Research Output

2019

Addendum: The FAIR Guiding Principles for scientific data management and stewardship

Wilkinson, M. D., Dumontier, M., Aalbersberg, I. J., Appleton, G., Axton, M., Baak, A., Blomberg, N., Boiten, J. W., Da Silva Santos, L. B., Bourne, P. E., Bouwman, J., Brookes, A. J., Clark, T., Crosas, M., Dillo, I., Dumon, O., Edmunds, S., Evelo, C. T., Finkers, R., Gonzalez-Beltran, A. & 33 others, Gray, A. J. G., Groth, P., Goble, C., Grethe, J. S., Heringa, J., 't Hoen, P. A. C., Hooft, R., Kuhn, T., Kok, R., Kok, J., Lusher, S. J., Martone, M. E., Mons, A., Packer, A. L., Persson, B., Rocca-Serra, P., Roos, M., van Schaik, R., Sansone, S. A., Schultes, E., Sengstag, T., Slater, T., Strawn, G., Swertz, M. A., Thompson, M., van der Lei, J., van Mulligen, E., Velterop, J., Waagmeester, A., Wittenburg, P., Wolstencroft, K., Zhao, J. & Mons, B., 2019, In : Scientific Data. 6, 6.

Research output: Contribution to journalComment/Letter to the editorAcademic

Open Access
4 Citations (Scopus)

Genetic variation in phytochemicals in leaves of pepper (Capsicum) in relation to thrips resistance

Maharijaya, A., Vosman, B., Pelgrom, K., Wahyuni, Y., de Vos, R. C. H. & Voorrips, R. E., Feb 2019, In : Arthropod-Plant Interactions. 13, 1, p. 1-9

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
4 Citations (Scopus)

Haplotype estimation in polyploids using DNA sequence data

Motazedi, E., 2019, Wageningen: Wageningen University. 153 p.

Research output: Thesisinternal PhD, WU

Open Access

QTL mapping of insect resistance components of Solanum galapagense

Vosman, B., Kashaninia, A., van’t Westende, W., Meijer-Dekens, F., van Eekelen, H., Visser, R. G. F., de Vos, R. C. H. & Voorrips, R. E., Feb 2019, In : Theoretical and Applied Genetics. 132, 2, p. 531–541

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
5 Citations (Scopus)

The effect of plant development on thrips resistance in Capsicum

van Haperen, P., Voorrips, R. E., van Loon, J. J. A. & Vosman, B., Feb 2019, In : Arthropod-Plant Interactions. 13, 1, p. 11–18

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
1 Citation (Scopus)
2018

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
40 Citations (Scopus)
Open Access
10 Citations (Scopus)

Combining QTL mapping with transcriptome and metabolome profiling reveals a possible role for ABA signaling in resistance against the cabbage whitefly in cabbage

Broekgaarden, C., Pelgrom, K. T. B., Bucher, J., van Dam, N. M., Grosser, K., Pieterse, C. M. J., van Kaauwen, M., Steenhuis, G., Voorrips, R. E., de Vos, M., Vosman, B., Worrich, A. & van Wees, S. C. M., 6 Nov 2018, In : PLoS ONE. 13, 11, e0206103.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
2 Citations (Scopus)

Designing plant varieties with information technology

Visser, R. G. F. & Finkers, H. J., 2018, In : Prophyta - Focus on Europe. p. 28-30

Research output: Contribution to journalArticleProfessional

Open Access

Efficient algorithms for polyploid haplotype phasing

He, D., Saha, S., Finkers, R. & Parida, L., 9 May 2018, In : BMC Genomics. 19, Supplement 2, 110.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
8 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

13 Citations (Scopus)

Exploring natural genetic variation in tomato sucrose synthases on the basis of increased kinetic properties

Dinh, Q. D., Finkers, R., Westphal, A. H., van Dongen, W. M. A. M., Visser, R. G. F. & Trindade, L. M., 29 Oct 2018, In : PLoS ONE. 13, 10, e0206636.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
3 Citations (Scopus)

Genetic mapping in polyploids

Bourke, P. M., 2018, Wageningen: Wageningen University. 305 p.

