construction from F1 populations of outcrossing polyploids

    Bourke, P. M., van Geest, G., Voorrips, R. E., Jansen, J., Kranenburg, T., Shahin, A., Visser, R. G. F., Arens, P., Smulders, M. J. M. & Maliepaard, C., 15 Oct 2018, In : Bioinformatics. 34, 20, p. 3496-3502

    Research output: Contribution to journalArticleAcademicpeer-review

    Open Access
    Linkage Analysis
    Genetic Linkage
    Polyploidy
    Chrysanthemum
    Crops

    QTL detection in a breeding pedigree of diploid potato

    Korontzis, G., Malosetti, M., Mulder, H. A., Maliepaard, C. A., Víquez Zamora, A. M., Veerkamp, R. F. & van Eeuwijk, F. A., Sep 2018.

    Research output: Contribution to conferenceAbstractAcademic

    19 Citations (Scopus)

    Tools for Genetic Studies in Experimental Populations of Polyploids

    Bourke, P. M., Voorrips, R. E., Visser, R. G. F. & Maliepaard, C. A., 18 Apr 2018, In : Frontiers in Plant Science. 9, 513.

    Research output: Contribution to journalArticleAcademicpeer-review

    Open Access
    polyploidy
    inheritance (genetics)
    chromosome mapping
    alleles
    chromosomes
    2 Citations (Scopus)

    TriPoly: haplotype estimation for polyploids using sequencing data of related individuals

    Motazedi, E., de Ridder, D., Finkers, R., Baldwin, S., Thomson, S., Monaghan, K. & Maliepaard, C., 15 Nov 2018, In : Bioinformatics. 34, 22, p. 3864-3872

    Research output: Contribution to journalArticleAcademicpeer-review

    Polyploidy
    Haplotype
    Haplotypes
    Sequencing
    Chromosomes
    2017
    19 Citations (Scopus)

    An ultra-dense integrated linkage map for hexaploid chrysanthemum enables multi-allelic QTL analysis

    van Geest, G., Bourke, P. M., Voorrips, R. E., Marasek-Ciolakowska, A., Liao, Y., Post, A., van Meeteren, U., Visser, R. G. F., Maliepaard, C. & Arens, P., Dec 2017, In : Theoretical and Applied Genetics. 130, 12, p. 2527-2541

    Research output: Contribution to journalArticleAcademicpeer-review

    Open Access
    Chrysanthemum
    hexaploidy
    Lettuce
    chromosome mapping
    quantitative trait loci
    3 Citations (Scopus)

    Comparison of selection efficiency for spring barley (Hordeum vulgare L.) under organic and conventional farming conditions

    Kokare, A., Legzdina, L., Maliepaard, C., Niks, R. E. & Lammerts van Bueren, E. T., 2017, In : Crop Science. 57, 2, p. 626-636

    Research output: Contribution to journalArticleAcademicpeer-review

    spring barley
    organic production
    Hordeum vulgare
    ideotypes
    early selection
    7 Citations (Scopus)

    Genetic complexity of miscanthus cell wall composition and biomass quality for biofuels

    van der Weijde, T., Lessa Alvim Kamei, C., Severing, E., Torres Salvador, A. F., Gomez, L. D., Dolstra, O., Maliepaard, C. A., McQueen-Mason, S. J., Visser, R. G. F. & Trindade, L. M., 2017, In : BMC Genomics. 18, 15 p., 406.

    Research output: Contribution to journalArticleAcademicpeer-review

    Open Access
    Biofuels
    Biomass
    Cell Wall
    Sorghum
    Growth
    26 Citations (Scopus)

    Partial preferential chromosome pairing is genotype dependent in tetraploid rose

    Bourke, P. M., Arens, P., Voorrips, R. E., Esselink, D., Koning-Boucoiran, C. F. S., van 't Westende, W., Santos Leonardo, T., Wissink, P., Zheng, C., van Geest, G., Visser, R. G. F., Krens, F. A., Smulders, R. & Maliepaard, C., 2017, In : The Plant Journal. 90, 2, p. 330-343

    Research output: Contribution to journalArticleAcademicpeer-review

    Open Access
    Chromosome Pairing
    chromosome pairing
    Tetraploidy
    tetraploidy
    Rosa
    2016
    12 Citations (Scopus)

    A Systems genetics approach identifies gene regulatory networks associated with fatty acid composition in brassica rapa seed

    Basnet, R. K., Pino Del Carpio, D., Xiao, D., Bucher, J., Jin, M., Boyle, K., Fobert, P., Visser, R. G. F., Maliepaard, C. & Bonnema, G., 2016, In : Plant Physiology. 170, 1, p. 568-585

    Research output: Contribution to journalArticleAcademicpeer-review

    Open Access
    Brassica rapa
    Gene Regulatory Networks
    Seeds
    Fatty Acids
    fatty acid composition
    1 Citation (Scopus)

    Genetic control of water and nitrate capture and their use efficiency in lettuce (Lactuca sativa L.)

