Publications and communications of Tom Druet

Naji, M., Gualdrón Duarte, J. L., Forneris, N., & Druet, T. (31 January 2024). Inbreeding depression is associated with recent homozygous-by-descent segments in Belgian Blue beef cattle. Genetics, Selection, Evolution, 56 (1), 10. doi:10.1186/s12711-024-00878-7

Gualdrón Duarte, J. L., Yuan, C., Gori, A.-S., Moreira, G. C. M., Takeda, H., Coppieters, W., Charlier, C., Georges, M., & Druet, T. (28 November 2023). Sequenced-based GWAS for linear classification traits in Belgian Blue beef cattle reveals new coding variants in genes regulating body size in mammals. Genetics, Selection, Evolution, 55 (1), 83. doi:10.1186/s12711-023-00857-4

Lee, Y. L., Bosse, M., Takeda, H., Moreira, G. C. M., Karim, L., Druet, T., Oget-Ebrad, C., Coppieters, W., Veerkamp, R. F., Groenen, M. A. M., Georges, M., Bouwman, A. C., & Charlier, C. (01 May 2023). High-resolution structural variants catalogue in a large-scale whole genome sequenced bovine family cohort data. BMC Genomics, 24 (1), 225. doi:10.1186/s12864-023-09259-8

Wilmot, H., Druet, T., Hulsegge, I., Gengler, N., & Calus, M. P. L. (30 March 2023). Estimation of inbreeding, between-breed genomic relatedness and definition of sub-populations in red-pied cattle breeds. Animal, 17 (5), 100793. doi:10.1016/j.animal.2023.100793

Druet, T., Flori, L., & Gautier, M. (08 July 2022). Partitioning of autozygosity in different age-based classes in cattle populations with different demographic histories [Paper presentation]. World Congress on Genetics Applied to Livestock Production, Rotterdam, Netherlands.

Gualdron Duarte, J. L., Gori, A.-S., Costa Monteiro Moreira, G., Georges, M., Charlier, C., & Druet, T. (08 July 2022). Sequence-based multi-trait genome-wide association study for linear classification traits in Belgian Blue beef cattle [Paper presentation]. World Congress on Genetics Applied to Livestock Production, Rotterdam, Netherlands.

Lee, Y. L., Bosse, M., Coppieters, W., Veerkamp, R., Karim, L., Oget, C., Druet, T., Groenen, M., Georges, M., Bouwman, A., & Charlier, C. (08 July 2022). Rare CNVs in the bovine genome are not captured well by 50K density genotyping array SNPs [Paper presentation]. World Congress on Genetics Applied to Livestock Production, Rotterdam, Netherlands.

Oget, C., Costa Monteiro Moreira, G., Karim, L., Coppieters, W., Charlier, C., Georges, M., & Druet, T. (08 July 2022). Fine-Scale Study of Meiotic Recombination in Cattle [Paper presentation]. World Congress on Genetics Applied to Livestock Production, Rotterdam, Netherlands.

Rombouts, T., Druet, T., Gualdron Duarte, J. L., Ahariz, N., Karim, L., Coppieters, W., De Smet, S., Georges, M., & Charlier, C. (08 July 2022). A hypomorphic mutation in the ATP2A1 gene increases muscle mass yet compromises meat quality of Belgian Blue cattle [Paper presentation]. World Congress on Genetics Applied to Livestock Production, Rotterdam, Netherlands.

Yuan, C., Tang, L., Lopdell, T., Oget, C., Costa Monteiro Moreira, G., Gualdron Duarte, J. L., Cheng, Z., Salavati, M., Wathes, D. C., Crowe, M. A., GplusE consortium, Coppieters, W., Charlier, C., Druet, T., Georges, M., & Takeda, H. (08 July 2022). Enrichment of causative variants in tissue-specific and shared ATAC-Seq peaks in cattle [Paper presentation]. World Congress on Genetics Applied to Livestock Production, Rotterdam, Netherlands.

Druet, T., Naji, M., Forneris, N., Flori, L., & Gautier, M. (29 June 2022). Understanding and managing inbreeding with runs of homozygosity in animal populations [Paper presentation]. 6th Polish Congress of Genetics, Krakow, Poland.