Research output: Thesisinternal PhD, WU

Open Access

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
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
13 Citations (Scopus)

QTLTableMiner++: Semantic mining of QTL tables in scientific articles

Singh, G., Kuzniar, A., van Mulligen, E. M., Gavai, A., Bachem, C. W., Visser, R. G. F. & Finkers, R., 25 May 2018, In : BMC Bioinformatics. 19, 183.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
2 Citations (Scopus)

Reduced phloem uptake of Myzus persicae on an aphid resistant pepper accession

Sun, M., Voorrips, R. E., Steenhuis-Broers, G., van't Westende, W. & Vosman, B., 27 Jun 2018, In : BMC Plant Biology. 18, 1, 138.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
9 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
25 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

2 Citations (Scopus)
2017

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
20 Citations (Scopus)

Bladluisresistentie in Paprika: Groene Veredeling Paprika

Sun, M., Voorrips, R. E., van 't Westende, W. P. C. & Vosman, B., Jun 2017, 2 p. Wageningen : Wageningen University & Research.

Research output: Other contributionPamphlet

Open Access

Conclusive evidence for hexasomic inheritance in chrysanthemum based on analysis of a 183 k SNP array

van Geest, G., Voorrips, R. E., Esselink, D., Post, A., Visser, R. G. F. & Arens, P., 2017, In : BMC Genomics. 18, 585.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
15 Citations (Scopus)

Erratum to: Genetic structure of a QTL hotspot on chromosome 2 in sweet cherry indicates positive selection for favorable haplotypes

Cai, L., Voorrips, R. E., van de Weg, E., Peace, C. & Iezzoni, A., 2017, In : Molecular Breeding. 37, 8, 100.

Research output: Contribution to journalComment/Letter to the editorAcademic

Open Access

Evaluation of LD decay and various LD-decay estimators in simulated and SNP-array data of tetraploid potato

Vos, P. G., Paulo, M. J., Voorrips, R. E., Visser, R. G. F., van Eck, H. J. & van Eeuwijk, F. A., 2017, In : Theoretical and Applied Genetics. 130, 1, p. 123-135

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
35 Citations (Scopus)

Genetic architecture of plant stress resistance: multi-trait genome-wide association mapping

Thoen, H. P. M., Davila Olivas, N. H., Kloth, K. J., Coolen, S., Huang, P., Aarts, M. G. M., Molenaar, J. A., Bakker, J., Bouwmeester, H. J., Broekgaarden, C., Bucher, J., Busscher-Lange, J., Cheng, X., van Dijk-Fradin, E. F., Jongsma, M. A., Julkowska, M. M., Keurentjes, J. J. B., Ligterink, W., Pieterse, C. M. J., Ruyter-Spira, C. P. & 13 others, Smant, G., van Schaik, C. C., van Wees, S. C. M., Visser, R. G. F., Voorrips, R. E., Vosman, B., Vreugdenhil, D., Warmerdam, S., Wiegers, G. L., van Heerwaarden, J., Kruijer, W. T., van Eeuwijk, F. A. & Dicke, M., 2017, In : New Phytologist. 213, 3, p. 1346-1362

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
57 Citations (Scopus)

Genetic structure of a QTL hotspot on chromosome 2 in sweet cherry indicates positive selection for favorable haplotypes

Cai, L., Voorrips, R. E., van de Weg, E., Peace, C. & Iezzoni, A., 2017, In : Molecular Breeding. 37, 7, 10 p., 85.

Research output: Contribution to journalArticleAcademicpeer-review

13 Citations (Scopus)

Genome-wide association analysis for lodging tolerance and plant height in a diverse European hexaploid oat collection

Tumino, G., Voorrips, R. E., Morcia, C., Ghizzoni, R., Germeier, C. U., Caldas Paulo, J., Terzi, V. & Smulders, M. J. M., 2017, In : Euphytica. 213, 8, 163.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
14 Citations (Scopus)

Managing Variant Calling Files the Big Data Way: Using HDFS and Apache Parquet

Boufea, A., Finkers, H. J., van Kaauwen, M. P. W., Kramer, M. R. & Athanasiadis, I. N., 2017, BDCAT '17 Proceedings of the Fourth IEEE/ACM International Conference on Big Data Computing, Applications and Technologies. ACM, p. 219-226

Research output: Chapter in Book/Report/Conference proceedingChapter

Open Access
1 Citation (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
28 Citations (Scopus)

Reduced phloem uptake of Myzus persicae on an aphid resistant pepper accession

Sun, M., Voorrips, R. E., van 't Westende, W. P. C. & Vosman, B., Jun 2017.