    Kerbiriou, P. J., Maliepaard, C. A., Stomph, T. J., Koper, M., Froissart, D., Roobeek, I., Lammerts Van Bueren, E. T. & Struik, P. C., 2016, In : Frontiers in Plant Science. 7, 343.

    Research output: Contribution to journalArticleAcademicpeer-review

    Open Access
    Lactuca sativa
    lettuce
    nitrates
    shoots
    quantitative trait loci
    20 Citations (Scopus)
    Open Access
    base maps
    Tetraploidy
    tetraploidy
    chromosome mapping
    gardens
    8 Citations (Scopus)

    Inheritance and QTL analysis of the determinants of flower color in tetraploid cut roses

    Gitonga, V. W., Stolker, R., Koning-Boucoiran, C. F. S., Aelaei, M., Visser, R. G. F., Maliepaard, C. & Krens, F. A., 2016, In : Molecular Breeding. 36, 10, 143.

    Research output: Contribution to journalArticleAcademicpeer-review

    Open Access
    Tetraploidy
    tetraploidy
    quantitative trait loci
    inheritance (genetics)
    Rosa
    10 Citations (Scopus)

    Integrating haplotype-specific linkage maps in tetraploid species using SNP markers

    Bourke, P. M., Voorrips, R. E., Kranenburg, T., Jansen, H., Visser, R. G. F. & Maliepaard, C., 2016, In : Theoretical and Applied Genetics. 129, 11, p. 2211-2226 16 p.

    Research output: Contribution to journalArticleAcademicpeer-review

    Open Access
    Tetraploidy
    Solanum tuberosum
    Haplotypes
    tetraploidy
    chromosome mapping
    24 Citations (Scopus)

    Integration of multi-omics data for prediction of phenotypic traits using random forest

    Acharjee, A., Kloosterman, B., Visser, R. G. F. & Maliepaard, C., 2016, In : BMC Bioinformatics. 17, 5, 180.

    Research output: Contribution to journalArticleAcademicpeer-review

    Open Access
    Random Forest
    Gene expression
    Metabolites
    Gene Expression
    Prediction
    4 Citations (Scopus)

    Multi-trait QTL analysis for agronomic and quality characters of Agaricus bisporus (button mushrooms)

    Gao, W., Baars, J. J. P., Maliepaard, C., Visser, R. G. F., Zhang, J. & Sonnenberg, A. S. M., 2016, In : AMB Express. 6, 67.

    Research output: Contribution to journalArticleAcademicpeer-review

    Open Access
    Agaricus
    Agaricales
    Chromosomes, Human, Pair 10
    Genetic Recombination
    Soil
    2 Citations (Scopus)

    Systems genetics reveals key genetic elements of drought induced gene regulation in diploid potato

    van Muijen, D., Kumari, A., Maliepaard, C., Visser, R. G. F. & van der Linden, G., 2016, In : Plant, Cell & Environment. 39, 9, p. 1895-1908

    Research output: Contribution to journalArticleAcademicpeer-review

    Droughts
    Solanum tuberosum
    Diploidy
    diploidy
    drought
    2015
    1 Citation (Scopus)
    Metabolomics
    Phytochemicals
    Transcription
    Lycopersicon esculentum
    Fruits
    5 Citations (Scopus)

    Development of the WagRhSNP AXIOM SNP Array Based on Sequences from Tetraploid Cut Roses and Garden Roses

    Smulders, M. J. M., Voorrips, R. E., Esselink, G., Santos Leonardo, T. M., van 't Westende, W. P. C., Vukosavljev, M., Koning-Boucoiran, C. F. S., van de Weg, W. E., Arens, P. F. P., Schulz, D., Debener, T., Bellon, L., Mittmann, M., Pirani, A., Webster, T., Brew, F., Cox, P. & Maliepaard, C. A., 2015, Proceedings VIth International Symposiul on Rose Research and Cultivation. Debener, T. & Linde, M. (eds.). ISHS, Vol. 1064. p. 177-184

    Research output: Chapter in Book/Report/Conference proceedingConference paperAcademicpeer-review

    tetraploidy
    gardens
    Rosa
    alleles
    vegetable crops
    15 Citations (Scopus)

    QTL analysis for stomatal functioning in tetraploid Rosa x hybrida grown at high relative air humidity and its implications on postharvest longevity

    Carvalho, D. R. A., Koning, C. F. S., Fanourakis, D., Vasconcelos, M. W., Carvalho, S. M. P., Heuvelink, E., Krens, F. A. & Maliepaard, C. A., 2015, In : Molecular Breeding. 35, 11 p., 172.

