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Genomic Prediction of Grain Yield and Drought-Adaptation Capacity in Sorghum Is Enhanced by Multi-Trait Analysis.

Velazco JG, Jordan DR, Mace ES, Hunt CH, Malosetti M, van Eeuwijk FA.

Front Plant Sci. 2019 Jul 31;10:997. doi: 10.3389/fpls.2019.00997. eCollection 2019.


Significance testing and genomic inflation factor using high-density genotypes or whole-genome sequence data.

van den Berg S, Vandenplas J, van Eeuwijk FA, Lopes MS, Veerkamp RF.

J Anim Breed Genet. 2019 Jun 19. doi: 10.1111/jbg.12419. [Epub ahead of print]


Construction of Genetic Linkage Maps in Multiparental Populations.

Zheng C, Boer MP, van Eeuwijk FA.

Genetics. 2019 Aug;212(4):1031-1044. doi: 10.1534/genetics.119.302229. Epub 2019 Jun 10.


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

Bustos-Korts D, Dawson IK, Russell J, Tondelli A, Guerra D, Ferrandi C, Strozzi F, Nicolazzi EL, Molnar-Lang M, Ozkan H, Megyeri M, Miko P, Çakır E, Yakışır E, Trabanco N, Delbono S, Kyriakidis S, Booth A, Cammarano D, Mascher M, Werner P, Cattivelli L, Rossini L, Stein N, Kilian B, Waugh R, van Eeuwijk FA.

Plant J. 2019 May 20. doi: 10.1111/tpj.14414. [Epub ahead of print]


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

van Eeuwijk FA, Bustos-Korts D, Millet EJ, Boer MP, Kruijer W, Thompson A, Malosetti M, Iwata H, Quiroz R, Kuppe C, Muller O, Blazakis KN, Yu K, Tardieu F, Chapman SC.

Plant Sci. 2019 May;282:23-39. doi: 10.1016/j.plantsci.2018.06.018. Epub 2018 Jun 30.


Combining pedigree and genomic information to improve prediction quality: an example in sorghum.

Velazco JG, Malosetti M, Hunt CH, Mace ES, Jordan DR, van Eeuwijk FA.

Theor Appl Genet. 2019 Jul;132(7):2055-2067. doi: 10.1007/s00122-019-03337-w. Epub 2019 Apr 9.


Imputation to whole-genome sequence using multiple pig populations and its use in genome-wide association studies.

van den Berg S, Vandenplas J, van Eeuwijk FA, Bouwman AC, Lopes MS, Veerkamp RF.

Genet Sel Evol. 2019 Jan 24;51(1):2. doi: 10.1186/s12711-019-0445-y.


Assessment of heterosis in two Arabidopsis thaliana common-reference mapping populations.

van Hulten MHA, Paulo MJ, Kruijer W, Blankestijn-De Vries H, Kemperman B, Becker FFM, Yang J, Lauss K, Stam ME, van Eeuwijk FA, Keurentjes JJB.

PLoS One. 2018 Oct 12;13(10):e0205564. doi: 10.1371/journal.pone.0205564. eCollection 2018.


Recursive Algorithms for Modeling Genomic Ancestral Origins in a Fixed Pedigree.

Zheng C, Boer MP, van Eeuwijk FA.

G3 (Bethesda). 2018 Oct 3;8(10):3231-3245. doi: 10.1534/g3.118.200340.


Accurate Genotype Imputation in Multiparental Populations from Low-Coverage Sequence.

Zheng C, Boer MP, van Eeuwijk FA.

Genetics. 2018 Sep;210(1):71-82. doi: 10.1534/genetics.118.300885. Epub 2018 Jul 25.


Natural variation of YELLOW SEEDLING1 affects photosynthetic acclimation of Arabidopsis thaliana.

van Rooijen R, Kruijer W, Boesten R, van Eeuwijk FA, Harbinson J, Aarts MGM.

Nat Commun. 2017 Nov 10;8(1):1421. doi: 10.1038/s41467-017-01576-3.


Modelling spatial trends in sorghum breeding field trials using a two-dimensional P-spline mixed model.

Velazco JG, Rodríguez-Álvarez MX, Boer MP, Jordan DR, Eilers PHC, Malosetti M, van Eeuwijk FA.

Theor Appl Genet. 2017 Jul;130(7):1375-1392. doi: 10.1007/s00122-017-2894-4. Epub 2017 Apr 3.


The potential of probabilistic graphical models in linkage map construction.

Wang H, van Eeuwijk FA, Jansen J.