Research output: Contribution to conferencePosterAcademic

Resistentie tegen bladluizen in paprika

Vosman, B., Sun, M., van 't Westende, W. P. C. & Voorrips, R. E., 18 Jan 2017.

Research output: Contribution to conferencePosterAcademic

Toward better data sharing methods for genebanks

Papoutsoglou, E., Kaliyaperumal, R., Van Hintum, T., Visser, R. G. F., Athanasiadis, I. N. & Finkers, R., 2017. 6 p.

Research output: Contribution to conferenceConference paper

Open Access
2016

A high-density, multi-parental SNP genetic map on apple validates a new mapping approach for outcrossing species

Di Pierro, E. A., Gianfranceschi, L., Di Guardo, M., Koehorst-Van Putten, H. J. J., Kruisselbrink, J. W., Longhi, S., Troggio, M., Bianco, L., Muranty, H., Pagliarani, G., Bink, M. C. A. M., Voorrips, R. E. & van de Weg, E., 2016, In : Horticulture Research. 3, 16057.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
32 Citations (Scopus)

Antibiosis resistance against larval cabbage root fly, Delia radicum, in wild Brassica-species

Wang, S., Voorrips, R. E., Steenhuis-Broers, G., Vosman, B. & van Loon, J. J. A., 1 Jun 2016, In : Euphytica. 17 p.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
5 Citations (Scopus)

Aphid resistance in a Capsicum collection

Voorrips, R. E., Steenhuis-Broers, M. M., van 't Westende, W. P. C. & Vosman, B., 2016, 2016 Proceedings of the XVIth EUCARPIA Capsicum and Eggplant Working Group Meeting. Ertsey-Peregi, K., Fustos, Z., Palotas, G. & Csillery, G. (eds.). Budapest, Hungary: Eucarpia

Research output: Chapter in Book/Report/Conference proceedingConference paper

Genome-wide association analysis of the anthocyanin and carotenoid contents of rose petals

Schulz, D. F., Schott, R. T., Voorrips, R. E., Smulders, R., Linde, M. & Debener, T., 2016, In : Frontiers in Plant Science. 7, DECEMBER2016, 1798.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
17 Citations (Scopus)
Open Access
22 Citations (Scopus)

Improved utilization of crop diversity for rationalized breeding using data interoperability

Finkers, H. J., 2016, Enhancing crop genepool use: capturing wild relative and landrace diversity for crop improvement. Maxted, N., Dulloo, M. E. & Ford-Lloyd, M. V. (eds.). CAB International, p. 436-440

Research output: Chapter in Book/Report/Conference proceedingChapter

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
12 Citations (Scopus)

PediHaplotyper: software for consistent assignment of marker haplotypes in pedigrees

Voorrips, R. E., Bink, M. C. A. M., Kruisselbrink, J. W., Koehorst-van Putten, H. J. J. & van de Weg, E., 2016, In : Molecular Breeding. 36, 119.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
21 Citations (Scopus)

Population structure and genome-wide association analysis for frost tolerance in oat using continuous SNP array signal intensity ratios

Tumino, G., Voorrips, R. E., Rizza, F., Badeck, F. W., Morcia, C., Ghizzoni, R., Germeier, C. U., Paulo, M. J., Terzi, V. & Smulders, M. J. M., 2016, In : Theoretical and Applied Genetics. 129, 9, p. 1711-1724

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
13 Citations (Scopus)

Probabilistic Multilocus Haplotype Reconstruction in Outcrossing Tetraploids

Zheng, C., Voorrips, R. E., Jansen, J., Hackett, C. A., Ho, J. & Bink, M. C. A. M., 2016, In : Genetics. 203, 1, p. 119-131

