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INRA UMR 1313 Génétique Animale et Biologie Intégrative
Domaine de Vilvert, Bat 211, 78352 Jouy en Josas
Tel : +33 (0) 1 34 65 22 00

Email : denis.laloe(at)inrae.fr

Équipe Populations, statistique et génome (PSGEN)

CV

1980 : Diplôme d'ingénieur agronome de l’ENSA de Rennes
1983 : DEA de Génétique Quantitative (Paris XI)
Responsable de l’unité informatique de l’UPRA Porcine
1987 : Ingénieur de Recherches INRA
1993 : DEA de Modélisation stochastique et Statistique ( Paris XI)

2015 : HDR (INP Toulouse)

Domaines de recherche

Génétique des populations, analyse de la structuration génétique des populations d’élevage, analyse des données x-omiques, génétique quantitative.

Présentations orales

• Interventions dans le master européen PRIAM, septembre 2018 : Multivariate Factorial Analyses
• Interventions dans le module doctoral "Environmental Genetics" (doctoral schools ABIES/GAIA), mai 2016
  • D Laloë, 2016. Links with instrumental covariables. Factorial methods [Vidéo] 
  • D Laloë, T Zerjal, X Rognon, 2016.Multivariate Data Analysis [Vidéo]
    • 1. An introduction with a focus on Principal Components Analysis on SNP data.
    • 2. Geometrical aspects - the inertia.
• D Laloë, A Rau. 2016. From genotype to phenotype: what statistical methods to integrate heterogeneous data. Journées bioinformatiques de l'INRA, Toulouse, 22 mars 2016
• D Laloë, T Zerjal. 2013. Landscape Genomics and Multivariate Analyses. Examples and prospects for poultry. WPSA, 8th European Genetics Symposium, Venice Italy, 25-27 september 2013 [Landscapenomix_2013]
• D Laloë, 2010. Evaluation génétique. Les fondements.Séminaire du département de Génétique Animale, 18-21 octobre 2010. [Fondements_evalgenet.2010]
• D Laloë, B Salmi. 2012. Analyse factorielle multiple et intégration de données. Application à la variabilité de la qualité de viande de porc.Réunion du réseau "Statomique", 15 mai 2012.[AFM_2012]
• D Laloë, M Gautier. 2012. Interprétation génétique des ACP entre groupes appliquées aux SNP. Séminaire du laboratoire TIMC-IMAG, université Joseph Fourier, Grenoble, 14 juin 2012. [ACP_SNP_2012]
• D Laloë, T Zerjal. 2013. Diversita genetica degli animali domestici. Qualche esempio e un po’ di teoria.Università di Pisa, 24 maggio 2013. [diversitagenetica_2013]

Publications et autres productions récentes

Divers

Ducrocq, V., Laloë, D., Swaminathan, M., Rognon, X., Tixier-Boichard, M., & Zerjal, T. (2018). Genomics for ruminants in developing countries: From principles to practice. Frontiers in genetics, 9, 251., https://doi.org/10.3389/fgene.2018.00251

Danchin-Burge, C., Danvy, S., Laloë, D., Verrier, E. (2017). Création d’un observatoire de la VARiabilité génétique des RUMinants et des Equidés (VARUME). Innovations Agronomiques, 55, 235-245. , DOI : 10.15454/1.5137783633347627E12

Laloë, D. 2015. Approches géométriques de l'analyse de données génétiques (Doctoral dissertation - Habilitation à diriger des recherches, Institut National Polytechnique de Toulouse).Verrier, É., & Laloë, D. (2015). Les animaux convoqués dans la propagande de guerre: dessins de presse, affiches et cartes postales en 1914-1918. Ethnozootechnie, (98), 65-76.

Verrier, E., Audiot, A., Bertrand, C., Chapuis, H., Charvolin, E., Danchin-Burge, C., ... & Laloë, D. 2015. Assessing the risk status of livestock breeds: a multi-indicator method applied to 178 French local breeds belonging to ten species. Animal Genetic Resources Information= Bulletin de information sur les ressources génétiques animales= Boletín de información sobre recursos genéticos animales, (57), 105-118.