    Research output: Contribution to journalArticleAcademicpeer-review

    Tetraploidy
    Quantitative Trait Loci
    Humidity
    tetraploidy
    quantitative trait loci
    11 Citations (Scopus)

    Quantitative Trait Locus Analysis of seed germination and seedling vigour in Brassica rapa reveals QTL hotspots and epistatic interactions

    Basnet, R. K., Duwal, A., Tiwari, D. N., Xiao, D., Monakhos, S., Bucher, J., Visser, R. G. F., Groot, S. P. C., Bonnema, A. B. & Maliepaard, C. A., 2015, In : Frontiers in Plant Science. 6, 32 p., 1032.

    Research output: Contribution to journalArticleAcademicpeer-review

    Open Access
    Brassica rapa
    vigor
    quantitative trait loci
    seed germination
    seedlings
    29 Citations (Scopus)

    The double-reduction landscape in tetraploid potato as revealed by a high-density linkage map

    Bourke, P. M., Voorrips, R. E., Visser, R. G. F. & Maliepaard, C., 2015, In : Genetics. 201, 3, p. 853-863

    Research output: Contribution to journalArticleAcademicpeer-review

    Tetraploidy
    Solanum tuberosum
    Genetic Linkage
    Polyploidy
    Centromere
    3 Citations (Scopus)

    Understanding the genetic basis of potato development using a multi-trait QTL analysis

    Hurtado-Lopez, P. X., Tessema, B. B., Schnabel, S. K., Maliepaard, C. A., van der Linden, C. G., Eilers, P. H. C., Jansen, J., van Eeuwijk, F. A. & Visser, R. G. F., 2015, In : Euphytica. 204, 1, p. 229-241

    Research output: Contribution to journalArticleAcademicpeer-review

    Open Access
    Plant Development
    Solanum tuberosum
    quantitative trait loci
    potatoes
    Photoperiod
    46 Citations (Scopus)
    Open Access
    transcriptome
    single nucleotide polymorphism
    Rosa
    RNA
    genes
    2014
    15 Citations (Scopus)
    Glucosinolates
    thermal degradation
    Metabolomics
    Brassica
    Vegetables
    15 Citations (Scopus)

    Capturing flavors from Capsicum baccatum by introgression in sweet pepper

    Eggink, P. M., Tikunov, Y. M., Maliepaard, C. A., Haanstra, J. P. W., de Rooij, H., Vogelaar, A., Gutteling, E. W., Freymark, G., Bovy, A. G. & Visser, R. G. F., 2014, In : Theoretical and Applied Genetics. 127, 2, p. 373-390

    Research output: Contribution to journalArticleAcademicpeer-review

    Capsicum baccatum
    Capsicum
    sweet peppers
    introgression
    Fruit
    24 Citations (Scopus)

    Genetic variation, heritability and genotype by environment interaction of morphological traits in a tetraploid rose population

    Gitonga, V. W., Koning, C. F. S., Verlinden, K., Dolstra, O., Visser, R. G. F., Maliepaard, C. A. & Krens, F. A., 2014, In : BMC Genetics. 15, 23 p., 146.

    Research output: Contribution to journalArticleAcademicpeer-review

    Open Access
    Tetraploidy
    Genotype
    Kenya
    Population
    Chlorophyll
    2 Citations (Scopus)

    Metabolic diversity in apple germplasm

    Khan, S. A., Tikunov, Y. M., Chibon, P. Y. F. R. P., Maliepaard, C. A., Beekwilder, M. J., Jacobsen, E. & Schouten, H. J., 2014, In : Plant Breeding. 133, 2, p. 281-290

    Research output: Contribution to journalArticleAcademicpeer-review

    Catechin
    Malus
    phenolic compounds
    germplasm
    Enoyl-CoA Hydratase
    6 Citations (Scopus)

    Performance of spring barley (Hordeum vulgare) varieties under organic and conventional conditions