Theor Appl Genet. 2017 Feb;130(2):433-444. doi: 10.1007/s00122-016-2824-x. Epub 2016 Dec 5.


A method for sensitivity analysis to assess the effects of measurement error in multiple exposure variables using external validation data.

Agogo GO, van der Voet H, van 't Veer P, Ferrari P, Muller DC, Sánchez-Cantalejo E, Bamia C, Braaten T, Knüppel S, Johansson I, van Eeuwijk FA, Boshuizen HC.

BMC Med Res Methodol. 2016 Oct 13;16(1):139.


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

Thoen MP, Davila Olivas NH, Kloth KJ, Coolen S, Huang PP, Aarts MG, Bac-Molenaar JA, Bakker J, Bouwmeester HJ, Broekgaarden C, Bucher J, Busscher-Lange J, Cheng X, Fradin EF, Jongsma MA, Julkowska MM, Keurentjes JJ, Ligterink W, Pieterse CM, Ruyter-Spira C, Smant G, Testerink C, Usadel B, van Loon JJ, van Pelt JA, van Schaik CC, van Wees SC, Visser RG, Voorrips R, Vosman B, Vreugdenhil D, Warmerdam S, Wiegers GL, van Heerwaarden J, Kruijer W, van Eeuwijk FA, Dicke M.

New Phytol. 2017 Feb;213(3):1346-1362. doi: 10.1111/nph.14220. Epub 2016 Oct 4.


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

Vos PG, Paulo MJ, Voorrips RE, Visser RG, van Eck HJ, van Eeuwijk FA.

Theor Appl Genet. 2017 Jan;130(1):123-135. doi: 10.1007/s00122-016-2798-8. Epub 2016 Oct 3.


Evaluation of a two-part regression calibration to adjust for dietary exposure measurement error in the Cox proportional hazards model: A simulation study.

Agogo GO, van der Voet H, Van't Veer P, van Eeuwijk FA, Boshuizen HC.

Biom J. 2016 Jul;58(4):766-82. doi: 10.1002/bimj.201500009. Epub 2016 Mar 22.


Back to Acid Soil Fields: The Citrate Transporter SbMATE Is a Major Asset for Sustainable Grain Yield for Sorghum Cultivated on Acid Soils.

Carvalho G Jr, Schaffert RE, Malosetti M, Viana JH, Menezes CB, Silva LA, Guimaraes CT, Coelho AM, Kochian LV, van Eeuwijk FA, Magalhaes JV.

G3 (Bethesda). 2015 Dec 17;6(2):475-84. doi: 10.1534/g3.115.025791.


Genomic prediction using imputed whole-genome sequence data in Holstein Friesian cattle.

van Binsbergen R, Calus MP, Bink MC, van Eeuwijk FA, Schrooten C, Veerkamp RF.

Genet Sel Evol. 2015 Sep 17;47:71. doi: 10.1186/s12711-015-0149-x.


Root phenotyping: from component trait in the lab to breeding.

Kuijken RC, van Eeuwijk FA, Marcelis LF, Bouwmeester HJ.

J Exp Bot. 2015 Sep;66(18):5389-401. doi: 10.1093/jxb/erv239. Epub 2015 Jun 12. Review.


Reconstruction of Genome Ancestry Blocks in Multiparental Populations.

Zheng C, Boer MP, van Eeuwijk FA.

Genetics. 2015 Aug;200(4):1073-87. doi: 10.1534/genetics.115.177873. Epub 2015 Jun 4.


Marker-based estimation of heritability in immortal populations.

Kruijer W, Boer MP, Malosetti M, Flood PJ, Engel B, Kooke R, Keurentjes JJ, van Eeuwijk FA.

Genetics. 2015 Feb;199(2):379-98. doi: 10.1534/genetics.114.167916. Epub 2014 Dec 19. Erratum in: Genetics. 2015 May;200(1):385.


Use of two-part regression calibration model to correct for measurement error in episodically consumed foods in a single-replicate study design: EPIC case study.

Agogo GO, van der Voet H, van't Veer P, Ferrari P, Leenders M, Muller DC, Sánchez-Cantalejo E, Bamia C, Braaten T, Knüppel S, Johansson I, van Eeuwijk FA, Boshuizen H.

PLoS One. 2014 Nov 17;9(11):e113160. doi: 10.1371/journal.pone.0113160. eCollection 2014.


A general modeling framework for genome ancestral origins in multiparental populations.

Zheng C, P Boer M, van Eeuwijk FA.

Genetics. 2014 Sep;198(1):87-101. doi: 10.1534/genetics.114.163006.


