REML Implementations of Kernel-based Multi-environment Genomic Prediction Models

Authors: Melsen, Killian A. C., Gezan, Salvador, van Eeuwijk, Fred, Peeters, Carel F. W.

Subject Terms: Statistics - Methodology

Access URL: http://arxiv.org/abs/2501.06844

Improving Genomic Prediction using High-dimensional Secondary Phenotypes: the Genetic Latent Factor Approach

Authors: Melsen, Killian A. C., Kunst, Jonathan F., Crossa, José, Krause, Margaret R., van Eeuwijk, Fred A., Kruijer, Willem, Peeters, Carel F. W.

Subject Terms: Statistics - Methodology, Quantitative Biology - Quantitative Methods

Access URL: http://arxiv.org/abs/2408.09876

Modelling methane production of dairy cows: A hierarchical Bayesian stochastic approach

Authors: Levrault, Cécile M., Ogink, Nico W.M., Dijkstra, Jan, Groot Koerkamp, Peter W.G., Nichols, Kelly, van Eeuwijk, Fred A., Peeters, Carel F.W.

Source: In Computers and Electronics in Agriculture January 2025 228

Penalized factorial regression as a flexible and computationally attractive reaction norm model for prediction in the presence of GxE: Penalized factorial regression as a flexible and...: V. Avagyan et al.

Authors: Avagyan, Vahe, Boer, Martin P., Solin, Junita, van Dijk, Aalt D. J., Bustos-Korts, Daniela, van Rossum, Bart-Jan, Ramakers, Jip J. C., van Eeuwijk, Fred, Kruijer, Willem

Source: Theoretical & Applied Genetics; Apr2025, Vol. 138 Issue 4, p1-12, 12p

A diversity of resistance sources to Fusarium oxysporum f. sp. pisi found within grass pea germplasm

Authors: Sampaio, Ana Margarida, Vitale, Stefania, Turrà, David, Di Pietro, Antonio, Rubiales, Diego, van Eeuwijk, Fred, Vaz Patto, Maria Carlota

Source: Plant and Soil, 2021 Jun 01. 463(1/2), 19-38.

Access URL: https://www.jstor.org/stable/27293273

Spatial Models for Field Trials

Authors: Rodríguez-Álvarez, María Xosé, Boer, Martin P., van Eeuwijk, Fred A., Eilers, Paul H. C.

Subject Terms: Statistics - Methodology, Statistics - Applications

Access URL: http://arxiv.org/abs/1607.08255

Species-wide inventory of Arabidopsis thaliana organellar variation reveals ample phenotypic variation for photosynthetic performance.

Authors: Theeuwen, Tom P. J. M., Wijfjes, Raúl Y., Dorussen, Delfi, Lawson, Aaron W., Lind, Jorrit, Kaining Jin, Boekeloo, Janhenk, Tijink, Dillian, Hall, David, Hanhart, Corrie, Becker, Frank F. M., van Eeuwijk, Fred A., Kramer, David M., Wijnker, Erik, Harbinson, Jeremy, Koornneef, Maarten, Aarts, Mark G. M.

Source: Proceedings of the National Academy of Sciences of the United States of America; 12/3/2024, Vol. 121 Issue 49, p1-12, 35p

Subject Terms: GENETIC variation, CHLOROPLAST DNA, PHENOTYPES, ARABIDOPSIS thaliana, PHENOTYPIC plasticity

Allelic variants confer Arabidopsis adaptation to small regional environmental differences.

Authors: Wijfjes, Raúl Y., Boesten, René, Becker, Frank F. M., Theeuwen, Tom P. J. M., Snoek, Basten L., Mastoraki, Maria, Verheijen, Jelle J., Güvencli, Nuri, Denkers, Lissy‐Anne M., Koornneef, Maarten, van Eeuwijk, Fred A., Smit, Sandra, de Ridder, Dick, Aarts, Mark G. M.

Source: Plant Journal; Nov2024, Vol. 120 Issue 4, p1662-1681, 20p

Subject Terms: PLANT adaptation, GENETIC variation, ARABIDOPSIS thaliana, IRON deficiency, CLIMATE change, FLOWERING time

Marker-based estimation of heritability in immortal populations

Authors: Kruijer, Willem, Boer, Martin, Malosetti, Marcos, Flood, Padraic J., Engel, Bas, Kooke, Rik, Keurentjes, Joost, van Eeuwijk, Fred

Source: Genetics (2015), Vol. 199(2), p. 379-398

Subject Terms: Statistics - Applications, Quantitative Biology - Populations and Evolution, 62P10

Access URL: http://arxiv.org/abs/1412.6779

Corrigendum to “Modelling methane production of dairy cows: A hierarchical Bayesian stochastic approach” [Comput. Electron. Agric. 228 (2025) 109683]

Authors: Levrault, Cécile M. ^{a, ⁎}, Ogink, Nico W.M. ^{a, b}, Dijkstra, Jan ^c, Groot Koerkamp, Peter W.G. ^a, Nichols, Kelly ^c, van Eeuwijk, Fred A. ^d, Peeters, Carel F.W. ^d

Source: In Computers and Electronics in Agriculture March 2025 230

Dietary Intakes of Vegetable Protein, Folate,and Vitamins B-6 and B-12 Are Partially Correlated with Physical Functioning of Dutch Older Adults Using Copula Graphical Models

Authors: Behrouzi, Pariya ^*, Grootswagers, Pol, Keizer, Paul L C, Smeets, Ellen T H C, Feskens, Edith J M, de Groot, Lisette C P G M, van Eeuwijk, Fred A