De Los Rios-Perez, L., Druet, T., Goldammer, T., & Wittenburg, D. (2022). Analysis of Autozygosity Using Whole-Genome Sequence Data of Full-Sib Families in Pikeperch (Sander lucioperca). Frontiers in Genetics. doi:10.3389/fgene.2021.786934

Druet, T., & Gautier, M. (2022). A hidden Markov model to estimate homozygous-by-descent probabilities associated with nested layers of ancestors. Theoretical Population Biology, 145, 38-51. doi:10.1016/j.tpb.2022.03.001

Kadri, N. K., Zhang, J., Oget-Ebrad, C., Wang, Y., Couldrey, C., Spelman, R., Charlier, C., Georges, M., & Druet, T. (2022). High male specific contribution of the X-chromosome to individual global recombination rate in dairy cattle. BMC Genomics, 23 (1), 114. doi:10.1186/s12864-022-08328-8

Magnier, J., Druet, T., Naves, M., Ouvrard, M., Raoul, S., Janelle, J., Moazami-Goudarzi, K., Lesnoff, M., Tillard, E., Gautier, M., & Flori, L. (2022). The genetic history of Mayotte and Madagascar cattle breeds mirrors the complex pattern of human exchanges in Western Indian Ocean. G3: Genes, Genomes, Genetics, 12 (4). doi:10.1093/g3journal/jkac029

Oget, C., Kadri, N. K., Moreira, G. C. M., Karim, L., Coppieters, W., Georges, M., & Druet, T. (2022). Benchmarking phasing software with a whole-genome sequenced cattle pedigree. BMC Genomics, 23 (1), 130. doi:10.1186/s12864-022-08354-6

Alemu, S. W., Kadri, N. K., Harland, C., Faux, P., Charlier, C., Caballero, A., & Druet, T. (2021). An evaluation of inbreeding measures using a whole-genome sequenced cattle pedigree. Heredity, 126, 410-423. doi:10.1038/s41437-020-00383-9

Caballero, A., Villanueva, B., & Druet, T. (2021). On the estimation of inbreeding depression using different measures of inbreeding from molecular markers. Evolutionary Applications, 14, 416-428. doi:10.1111/eva.13126

Lee, Y.-L., Takeda, H., Costa Monteiro Moreira, G., Karim, L., Mullaart, E., Coppieters, W., Appeltant, R., Veerkamp, R. F., Groenen, M. A. M., Georges, M., Bosse, M., Druet, T., Bouwman, A. C., & Charlier, C. (2021). A 12 kb multi-allelic copy number variation encompassing a GC gene enhancer is associated with mastitis resistance in dairy cattle. PLoS Genetics, 17 (7), 1009331. doi:10.1371/journal.pgen.1009331

Cardoso Esteves, S. M., Iacono, F., Jadoul, A., Banneux, S., Cardol, P., Druet, T., Hanikenne, M., & Houet, R. (Other coll.). (17 November 2020). A MAGIC design to study metal homeostasis in Chlamydomonas reinhardtii [Poster presentation]. EMBL Conference: From functional genomics to systems biology.

Druet, T., & Legarra, A. (2020). Theoretical and empirical comparisons of expected and realized relationships for the X-chromosome. Genetics, selection, evolution : GSE, 52 (1), 50. doi:10.1186/s12711-020-00570-6

Druet, T., Oleński, K., Flori, L., Bertrand, A., Olech, W., Tokarska, M., Kaminski, S., & Gautier, M. (2020). Genomic Footprints of Recovery in the European Bison. Journal of Heredity, 111 (2), 194-203. doi:10.1093/jhered/esaa002

Gualdron Duarte, J. L., Gori, A.-S., Hubin, X., Lourenco, D., Charlier, C., Misztal, I., & Druet, T. (2020). Performances of Adaptive MultiBLUP, Bayesian regressions, and weighted-GBLUP approaches for genomic predictions in Belgian Blue beef cattle. BMC Genomics, 21 (1), 545. doi:10.1186/s12864-020-06921-3

Zhang, J., Kadri, N. K., Mullaart, E., Spelman, R., Fritz, S., Boichard, D., Charlier, C., Georges, M., & Druet, T. (2020). Genetic architecture of individual variation in recombination rate on the X chromosome in cattle. Heredity, 125 (5), 304-316. doi:10.1038/s41437-020-0341-9

