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portrait Matthieu FalqueMatthieu FALQUE


Génétique Quantitative et Évolution - Le Moulon
INRA - Université Paris-Sud - CNRS - AgroParisTech
Ferme du Moulon
F-91190 Gif-sur-Yvette
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(33) 1 69 33 23 64


> Education and Positions

Currently Member of the RAMDAM team (Recombination of Alleles in Meiosis: Determinism, Applications, Modeling), affiliated with the Labex Saclay Plant Sciences

HDR (ability to supervise PhD students) 2015, University of Orsay, France

Currently Head of the ACEP team (Atelier Cartographie Expression Polymorphisme)

Since 1998: Ingénieur de Recherche (INRA) at UMR GQE - Le Moulon, Gif-sur-Yvette, France

Postdoc in Plant Population Genetics (1997-1998) CNRS, Lille France

Postdoc in Plant Population Genetics (1995-1997) NIOO-CTO, Heteren-Wageningen, The Netherlands

Postdoc in Plant Molecular Genetics (1994-1995) CIRAD, Montpellier, France

Ph.D. in Plant Biology (1994), Univ Toulouse, France

DNA double-strand breaks


> Research interests: plant genetics, molecular markers, linkage mapping, meiosis and recombination, modeling

My research in the RAMDAM team

Starting from linkage mapping for plant breeding applications, my research now mostly focuses on quantitative characterization of mechanisms of crossover formation. In particular, I have been developing with Olivier Martin mathematical models to simulate crossover interference. These models take into account the two different pathways of crossover formation which have been discovered in several organisms. We have used this model to unveil the existence of these two pathways in Maize and to investigate quantitative properties of crossover formation mechanisms in different species. In particular, we have demonstrated in Tomato that crossovers produced by two different pathways still can interfere with each other out to distances of about 6 microns.

Yeast tetrads with segregating fluorescent markers Flow cytometry analyses of spores

Linkage map of Maize chrom 1

My research in the ACEP group

The ACEP group is an internal platform of services in the fields of genetic map construction and analyses of DNA polymorphism and gene expression. We provide DNA analysis service and keep a technological watch in molecular marker technologies. I also develop software tools for automated genetic mapping with large numbers of markers, and I have constructed high-density genetic maps in several plant species.

Current Projects

1. Linkage-based analysis of structural variation by detecting signatures of duplications and translocations from genetic segregation data

2. Quantifying across successive generations how linkage slows down genetic progress and how to best use new technologies that enhance recombination rates.

> Teaching activities

Occasional teaching for students and professionals from breeding companies on molecular markers, genetic mapping, and plant genomics for breeding.

> Selected publications

Full list available on Google scholar

Meiosis and crossover interference

Tourrette E, Bernardo R, Falque M, Martin OC (2019) Assessing by Modeling the Consequences of Increased Recombination in Recurrent Selection of Oryza sativa and Brassica rapa. G3, Epub ahead of print.

Termolino P, Falque M, Aiese Cigliano R, Cremona G, Paparo R, Ederveen A, Martin OC, Consiglio FM, Conicella C (2019) Recombination suppression in heterozygotes for a pericentric inversion induces the interchromosomal effect on crossovers in Arabidopsis. Plant J, Epub ahead of print..

Raffoux X., Bourge M., Dumas F., Martin O. C. and Falque M. (2018) Role of cis, trans, and Inbreeding Effects on Meiotic Recombination in Saccharomyces cerevisiae. Genetics, 210 (4) 1213-1226.

Raffoux X., Bourge M., Dumas F., Martin O. C., Falque M. (2018) High-throughput measurement of recombination rates and genetic interference in Saccharomyces cerevisiae. Yeast, 35 (6) 431-442.

Pelé A., Falque M., Trotoux G., Eber F., Negre S., Gilet M., Huteau V., Lode M., Jousseaume T., Dechaumet S., Morice J., Poncet C., Coriton O., Martin O. C., Rousseau-Gueutin M., Chevre A. M. (2017) Amplifying recombination genome-wide and reshaping crossover landscapes in Brassicas. PLoS Genet, 13 (5) e1006794.

Sidhu G.K., Fang C., Olson M.A., Falque M., Martin O.C., and  Pawlowski W.P.(2015) Recombination patterns in maize reveal limits to crossover homeostasis. PNAS 1514265112 .

Anderson L.K. , ... and  Falque M. (2014) Combined fluorescent and electron microscopic imaging unveils the specific properties of two classes of meiotic crossovers. PNAS 111 (37) 13415-13420. Highlighted in the INRA news.

Basu-Roy S., Gauthier F., Giraut L., Mezard C., Falque M.1, and O. C. Martin1 (2013) Hot Regions of Non-Interfering Crossovers Coexist with a Non-Uniformly Interfering Pathway in Arabidopsis thaliana. Genetics 195: 769–779.  1 equal contributions of 2 last authors.