A new method to infer causal phenotype networks using QTL and phenotypic information.

Wang H, van Eeuwijk FA.

PLoS One. 2014 Aug 21;9(8):e103997. doi: 10.1371/journal.pone.0103997. eCollection 2014.


Variation in broccoli cultivar phytochemical content under organic and conventional management systems: implications in breeding for nutrition.

Renaud EN, Lammerts van Bueren ET, Myers JR, Paulo MJ, van Eeuwijk FA, Zhu N, Juvik JA.

PLoS One. 2014 Jul 16;9(7):e95683. doi: 10.1371/journal.pone.0095683. eCollection 2014.


Accuracy of imputation to whole-genome sequence data in Holstein Friesian cattle.

van Binsbergen R, Bink MC, Calus MP, van Eeuwijk FA, Hayes BJ, Hulsegge I, Veerkamp RF.

Genet Sel Evol. 2014 Jul 15;46:41. doi: 10.1186/1297-9686-46-41.


Identification of agronomically important QTL in tetraploid potato cultivars using a marker-trait association analysis.

D'hoop BB, Keizer PL, Paulo MJ, Visser RG, van Eeuwijk FA, van Eck HJ.

Theor Appl Genet. 2014 Mar;127(3):731-48. doi: 10.1007/s00122-013-2254-y. Epub 2014 Jan 10.


Multi-trait and multi-environment QTL analyses of yield and a set of physiological traits in pepper.

Alimi NA, Bink MC, Dieleman JA, Magán JJ, Wubs AM, Palloix A, van Eeuwijk FA.

Theor Appl Genet. 2013 Oct;126(10):2597-625. doi: 10.1007/s00122-013-2160-3. Epub 2013 Aug 1.


The statistical analysis of multi-environment data: modeling genotype-by-environment interaction and its genetic basis.

Malosetti M, Ribaut JM, van Eeuwijk FA.

Front Physiol. 2013 Mar 12;4:44. doi: 10.3389/fphys.2013.00044. eCollection 2013.


Maximizing genetic differentiation in core collections by PCA-based clustering of molecular marker data.

van Heerwaarden J, Odong TL, van Eeuwijk FA.

Theor Appl Genet. 2013 Mar;126(3):763-72. doi: 10.1007/s00122-012-2016-2. Epub 2012 Nov 21.


Quality of core collections for effective utilisation of genetic resources review, discussion and interpretation.

Odong TL, Jansen J, van Eeuwijk FA, van Hintum TJ.

Theor Appl Genet. 2013 Feb;126(2):289-305. doi: 10.1007/s00122-012-1971-y. Epub 2012 Sep 15. Review.


Studying the genetic basis of drought tolerance in sorghum by managed stress trials and adjustments for phenological and plant height differences.

Sabadin PK, Malosetti M, Boer MP, Tardin FD, Santos FG, Guimarães CT, Gomide RL, Andrade CL, Albuquerque PE, Caniato FF, Mollinari M, Margarido GR, Oliveira BF, Schaffert RE, Garcia AA, van Eeuwijk FA, Magalhaes JV.

Theor Appl Genet. 2012 May;124(8):1389-402. doi: 10.1007/s00122-012-1795-9.


Genome-wide association studies for agronomical traits in a world wide spring barley collection.

Pasam RK, Sharma R, Malosetti M, van Eeuwijk FA, Haseneyer G, Kilian B, Graner A.

BMC Plant Biol. 2012 Jan 27;12:16. doi: 10.1186/1471-2229-12-16.


A mixed model QTL analysis for sugarcane multiple-harvest-location trial data.

Pastina MM, Malosetti M, Gazaffi R, Mollinari M, Margarido GR, Oliveira KM, Pinto LR, Souza AP, van Eeuwijk FA, Garcia AA.

Theor Appl Genet. 2012 Mar;124(5):835-49. doi: 10.1007/s00122-011-1748-8. Epub 2011 Dec 13.


On the increase of predictive performance with high-level data fusion.

Doeswijk TG, Smilde AK, Hageman JA, Westerhuis JA, van Eeuwijk FA.

Anal Chim Acta. 2011 Oct 31;705(1-2):41-7. doi: 10.1016/j.aca.2011.03.025. Epub 2011 Mar 17.


Determination of genetic structure of germplasm collections: are traditional hierarchical clustering methods appropriate for molecular marker data?

Odong TL, van Heerwaarden J, Jansen J, van Hintum TJ, van Eeuwijk FA.