    Kokare, A., Legzdina, L., Beinarovica, I., Niks, R. E., Maliepaard, C. A. & Lammerts Van Bueren, E., 2014, In : Euphytica. 197, 2, p. 279-293

    Research output: Contribution to journalArticleAcademicpeer-review

    Organic Agriculture
    spring barley
    Hordeum
    Hordeum vulgare
    yield components
    4 Citations (Scopus)

    Possibilities and challenges of the potato genome sequence

    Visser, R. G. F., Bachem, C. W. B., Borm, T. J. A., de Boer, J. M., van Eck, H. J., Finkers, H. J., van der Linden, G., Maliepaard, C. A., Uitdewilligen, J. G. A. M. L., Voorrips, R. E., Vos, P. G. & Wolters, A. M. A., 2014, In : Potato Research. 57, 3-4, p. 327-330

    Research output: Contribution to journalArticleAcademicpeer-review

    Open Access
    Solanum tuberosum
    Haplotypes
    haplotypes
    potatoes
    Genome
    2013

    Comparison of Regularized Regression Methods for ~Omics Data

    Acharjee, A., Finkers, H. J., Visser, R. G. F. & Maliepaard, C. A., 2013, In : Metabolomics : Open Access. 3, 3, 9 p., 126.

    Research output: Contribution to journalArticleAcademicpeer-review

    potato
    carotenoid
    prediction
    comparison
    method

    Genetic Analysis of Tetraploid F1 Populations Using SNP Markers

    Voorrips, R. E., Maliepaard, C. A. & Smulders, M. J. M., 2013.

    Research output: Contribution to conferenceAbstractAcademic

    tetraploidy
    genetic techniques and protocols
    Rosa
    polyploidy
    meiosis
    17 Citations (Scopus)
    Open Access
    Brassica rapa
    Seeds
    Genome
    Plant Oils
    Haploidy
    124 Citations (Scopus)
    Lycopersicon esculentum
    MicroRNAs
    microRNA
    fruiting
    Fruit
    22 Citations (Scopus)

    Relation between HLA genes, human skin volatiles and attractiveness of humans to malaria mosquitoes

    Verhulst, N. O., Beijleveld, H., Qiu, Y. T., Maliepaard, C. A., Verduyn, W., Haasnoot, G. W., Claas, F. H. J., Mumm, R., Bouwmeester, H. J., Takken, W., van Loon, J. J. A. & Smallegange, R. C., 2013, In : Infection, Genetics and Evolution. 18, p. 87-93

    Research output: Contribution to journalArticleAcademicpeer-review

    Open Access
    malaria
    HLA Antigens
    antigen
    Culicidae
    mosquito
    2012
    40 Citations (Scopus)

    A taste of sweet pepper: Volatile and non-volatile chemical composition of fresh sweet pepper (Capsicum annuum) in relation to sensory evaluation of taste

    Eggink, P. M., Maliepaard, C. A., Tikunov, Y. M., Haanstra, J. P. W., Bovy, A. G. & Visser, R. G. F., 2012, In : Food Chemistry. 132, 1, p. 301-310

    Research output: Contribution to journalArticleAcademicpeer-review

    Capsicum
    Flavors
    sweet peppers
    Capsicum annuum
    sensory evaluation
    15 Citations (Scopus)

    Dynamics of senescence-related QTLs in potato

    Hurtado Lopez, P. X., Schnabel, S. K., Zaban, A., Vetelainen, M., Virtanen, E., Eilers, P., van Eeuwijk, F. A., Visser, R. G. F. & Maliepaard, C. A., 2012, In : Euphytica. 183, 3, p. 289-302

    Research output: Contribution to journalArticleAcademicpeer-review

    Open Access
    Solanum tuberosum
    quantitative trait loci
    potatoes
    Chromosomes, Human, Pair 4
    chromosomes
    5 Citations (Scopus)

    Prediction of sweet pepper (Capsicum annuum) flavour over different harvests

    Eggink, P. M., Maliepaard, C. A., Tikunov, Y. M., Haanstra, J. P. W., Pohu-Flament, L. M. M., de Wit-Maljaars, S. C., Willeboordse-Vos, F., Bos, S., Benning-de Waard, C., de Grauw-van Leeuwen, P. J., Freymark, G., Bovy, A. G. & Visser, R. G. F., 2012, In : Euphytica. 187, 1, p. 117-131

    Research output: Contribution to journalArticleAcademicpeer-review

    Capsicum
    sweet peppers
    Capsicum annuum
    Fructose
    Breeding