Bauer E.1, Falque M.1, ..., and Schoen C.-C. (2013) Intraspecific variation of recombination rate in maize. Genome Biology, 14:R103. 1equal contributions of 2 first authors

Gauthier F., Martin, O.C., and Falque M.  (2011). CODA (CrossOver Distribution Analyzer): quantitative characterization of crossover position patterns along chromosomes. BMC Bioinformatics 12:27.

Falque M., Anderson L. K., Stack S. M., Gauthier F. and Martin O.C. (2009). Two Types of Meiotic Crossovers Coexist in Maize. The Plant Cell 21: 3915–3925. Raw RN position data available here

Falque M., Mercier R., Mézard C., de Vienne D., and  Martin O.C. (2007). Patterns of recombination rate along chromosomes : importance of interference and obligate chiasma. Genetics 176:1453-1467.

Genetic mapping

Kreplak J, ..., Falque M, ..., Wincker P, Burstin J (2019) A reference genome for pea provides insight into legume genome evolution. Nat Genet, 51 (9) 1411–1422.

Courret C., Gérard P. R., Ogereau D., Falque M., Moreau L., Montchamp-Moreau C. (2019) X-chromosome meiotic drive in Drosophila simulans: a QTL approach reveals the complex polygenic determinism of Paris drive suppression. Heredity, 122 (6) 906–915. doi:10.1038/s41437-018-0163-1

Martinez Palacios P., Jacquemot M.-P., Tapie M., Rousselet A., Diop M., Remoué C., Falque M., Lloyd A., Jenczewski E., Lassalle G., Chévre A.-M., Lelandais C., Crespi M., Brabant P., Joets J., Alix K. (2019) Assessing the Response of Small RNA Populations to Allopolyploidy Using Resynthesized Brassica napus Allotetraploids. Molecular Biology and Evolution, 36 (4) 709–726. doi:10.1093/molbev/msz007

Virlouvet L., El Hage F., Griveau Y., Jacquemot M.-P., Gineau E., Baldy A., Legay S., Horlow C., Combes V., Bauland C., Palafre C., Falque M., Moreau L., Coursol S., Méchin V., Reymond M. (2019) Water Deficit-Responsive QTLs for Cell Wall Degradability and Composition in Maize at Silage Stage. Frontiers in Plant Science, 10 488. doi:10.3389/fpls.2019.00488

Giraud H., Bauland C., Falque M., Madur D., Combes V., Jamin P., Monteil C., Laborde J., Palaffre C., Gaillard A., Blanchard P., Charcosset A., Moreau L. (2017) Reciprocal Genetics: Identifying QTLs for General and Specific Combining Abilities in Hybrids Between Multiparental Populations from Two Maize (Zea mays L.) Heterotic Groups. Genetics, 207 (3) 1167-1180.

Giraud H., Bauland C., Falque M., Madur D., Combes V., Jamin P., Monteil C., Laborde J., Palaffre C., Gaillard A., Blanchard P., Charcosset A., Moreau L. (2017) Linkage Analysis and Association Mapping QTL Detection Models for Hybrids Between Multiparental Populations from Two Heterotic Groups: Application to Biomass Production in Maize (Zea mays L.). G3 (Bethesda), 7 (11) 3649-3657.

Boutet G., Carvalho S.A., Falque M., Peterlongo P., Lhuillier E., Bouchez O., Lavaud C., Pilet-Nayel M.L., Rivière N. &  Baranger A. (2016) SNP discovery and genetic mapping using genotyping by sequencing of whole genome genomic DNA from a pea RIL population. BMC Genomics 17:121

Tayeh, N., Aluome C., Falque M., Jacquin F., Klein A., Chauveau A., Bérard A., Houtin H., Ron, C., Kreplak J., Boucherot K., Martin C., Baranger A., Pilet-Nayel M.L., Warkentin T.D., Brunel D., Marget P., Le Paslier M.C., Aubert G., and  Burstin J. (2015) Development of two major resources for pea genomics: the GenoPea 13.2K SNP Array and a high-density, high-resolution consensus genetic map. The Plant Journal 84 : 1257-1273

Bauer E.1, Falque M.1, ..., and Schoen C.-C. (2013) Intraspecific variation of recombination rate in maize. Genome Biology, 14:R103. 1 equal contributions of 2 first authors

Ganal M.W. , ..., and Falque M. (2011) A Large Maize (Zea mays L.) SNP Genotyping Array: Development and Germplasm Genotyping, and Genetic Mapping to Compare with the B73 Reference Genome. PLoS ONE 6(12): e28334 .

Falque M., Décousset L., Dervins D., Jacob A.M., Joets J., Martinant J.P., Raffoux X.,  Ribière N., Ridel C., Samson D.,  Charcosset A. and Murigneux A. (2005) Linkage mapping of 1454 new maize candidate gene loci. Genetics 170: 1957-1966.