Research Output 2011 2018

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2018
33 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
11 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
9 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
7 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
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
17 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
11 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)

High-density SNP-based genetic maps for the parents of an outcrossed and a selfed tetraploid garden rose cross, inferred from admixed progeny using the 68k rose SNP array

Vukosavljev, M., Arens, P., Voorrips, R. E., Van'T Westende, W. P. C., Esselink, G. D., Bourke, P. M., Cox, P., Van De Weg, W. E., Visser, R. G. F., Maliepaard, C. & Smulders, M. J. M., 2016, In : Horticulture Research. 3, 16052.

Research output: Contribution to journalArticleAcademicpeer-review

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
23 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
3 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
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
13 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
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
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
2011
298 Citations (Scopus)

Finished Genome of the Fungal Wheat Pathogen Mycosphaerella graminicola Reveals Dispensome Structure, Chromosome Plasticity, and Stealth Pathogenesis

Goodwin, S. B., Ben M'Barek, S., Dhillon, B., Wittenberg, A. H. J., Crane, C. F., Hane, J. K., Foster, A. J., van der Lee, T. A. J., Grimwood, J., Aerts, A., Antoniw, J., Bailey, A., Bluhm, B., Bowler, J., Bristow, J., van der Burgt, A., Canto-Canché, B., Churchill, A. C. L., Conde-Ferràez, L., Cools, H. J. & 37 others, Coutinho, P. M., Csukai, M., Dehal, P., de Wit, P. J. G. M., Donzelli, B., van de Geest, H. C., van Ham, R. C. H. J., Hammond-Kosack, K. E., Henrissat, B., Kilian, A., Kobayashi, A. K., Koopmann, E., Kourmpetis, Y., Kuzniar, A., Lindquist, E., Lombard, V., Maliepaard, C. A., Martins, N., Mehrabi, A., Nap, J. P. H., Ponomarenko, A., Rudd, J. J., Salamov, A., Schmutz, J., Schouten, H. J., Shapiro, H., Stergiopoulos, I., Torriani, S. F. F., Tu, H., de Vries, R. P., Waalwijk, C., Ware, S. B., Wiebenga, A., Zwiers, L. H., Oliver, R. P., Grigoriev, I. V. & Kema, G. H. J., 2011, In : Plos Genetics. 7, 6, 17 p., e1002070.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Fungal Genome
Chromosome Structures
Mycosphaerella graminicola
Triticum
plasticity