Faux, P., Geurts, P., & Druet, T. (27 June 2019). A Random Forests Framework for Modeling Haplotypes as Mosaics of Reference Haplotypes. Frontiers in Genetics, 10, 562. doi:10.3389/fgene.2019.00562

Bertrand, A., Kadri, N. K., Flori, L., Gautier, M., & Druet, T. (2019). RZooRoH: An R package to characterize individual genomic autozygosity and identify homozygous-by-descent segments. Methods in Ecology and Evolution, 10 (6), 860-866. doi:10.1111/2041-210X.13167

Kadri, N. K., Harland, C., Charlier, C., Karim, L., Cambisano, N., Deckers, M., Mullaart, E., Coppieters, W., Georges, M., & Druet, T. (2018). High resolution mapping of cross-over events in cattle using NGS data. In Proceedings of the World Congress on Genetics Applied to Livestock Production.

Druet, T., & Gautier, M. (October 2017). A model-based approach to characterize individual inbreeding at both global and local genomic scales. Molecular Ecology, 26, 5820-5841. doi:10.1111/mec.14324

Faux, P., & Druet, T. (2017). A strategy to improve phasing of whole-genome sequenced individuals through integration of familial information from dense genotype panels. Genetics, Selection, Evolution, 49 (1), 46. doi:10.1186/s12711-017-0321-6

Hess, M., Druet, T., Hess, A., & Garrick, D. (2017). Fixed-length haplotypes can improve genomic prediction accuracy in an admixed dairy cattle population. Genetics, Selection, Evolution, 49 (1), 54. doi:10.1186/s12711-017-0329-y

Sole Berga, M., Gori, A.-S., Faux, P., Bertrand, A., Farnir, F., Gautier, M., & Druet, T. (2017). Age-based partitioning of individual genomic inbreeding levels in Belgian Blue cattle. Genetics, Selection, Evolution, 49 (1), 92. doi:10.1186/s12711-017-0370-x

Kadri, N. K., Harland, C., Faux, P., Cambisano, N., Karim, L., Coppieters, W., Fritz, S., Mullaart, E., Baurain, D., Boichard, D., Spelman, R., Charlier, C., Georges, M., & Druet, T. (2016). Coding and noncoding variants in HFM1, MLH3, MSH4, MSH5, RNF212, and RNF212B affect recombination rate in cattle. Genome Research, 26 (10), 1323-1332. doi:10.1101/gr.204214.116

Murgiano, L., Waluk, D. P., Towers, R., Wiedemar, N., Dietrich, J., Jagannathan, V., Drogemuller, M., Balmer, P., Druet, T., Galichet, A., Penedo, M. C., Muller, E. J., Roosje, P., Welle, M. M., & Leeb, T. (2016). An Intronic MBTPS2 Variant Results in a Splicing Defect in Horses with Brindle Coat Texture. G3: Genes, Genomes, Genetics, 6 (9), 2963-70. doi:10.1534/g3.116.032433

Sartelet, A.* , Li, W.* , Pailhoux, E., Richard, C., Tamma, N., Karim, L., Fasquelle, C., Druet, T., Coppieters, W., Georges, M., & Charlier, C. (2015). Genome-wide next-generation DNA and RNA sequencing reveals a mutation that perturbs splicing of the phosphatidylinositol glycan anchor biosynthesis class H gene (PIGH) and causes arthrogryposis in Belgian Blue cattle. BMC Genomics, 16 (316). doi:10.1186/s12864-015-1528-y
* These authors have contributed equally to this work.

Druet, T., & Georges, M. (22 August 2014). Pedigree-based haplotype reconstruction, identification of cross-overs and detection of map and genotyping errors using PHASEBOOK [Paper presentation]. 10 th World Congress of Genetics Applied to Livestock Production.