Theor Appl Genet. 2011 Jul;123(2):195-205. doi: 10.1007/s00122-011-1576-x. Epub 2011 Apr 7.


Gene and QTL detection in a three-way barley cross under selection by a mixed model with kinship information using SNPs.

Malosetti M, van Eeuwijk FA, Boer MP, Casas AM, Elía M, Moralejo M, Bhat PR, Ramsay L, Molina-Cano JL.

Theor Appl Genet. 2011 May;122(8):1605-16. doi: 10.1007/s00122-011-1558-z. Epub 2011 Mar 4.


Analysis of natural allelic variation in Arabidopsis using a multiparent recombinant inbred line population.

Huang X, Paulo MJ, Boer M, Effgen S, Keizer P, Koornneef M, van Eeuwijk FA.

Proc Natl Acad Sci U S A. 2011 Mar 15;108(11):4488-93. doi: 10.1073/pnas.1100465108. Epub 2011 Feb 23.


Mixed model association scans of multi-environmental trial data reveal major loci controlling yield and yield related traits in Hordeum vulgare in Mediterranean environments.

Comadran J, Russell JR, Booth A, Pswarayi A, Ceccarelli S, Grando S, Stanca AM, Pecchioni N, Akar T, Al-Yassin A, Benbelkacem A, Ouabbou H, Bort J, van Eeuwijk FA, Thomas WT, Romagosa I.

Theor Appl Genet. 2011 May;122(7):1363-73. doi: 10.1007/s00122-011-1537-4. Epub 2011 Jan 30.


Gene regulatory networks from multifactorial perturbations using Graphical Lasso: application to the DREAM4 challenge.

Menéndez P, Kourmpetis YA, ter Braak CJ, van Eeuwijk FA.

PLoS One. 2010 Dec 20;5(12):e14147. doi: 10.1371/journal.pone.0014147.


Population structure and linkage disequilibrium unravelled in tetraploid potato.

D'hoop BB, Paulo MJ, Kowitwanich K, Sengers M, Visser RG, van Eck HJ, van Eeuwijk FA.

Theor Appl Genet. 2010 Oct;121(6):1151-70. doi: 10.1007/s00122-010-1379-5. Epub 2010 Jun 20.


Codominant scoring of AFLP in association panels.

Gort G, van Eeuwijk FA.

Theor Appl Genet. 2010 Jul;121(2):337-51. doi: 10.1007/s00122-010-1313-x. Epub 2010 Mar 17.


Detection and use of QTL for complex traits in multiple environments.

van Eeuwijk FA, Bink MC, Chenu K, Chapman SC.

Curr Opin Plant Biol. 2010 Apr;13(2):193-205. doi: 10.1016/j.pbi.2010.01.001. Review.


Mixed model approaches for the identification of QTLs within a maize hybrid breeding program.

van Eeuwijk FA, Boer M, Totir LR, Bink M, Wright D, Winkler CR, Podlich D, Boldman K, Baumgarten A, Smalley M, Arbelbide M, ter Braak CJ, Cooper M.

Theor Appl Genet. 2010 Jan;120(2):429-40. doi: 10.1007/s00122-009-1205-0. Epub 2009 Nov 17.


Genetic diversity in a crop metapopulation.

van Heerwaarden J, van Eeuwijk FA, Ross-Ibarra J.

Heredity (Edinb). 2010 Jan;104(1):28-39. doi: 10.1038/hdy.2009.110.


Estimating maize genetic erosion in modernized smallholder agriculture.

van Heerwaarden J, Hellin J, Visser RF, van Eeuwijk FA.

Theor Appl Genet. 2009 Sep;119(5):875-88. doi: 10.1007/s00122-009-1096-0. Epub 2009 Jul 4.


Patterns of genetic diversity and linkage disequilibrium in a highly structured Hordeum vulgare association-mapping population for the Mediterranean basin.

Comadran J, Thomas WT, van Eeuwijk FA, Ceccarelli S, Grando S, Stanca AM, Pecchioni N, Akar T, Al-Yassin A, Benbelkacem A, Ouabbou H, Bort J, Romagosa I, Hackett CA, Russell JR.

Theor Appl Genet. 2009 Jun;119(1):175-87. doi: 10.1007/s00122-009-1027-0. Epub 2009 May 5.


Modeling QTL for complex traits: detection and context for plant breeding.

Cooper M, van Eeuwijk FA, Hammer GL, Podlich DW, Messina C.

Curr Opin Plant Biol. 2009 Apr;12(2):231-40. doi: 10.1016/j.pbi.2009.01.006. Epub 2009 Mar 11. Review.


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