Quantitative Genetics & Genomics
The Quantitative Genetics and Genomics team studies the genetic architecture of quantitative traits and works on related statistical methods. These include methods for genome-wide association studies, QTL fine-mapping, phasing and missing genotypes imputation, estimation of identity-by-descent (IBD) relationships, whole-genome predictions or partitioning of the genetic variance in different components.
We are also working on the estimation of inbreeding levels and the study of inbreeding depression. We developed a model approach to identify homozygous-by-descent segments (often captured with runs-of-homozygosity) and to characterize individual inbreeding levels. We are studying the relationship between the distribution of these homozygous-by-descent segments and the recent past effective population size.
We are the academic group driving the implementation of genomic selection in the Belgian Blue Cattle Breed in close collaboration with the Walloon Breeding Organisation.
Selected publications
Genomic prediction of individual inbreeding levels for the management of genetic diversity in populations with small effective size. Forneris NS, Bosse M, Gautier M, Druet T. Molecular Ecology Resources, 25(4) (2025)
Genomic reconstruction of the successful establishment of a feralized bovine population on the subantarctic island of Amsterdam. Gautier M, Micol T, Camus L, Moazami-Goudarzi K, Naves M, Guéret E, Engelen S, Lemainque A, Colas F, Flori L, Druet, T. Molecular Biology and Evolution, 41(7) (2024)
Sequenced-based GWAS for linear classification traits in Belgian Blue beef cattle reveals new coding variants in genes regulating body size in mammals. Gualdrón Duarte JL, Yuan C, Gori AS, Moreira GC, Takeda H, Coppieters W, Georges M, Druet T. Genetics Selection Evolution, 55(1), 83 (2023)
A hidden Markov model to estimate homozygous-by-descent probabilities associated with nested layers of ancestors. Druet T, Gautier M. Theor Popul Biol 145:38-51 (2022)
An evaluation of inbreeding measures using a whole-genome sequenced cattle pedigree. Alemu SW, Kadri NK, Harland C, Faux P, Charlier C, Caballero A, Druet T. Heredity 126(3) :410-423 (2021)
A 12 kb multi-allelic copy number variation encompassing a GC gene enhancer is associated with mastitis resistance in dairy cattle. Lee YL, Takeda H, Costa Monteiro Moreira G, Karim L, Mullaart E, Coppieters W, GplusE consortium, Appeltant R, Veerkamp RF, Groenen MAM, Georges M, Bosse M, Druet T, Bouwman A, Charlier, C. PLoS Genetics, 17(7), e1009331 (2021)
On the estimation of inbreeding depression using different measures of inbreeding from molecular markers. Caballero A, Villanueva B, Druet T. Evol Appl 14(2):416-428 (2021)
RZooRoH: an R package to characterize individual genomic autozygosity and identify homozygous-by-descent segments. Bertrand AR, Kadri NK, Flori L, Gautier M, Druet T. Methods Ecol Evol 10(6):860-866 (2019)
A model-based approach to characterize individual inbreeding at both global and local genomic scales. Druet T, Gautier M. Mol Ecol 26: 5820-5841 (2017)
Coding and non-coding variants in HFM1, MLH3, MSH4, MSH5, RNF212 and RNF212B affect recombination rate in cattle. Kadri NK, 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. Genome Res 26: 1323-1332 (2016)
Towards genomic prediction from whole genome sequence data: impact of sequencing design on genotype imputation and accuracy of prediction. Druet T, Macleod IM, Hayes BJ. Heredity 112:39-47 (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. Kumar Kadri N, Sahana G, Charlier C, Iso-Touru T, Guldbrandten B, Karim L, Nielsen US, Panitz F, Aamand GP, Schulman N, Georges M, Vilkki J, Lund MS, Druet T. PloS Genetics 10:E1004049 (2014)
Ancestral haplotype-based association mapping with generalized linear mixed models accounting for stratification. Zhang Z, Guillaume F, Sartelet A, Charlier C, Georges M, Farnir F, Druet T. Bioinformatics, 28(19), 2467-2473 (2012)
Variants modulating the expression of a chromosome domain encompassing PLAG1 influence bovine stature. Karim L*, Takeda H*, Lin L*, Druet T*, Arias JAC, Baurain D, Cambisano N, Davis SR, Farnir F, Grisart B, Harris BL, Keehan MD, Littlejohn MD, Spelman RJ, Georges M, Coppieters W. *co-first. Nat Genetics 43: 405-413 (2011)
A hidden markov model combining linkage and linkage disequilibrium information for haplotype reconstruction and quantitative trait locus fine mapping. Druet T, Georges M. Genetics 184:789-798 (2010)