Kadri, N. K., Sahana, G., Guldbrandtsen, B., Lund, M. S., & Druet, T. (June 2014). Efficiency of haplotype-based methods to fine-map QTLs and embryonic lethal variants affecting fertility: Illustration with a deletion segregating in Nordic Red cattle. Livestock Science, 166, 167-175. doi:10.1016/j.livsci.2014.04.030

Druet, T., Ahariz, N., Cambisano, N., Tamma, N., Michaux, C., Coppieters, W., Charlier, C., & Georges, M. (2014). Selection in action: dissecting the molecular underpinnings of the increasing muscle mass of Belgian Blue Cattle. BMC Genomics, 15 (1), 796. doi:10.1186/1471-2164-15-796

Hayes, B. J., Daetwyler, H. D., Bowman, P. J., Chamberlian, A., Vander Jagt, C., Capitan, A., Pausch, H., Stothard, P., Liao, X., Schrooten, C., Mullaart, E., Fries, R., Guldbrandtsen, B., Lund, M. S., Boichard, D., Veerkamp, R. F., VanTassell, C. P., Gredler, B., Druet, T., ... Goddard, M. E. (2014). Genomic prediction from whole genome sequence in livestock: the 1000 bull genomes project. In Proceedings from the 10th World Congress of Genetics Applied to Livestock Production. American Society of Animal Science.

Kumar Kadri, N., Sahana, G., Charlier, C., Iso-Touru, T., Guldbrandtsen, B., Karim, L., Sander Nielsen, U., Panitz, F., Pedersen Aamand, G., Schulman, N., Georges, M., Vilkki, J., Sandø Lund, M., & Druet, T. (January 2014). A 660-Kb Deletion with Antagonistic Effects on Fertility and Milk Production Segregates at High Frequency in Nordic Red Cattle: Additional Evidence for the Common Occurrence of Balancing Selection in Livestock. PLoS Genetics, 10 (1), 1004049. doi:10.1371/journal.pgen.1004049

Sartelet, A.* , Stauber, T.* , Coppieters, W., Ludwig, C. F., Fasquelle, C., Druet, T., Zhang, Z., Ahariz, N., Cambisano, N., Jentsch, T. J., & Charlier, C. (January 2014). A missense mutation accelerating the gating of the lysosomal Cl-/H+-exchanger ClC-7/Ostm1 causes osteopetrosis with gingival hamartomas in cattle. Disease Models and Mechanisms, 7, 119-128. doi:10.1242/dmm.012500
* These authors have contributed equally to this work.

Schrooten, C., Dassonneville, R., Ducrocq, V., Brondum, R. F., Lund, M. S., Chen, J., Liu, Z., Gonzalez-Recio, O., Pena, J., & Druet, T. (2014). Error rate for imputation from the Illumina BovineSNP50 chip to the Illumina BovineHD chip. Genetics, Selection, Evolution, 46 (1), 10. doi:10.1186/1297-9686-46-10

Druet, T., Perez-Pardal, L., Charlier, C., & Gautier, M. (2013). Identification of large selective sweeps associated with major genes in cattle. Animal Genetics, 44 (6), 758-62. doi:10.1111/age.12073

Sartelet, A., Druet, T., Michaux, C., Fasquelle, C., Geron, S., Tamma, N., Zhang, Z., Coppieters, W., Georges, M., & Charlier, C. (15 March 2012). A splice site variant in the bovine RNF11 gene compromises growth and regulation of the inflammatory response. PLoS Genetics, 15 (3), 1002581. doi:10.1371/journal.pgen.1002581

Sandor, C., Li, W., Coppieters, W., Druet, T., Charlier, C., & Georges, M. (2012). Genetic variants in REC8, RNF212, and PRDM9 influence male recombination in cattle. PLoS Genetics, 8 (7), 1002854. doi:10.1371/journal.pgen.1002854

Lund, M. S., de Ross, S. P., de Vries, A. G., Druet, T., Ducrocq, V., Fritz, S., Guillaume, F., Guldbrandtsen, B., Liu, Z., Reents, R., Schrooten, C., Seefried, F., & Su, G. (2011). A common reference population from four European Holstein populations increases reliability of genomic predictions. Genetics, Selection, Evolution, 43 (1), 43. doi:10.1186/1297-9686-43-43

Cierco-Ayrolles, C., Dejean, S., Legarra, A., Gilbert, H., Druet, T., Ytournel, F., Estivals, D., & Mangin, B. (22 October 2010). Does probabilistic modelling of linkage disequilibrium evolution improve the accuracy of QTL location in animal pedigree? Genetics, Selection, Evolution, 42, 38. doi:10.1186/1297-9686-42-38

Fasquelle, C.* , Sartelet, A.* , Li, W., Dive, M., Tamma, N., Michaux, C., Druet, T., Huijbers, I. J., Isacke, C. M., Coppieters, W., Georges, M., & Charlier, C. (2009). Balancing selection of a frame-shift mutation in the MRC2 gene accounts for the outbreak of the Crooked Tail Syndrome in Belgian Blue Cattle. PLoS Genetics, 5 (9), 1000666. doi:10.1371/journal.pgen.1000666
* These authors have contributed equally to this work.