Genetic structuring of populations

Boushaba , N. , Boujenane, I., Moazami-Goudarzi, K., Flori, L., Saïdi-Mehtar, N., Tabet-Aoul, N., Laloë, D. (2018). Genetic diversity and relationships among six local cattle populations in semi-arid areas assessed by a bovine medium-density single nucleotide polymorphism data. Animal, 1-7. , DOI : 10.1017/S1751731118001179

Mahammi, F. Z., Gaouar, S. B. S., Laloë, D., Faugeras, R., Tabet‐Aoul, N., Rognon, X., ... & Saidi‐Mehtar, N. (2016). A molecular analysis of the patterns of genetic diversity in local chickens from western Algeria in comparison with commercial lines and wild jungle fowls. Journal of Animal Breeding and Genetics, 133(1), 59-70.

Mir, C., Zerjal, T., ...,Laloë, D., ... & Hearne, S. (2013). Out of America: tracing the genetic footprints of the global diffusion of maize. Theoretical and applied genetics, 126(11), 2671-2682.

D Laloë, M Gautier, 2011. On the genetic interpretation of Between-Group PCA on SNP data. HAL open archive n° hal-00661214. 

C Berthouly, J c Maillard, L Pham Doan, T Nhu Van  B Bed'Hom, G Leroy, H Hoang Thanh, D Laloë, N Bruneau, C Vu Chi, V Nguyen Dang, E Verrier and X Rognon. 2010. Revealing fine scale subpopulations structure in the Vietnamese H'mong cattle breed for conservation purposes. BMC Genetics 2010, 11:45

C. Berthouly, X. Rognon, T. Nhu Van, A. Berthouly, H. Thanh Hoang, B. Bed'Hom, D. Laloë, C. Vu Chi, E. Verrier, J.-C. Maillard, 2010. Genetic and morphometric characterization of a local Vietnamese Swamp Buffalo population. Journal of Animal Breeding and Genetics. 127, 1:74-84

M Gautier, D Laloë, L Moazami-Goudarzi. 2010. Insights into the genetic history of French cattle from dense SNP data on 47 worlwide breeds. PLOS ONE, 5:9, e13038

Laloë, D.; Moazami-Goudarzi, K.; Lenstra, J.A.; Marsan, P.A.; Azor, P.; Baumung, R.; Bradley, D.G.; Bruford, M.W.; Cañón, J.; Dolf, G.; Dunner, S.; Erhardt, G.; Hewitt, G.; Kantanen, J.; Obexer-Ruff, G.; Olsaker, I.; Rodellar, C.; Valentini, A.; Wiener, P. 2010. European Cattle Genetic Diversity Consortium and Econogene Consortium Spatial Trends of Genetic Variation of Domestic Ruminants in Europe. Diversity. 2, 932-945.

Mathieu Gautier, Laurence Flori, Andrea Riebler, Florence Jaffrezic, Denis Laloë, Ivo Gut, Katayoun Moazami-Goudarzi and Jean-Louis Foulley, 2009.  A whole genome bayesian scan for adaptive genetic divergence in West African cattle. BMC Genomics. 10:550

P K Rout, M B Joshi, A Mandal, D Laloë, L Singh, K Thangaraj. 2008. Microsatellite-based phylogeny of Indian domestic goats. BMC Genetics. 9:11

C. Berthouly, B. Bed’Hom, M.Tixier-Boichard, C.F. Chen, Y.P. Lee, D. Laloë, H. Legros, E. Verrier, X. Rognon, 2008. Using molecular markers and multivariate methods to study the genetic diversity on local european and asian chickens breeds. Animal Genetics. 39(2):121-129

D. Laloë, T. Jombart, A.B. Dufour, K. Moazami-Goudarzi, 2007. Consensus genetic structuring and typological value of markers using Multiple Co-Inertia Analysis. Genet Sel Evol. 39, 545-567.