Source: In The Journal of Nutrition March 2020 150(3):634-643

StatgenMPP: an R package implementing an IBD-based mixed model approach for QTL mapping in a wide range of multi-parent populations

Authors: Li, Wenhao, Boer, Martin P, van Rossum, Bart-Jan, Zheng, Chaozhi, Joosen, Ronny V L, van Eeuwijk, Fred A

Source: Bioinformatics. 38(22):5134-5136

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100164935480.0x000001&indx=1&recIds=ETOCvdc_100164935480.0x000001

Modelling strategies for assessing and increasing the effectiveness of new phenotyping techniques in plant breeding

Authors: van Eeuwijk, Fred A., Bustos-Korts, Daniela, Millet, Emilie J., Boer, Martin P., Kruijer, Willem, Thompson, Addie, Malosetti, Marcos, Iwata, Hiroyoshi, Quiroz, Roberto, Kuppe, Christian, Muller, Onno, Blazakis, Konstantinos N., Yu, Kang, Tardieu, Francois, Chapman, Scott C.

Source: In Plant Science May 2019 282:23-39

Reciprocal cybrids reveal how organellar genomes affect plant phenotypes

Authors: Flood, Pádraic J., Theeuwen, Tom P. J. M., Schneeberger, Korbinian, Keizer, Paul, Kruijer, Willem, Severing, Edouard, Kouklas, Evangelos, Hageman, Jos A., Wijfjes, Raúl, Calvo-Baltanas, Vanesa, Becker, Frank F. M., Schnabel, Sabine K., Willems, Leo A. J., Ligterink, Wilco, van Arkel, Jeroen, Mumm, Roland, Gualberto, José M., Savage, Linda, Kramer, David M., Keurentjes, Joost J. B., van Eeuwijk, Fred, Koornneef, Maarten, Harbinson, Jeremy, Aarts, Mark G. M., Wijnker, Erik

Source: Nature plants. 6(1):13-21

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100131039071.0x000001&indx=1&recIds=ETOCvdc_100131039071.0x000001

Volatilome—Genome-Wide Association Study on Wholemeal Maize Flour

Authors: Alves, Mara Lisa, Bento-Silva, Andreia, Gaspar, Daniel, Paulo, Manuel, Brites, Cláudia, Mendes-Moreira, Pedro, do Rosário Bronze, Maria, Malosetti, Marcos, van Eeuwijk, Fred, Patto, Maria Carlota Vaz

Source: Journal of agricultural and food chemistry. 68(29):7809-7818

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCRN624351913&indx=1&recIds=ETOCRN624351913

Multi-environment analysis of sorghum breeding trials using additive and dominance genomic relationships

Authors: Hunt, Colleen H., Hayes, Ben J., van Eeuwijk, Fred A., Mace, Emma S., Jordan, David R.

Source: Theoretical and applied genetics. 133(3):1009-1018

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100161956638.0x000001&indx=1&recIds=ETOCvdc_100161956638.0x000001

Bivariate GWA mapping reveals associations between aliphatic glucosinolates and plant responses to thrips and heat stress.

Authors: Arouisse, Bader, Thoen, Manus P.M., Kruijer, Willem, Kunst, Jonathan F., Jongsma, Maarten A., Keurentjes, Joost J.B., Kooke, Rik, de Vos, Ric C.H., Mumm, Roland, van Eeuwijk, Fred A., Dicke, Marcel, Kloth, Karen J.

Source: Plant Journal; Oct2024, Vol. 120 Issue 2, p674-686, 13p

Subject Terms: FRANKLINIELLA occidentalis, QUANTITATIVE genetics, PLANT metabolites, PLANT diversity, ARABIDOPSIS thaliana

Modeling QTL-by-environment interactions for multi-parent populations.

Authors: Wenhao Li, Boer, Martin P., Joosen, Ronny V. L., Chaozhi Zheng, Percival-Alwyn, Lawrence, Cockram, James, Van Eeuwijk, Fred A.

Source: Frontiers in Plant Science; 2024, p1-14, 14p

Subject Terms: GENETIC variation, MATRIX functions, HOME environment, WHEAT, CORN

Correcting for spatial heterogeneity in plant breeding experiments with P-splines

Authors: Rodríguez-Álvarez, María Xosé, Boer, Martin P., van Eeuwijk, Fred A., Eilers, Paul H.C.

Source: In Spatial Statistics March 2018 23:52-71

Exome sequences and multi‐environment field trials elucidate the genetic basis of adaptation in barley

Authors: Bustos‐Korts, Daniela, Dawson, Ian K., Russell, Joanne, Tondelli, Alessandro, Guerra, Davide, Ferrandi, Chiara, Strozzi, Francesco, Nicolazzi, Ezequiel L., Molnar‐Lang, Marta, Ozkan, Hakan, Megyeri, Maria, Miko, Peter, Çakır, Esra, Yakışır, Enes, Trabanco, Noemi, Delbono, Stefano, Kyriakidis, Stylianos, Booth, Allan, Cammarano, Davide, Mascher, Martin, Werner, Peter, Cattivelli, Luigi, Rossini, Laura, Stein, Nils, Kilian, Benjamin, Waugh, Robbie, van Eeuwijk, Fred A.

Source: Plant journal. 99(6):1172-1191

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100088948395.0x000001&indx=1&recIds=ETOCvdc_100088948395.0x000001