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
16 Citations (Scopus)

The FAIR Guiding Principles for scientific data management and stewardship: Comment

Wilkinson, M. D., Dumontier, M., Aalbersberg, I. J., Appleton, G., Axton, M., Baak, A., Blomberg, N., Boiten, J. W., Da Silva Santos, L. B., Bourne, P. E., Bouwman, J., Brookes, A. J., Clark, T., Crosas, M., Dillo, I., Dumon, O., Edmunds, S., Evelo, C. T., Finkers, R., Gonzalez-Beltran, A. & 33 others, Gray, A. J. G., Groth, P., Goble, C., Grethe, J. S., Heringa, J., 't Hoen, P. A. C., Hooft, R., Kuhn, T., Kok, R., Kok, J., Lusher, S. J., Martone, M. E., Mons, A., Packer, A. L., Persson, B., Rocca-Serra, P., Roos, M., van Schaik, R., Sansone, S. A., Schultes, E., Sengstag, T., Slater, T., Strawn, G., Swertz, M. A., Thompson, M., van der Lei, J., van Mulligen, E., Velterop, J., Waagmeester, A., Wittenburg, P., Wolstencroft, K., Zhao, J. & Mons, B., 2016, In : Scientific Data. 3, 160018.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
1476 Citations (Scopus)

Using phenomics and genomics to unlock landrace and wild relative diversity for crop improvement

Vosman, B., Pelgrom, K. T. B., Sharma, G., Voorrips, R. E., Broekgaarden, C., Pritchard, J., May, S., Adobor, S., Castellanos-Uribe, M., van Kaauwen, M. P. W., Finkers, H. J., Janssen, B., van Workum, W. & Ford-Lloyd, B., 2016, Enhancing crop genepool use: capturing wild relative and landrace diversity for crop improvement. Maxted, N., Dulloo, M. E. & Ford-Lloyd, B. V. (eds.). CABI, p. 1-9

Research output: Chapter in Book/Report/Conference proceedingChapter

Utilizing low-coverage sequence data in tomato recombinant inbred lines (S. lycopersicum x S. pimpinellifolium)

van Binsbergen, R., Bink, M. C. A. M., Finkers, H. J., Calus, M. P. L., Veerkamp, R. F. & van Eeuwijk, F. A., 2016, Plant Breeding: the art of bringing science to life - Abstracts of the 20th EUCARPIA General Congress. Kölliker, R. & Boller, B. (eds.). Agroscope, Institute for Sustainability Sciences ISS, p. 19 1 p.

Research output: Chapter in Book/Report/Conference proceedingAbstract

Open Access
2015

A case study on constructing a rearranged physical and genetic SNP marker map for tetraploid alfalfa

Voorrips, R. E., Jansen, J., Ho, J. & Bink, M. C. A. M., 2015, p. 100-100.

Research output: Contribution to conferenceAbstractAcademic

candYgene: enabling precision breeding through FAIR Data

Kuzniar, A., Gavai, A. K., Ridder, L. O., Bonino da Silva Santos, L. O., Singh, G., Visser, R. G. F. & Finkers, H. J., 2015.

Research output: Contribution to conferenceAbstract

Open Access

Detection of an inversion in the Ty-2 region between S. lycopersicum and S. habrochaites by a combination of de novo genome assembly and BAC cloning

Wolters, A. M. A., Caro Rios, C. M., Dong, S., Finkers, H. J., Gao, J., Visser, R. G. F., Wang, X., Du, Y. & Bai, Y., 2015, In : Theoretical and Applied Genetics. 128, 10, p. 1987-1997

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
4 Citations (Scopus)

Development and analysis of an 20K SNP array for potato (Solanum tuberosum): An insight in the breeding history

Vos, P. G., Uitdewilligen, J. G. A. M. L., Voorrips, R. E., Visser, R. G. F. & van Eck, H. J., 2015, In : Theoretical and Applied Genetics. 128, 12, p. 2387-2401

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
51 Citations (Scopus)