K. Moazami-Goudarzi, D. Laloë. 2002. Is a multivariate consensus representation of genetic relationships among populations always meaningful. Genetics. 162, 473-484

K Moazami-Goudarzi, D Laloë, JP Furet, F Grosclaude, 1997. Analysis of genetic relationships between 10 cattle breeds with 17 microsatellites. Animal Genetics. 28, 338-345

x-omics data analysis (Genomic evaluation, transcriptomics, etc.)

Doublet, A. C., Restoux, G., Fritz, S., Balberini, L., Fayolle, G., Hozé, C., ... & Croiseau, P. (2020). Intensified Use of Reproductive Technologies and Reduced Dimensions of Breeding Schemes Put Genetic Diversity at Risk in Dairy Cattle Breeds. Animals, 10(10), 1903. https://doi.org/10.3390/ani10101903Rau, A., Manansala, R., Flister, M. J., Rui, H., Jaffrézic, F., Laloë, D., & Auer, P. L. (2020). Individualized multi-omic pathway deviation scores using multiple factor analysis, Biostatistics, kxaa029, DOI: 10.1093/biostatistics/kxaa029
Doublet, A. C., Croiseau, P., Fritz, S., Michenet, A., Hozé, C., Danchin-Burge, C., ... & Restoux, G. (2019). The impact of genomic selection on genetic diversity and genetic gain in three French dairy cattle breeds. Genetics Selection Evolution, 51(1), 52.Biase, F. H., Hue, I., Dickinson, S. E., Jaffrezic, F., Laloe, D., Lewin, H. A., & Sandra, O. (2019). Fine-tuned adaptation of embryo–endometrium pairs at implantation revealed by transcriptome analyses in Bos taurus. PLoS biology, 17(4), e3000046.  https://doi.org/10.1371/journal.pbio.3000046

Bílková, B., Świderská, Z., Zita, L., Laloë, D., Charles, M., Beneš, V., Stopka, P., Vinkler, M. (2018). Domestic fowl breed variation in egg white protein expression: application of proteomics and transcriptomics. Journal of Agricultural and Food Chemistry. , DOI : 10.1021/acs.jafc.8b03099

Eynard, S., Croiseau, P., Laloë, D., Fritz, S., Calus, M. P. L., Restoux, G. (2018). Which individuals to choose to update the reference population? Minimizing the loss of genetic diversity in animal genomic selection programs. G3 - Genes Genomes Genetics, 8 (1), 113-121. , DOI : 10.1534/g3.117.1117

Laloë, D., Le Bourhis, D., Brochard, V., Fernandez-Gonzalez, A., Dube, D., Trigal, B., ... & Duranthon, V. 2015. Metabolomic analysis revealed differences between bovine cloned embryos with contrasting development abilities. Animal Reproduction, 12(3), 818-818.

Dillies M.A., Rau, A., ..., Laloë D., ... & Jaffrézic F. 2013. A comprehensive evaluation of normalization methods for Illumina high-throughput RNA sequencing data analysis. Briefings in bioinformatics, 14(6), 671-683.

R Rincent, D Laloë, S Nicolas, T Altmann, D Brunel, P Revilla, V M. Rodriguez, J Moreno-Gonzales, A E. Melchinger, E Bauer, C-C Schön, N Meyer, C Giauffret, C Bauland, P Jamin, J Laborde, H Monod, P Flament, A Charcosset,  L Moreau, 2012. Maximizing the Reliability of Genomic Selection by Optimizing the Calibration Set of Reference Individuals: Comparison of Methods in Two Diverse Groups of Maize Inbreds (Zea mays L.) Genetics, 192:715-728.

S Le Guillou, N Sdassi, J Laubier, B Passet, M Vilotte, J Castille,D Laloë, J Polyte, S Bouet, F Jaffrézic, E Cribiu, J-L Vilotte, F Le Provost, 2012. Overexpression of miR-30b in the developing mouse mammary gland development causes a lactation defect and delays involution. Plos ONE 7-9:e45727

Quantitative genetics : Models of genetic evaluation; estimation of genetic parameters.