Gengler, N., Wiggans, G. R., Thornton, L. L. M., Wright, J. R., & Druet, T. (2006). Accounting for heterogeneous variances in multitrait evaluation of Jersey type traits. Journal of Dairy Science, 89 (8), 3143-3151. doi:10.3168/jds.S0022-0302(06)72588-7

Gengler, N., Wiggans, G. R., Thornton, L., Wright, J., & Druet, T. (July 2005). Accounting for heterogeneous variances in multi-trait evaluation of Jersey type traits. Journal of Dairy Science, 83/88 (Suppl. 1/ Suppl. 1), 11.

Bormann, J., Wiggans, G. R., Druet, T., & Gengler, N. (2003). Within-herd effects of age at test day and lactation stage on test-day yields. Journal of Dairy Science, 86 (11), 3765-3774. doi:10.3168/jds.S0022-0302(03)73983-6

Druet, T., Solkner, J., Misztal, I., & Gengler, N. (2002). On the value of incorporating dominance effects in genetic evaluation of dairy cattle. In Proceedings of the 7th World Congress on Genetics Applied to LivestockProduction, Session 1 (pp. 1-4).

Gengler, N., Wiggans, G. R., Wright, J. R., & Druet, T. (24 July 2001). Simultaneous accounting for heterogeneity of (co) variance components in genetic evaluation of type traits. Journal of Dairy Science, 79/84/80 (Suppl. 1/ Suppl. 1/ Suppl. 1), 247.

Druet, T., Misztal, I., Duangjinda, M., Reverter, A., & Gengler, N. (2001). Estimation of genetic covariances with Method R. Journal of Animal Science, 79 (3), 605-615. doi:10.2527/2001.793605x

Druet, T., Sölkner, J., Fürst, C., & Gengler, N. (2001). Estimation of additive genetic variance of reproduction traits in Austrian Simmental. Interbull Bulletin, 27, 128-132.

Druet, T., Solkner, J., Groen, A. F., & Gengler, N. (2001). Additive and dominance genetic variance of fertility by method R and preconditioned conjugate gradient. Journal of Dairy Science, 84 (4), 987.e1-987.e16. doi:10.3168/jds.S0022-0302(01)74557-2

Gengler, N., & Druet, T. (2001). Impact of biotechnology on animal breeding and genetic progress. In R. Renaville & A. Burny (Eds.), Biotechnology in Animal Husbandry.

Bormann, J., Wiggans, G. R., Philpot, J. C., Druet, T., & Gengler, N. (24 July 2000). Estimation of variance components for cow and parity effects from test-day yields. Journal of Animal Science, 78/83 (Suppl. 1/ Suppl. 1), 63.

Gengler, N., Dusseldorf, T., Wiggans, G. R., Wright, J. R., & Druet, T. (2000). Multitrait genetic evaluation of Jersey type with integrated accounting for heterogeneous (co) variances. Interbull Bulletin, 25.

Gengler, N., Dusseldorf, T., Wiggans, G. R., Wright, J. R., & Druet, T. (2000). Joint estimation of variances and effects in the US Jersey type evaluation system. Interbull Bulletin, 34, 34-40.

Druet, T., Solkner, J., & Gengler, N. (September 1999). Use of multitrait evaluation procedures to improve reliability of early prediction of survival. Journal of Dairy Science, 82 (9), 2054.e1-2054.e16. doi:10.3168/jds.S0022-0302(99)75444-5

Druet, T., Sölkner, J., Groen, A. F., & Gengler, N. (1999). Improved genetic evaluation of survival using MACE to combine direct and correlated information from yield and functional traits. Interbull Bulletin, 21, 122.