Ducrocq, V., Laloë, D., Swaminathan, M., Rognon, X., Tixier-Boichard, M., Zerjal, T. (2018). Genomics for ruminants in developing countries: from principles to practice. Frontiers in Genetics, 9. , DOI : 10.3389/fgene.2018.00251

Wang, S., Laloë, D., Missant, F., Malm, S., Lewis, T., Verrier, E., Strandberg, E., Bonnett, B., Leroy, G. (2018). Breeding policies and management of pedigree dogs in 15 national kennel clubs. Veterinary Journal, 234, 130-135. , DOI : 10.1016/j.tvjl.2018.02.018

N.T. Pegolo, D. Laloë,  H.N. de Oliveira, R.B. Lobo,  M.-N. Fouilloux, 2012. Trends of the genetic connectedness measures among Nelore beef cattle herds. J. Anim. Breed. Genet. 129 :1, 20-29.

D. Laloë, 2011. La genèse et le développement des concepts de l'évaluation génétique classique. IN : Numéro spécial Amélioration génétique. Mulsan P., Bodin L., Coudurier B., Deretz S., Leroy P., Quillet E., Perez J.M. (Eds), INRA Prod. Anim. 24, 323-330

E. Venot,  M.N. Fouilloux, F. Forabosco, A. Fogh, T. Pabiou, M. Coffey,  J.Å. Eriksson,  D. Laloë, 2009. Beef without borders:  genetic parameters for Charolaise and Limousine Interbeef genetic evaluation of weaning weights. Proceedings of the 2009 Interbull meeting. Barcelone, Spain , August 21-24. Bulletin 40, 61-67 www-interbull.slu.se/bulletins/bulletin40/contents.html

E. Venot,  M.N. Fouilloux, F. Forabosco, A. Fogh, T. Pabiou, M. Coffey,  J.E. Eriksson, D. Laloë, 2009. Interbeef genetic evaluation of weaning weights for Charolaise and Limousine breeds. Proceedings of the 2009 Interbull meeting. Barcelone, Spain , August 21-24. Bulletin 40, 55-60 www-interbull.slu.se/bulletins/bulletin40/contents.html

M.N. Fouilloux, V Clément, D Laloë, 2008. Measuring connectedness among random effects in mixed linear models: from theory to practice in large-size genetic evaluations. Genet Sel Evol. 40, 145-159.

Jaffrézic F, Venot E, Laloë D, Vinet A, Renand G, 2004. Use of structured antedependence models for the genetic analysis of growth curves. J Anim Sci. 2004 Dec;82(12):3465-73.

F. Phocas, D. Laloë, 2004. Genetic parameters for birth and weaning traits in French specialized beef cattle breeds. Livestock Production Science. 89, 121-128.

F. Phocas, D. Laloë, 2004. Should genetic groups be fitted in BLUP evaluation ? Practical answer for the French AI beef sire evaluation. Genet Sel Evol. 36:325-345

D Laloë, F. Phocas, 2003. A proposal of criteria of robustness in genetic evaluation. Livestock Production Science. 80(3), 241-256.

F. Phocas, D. Laloë, 2003. Evaluation models and genetic parameters for calving difficulty in beef cattle. Journal of Animal Science. 81:933-938

M N Fouilloux, D Laloë, 2001. A sampling method for estimating the accuracy of predicted breeding values in genetic evaluation. Genet Sel Evol. 33, 473-486

D Laloë, F. Phocas, F Ménissier. 1996. Considerations about measures of precision and connectedness in mixed linear models of genetic evaluation. Genet Sel Evol. 28, 359-378.

D Laloë, 1993. Precision and information in linear models of genetic evaluation. Genet Sel Evol, 25, 557-576

Multivariate analysis applied to animal production

B. Salmi, C. Larzul,, M. Damon, L. Lefaucheur, J. Mourot, E. Laville, P. Gatellier, K. Méteau, D. Laloë, B. Lebret. 2010. Multivariate analysis to compare pig meat quality traits according to breed and rearing system . Proceedings of the 9^th World congress on Genetics applied to Livestock Production. Leipzig, August 1-6, 2010, 442

L. Canario, Y. Billon, J.C. Caritez, J.P. Bidanel, D. Laloë, 2009. Comparison of sow farrowing characteristics between a Chinese breed and three French breeds. Livestock Science. 125, 132-140