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Dr. Lydia Bousset – Research scientist at INRAE Rennes, France

Contact address

UMR1349 IGEPP, INRAE – Agrocampus Ouest – Université Rennes1, Domaine de la Motte, BP 35327, 35653 Le Rheu Cedex, France

Au fil des saisons... Career Since 2002: INRAE Scientist (CR) at IGEPP Rennes

2016-2017: Visiting scientist at CSIRO (Canberra, Australie) 2014 : Habilitation à diriger des recherches (Université de Rennes 1) 2001-2002: Post-doctoral fellow at CEFE - CNRS in Montpellier, France 2000-2001: Post-doctoral fellow at Justus Liebig University of Giessen, Germany 1996-2000: PhD in epidemiology (INAPG AgroParisTech, France) at INRA Grignon 1995-1996: Research master in phytopathology (University of Paris XI Orsay, France) 1994-1996: Engineer in agronomy (INAPG AgroParisTech, France) 1990-1994: Undergraduation, Licence and Master in plant biology (University of Paris XI Orsay, France) isTech, France) à l’INRA Grignon

Research interests

Epidemiology in metapopulations in agro-ecosystems

As an epidemiologist, I am studying biology and population genetics of phoma stem canker (Leptosphaeria maculans) in relation to the stability of oilseed rape resistances’ efficacy. The aim of my research is to formalise, link and quantify the processes occurring in the adaptive response of a fungal metapopulation on a on a network of fields on which selection pressures imposed by human actions are heterogeneous.

For this I am interested in inoculum production, migration, survival, and the integration of these processes into models allowing simulating strategies (combinations of tactics) at the scale of a network of fields. I am joining together conceptualisation work, participation to model development, experiments in field plots or farmer’s fields, studies of processes under controlled conditions, and using image analysis to quantify epidemiological processes. Because of the interdisciplinary nature of the subject, understanding the conditions favourable to interdisciplinary research is part of my thoughts.

Topics of interest

(corresponding publications indicated by numbers between brackets)

• Epidemiology of inoculum production and transmission between cropping seasons, depending on the severity of the epidemics, the effect of plant resistance, the reproduction regimes and survival. Case studies: phoma stem canker on oilseed rape [11, 12, 13, 23, 25, 26, s2, s4] and barley powdery mildew [2, 4, 5]
• Epidemiology of inoculum dispersal. Case study: phoma stem canker on oilseed rape [16, 10, 24, s1, s4], poplar rust [17]
• Image processing for the quantification of epidemiological parameters [29, p4]
• Characterisation of pH and redox in plants and fungi. Case studies: rice [27] many fungi [28]
• Population structure depending on environmental characteristics, reproduction regime and adaptation to selection pressures induced by plant resistance and pesticides. Case studies: phoma stem canker [15, 22, 26, p3], poplar rust [17], barley powdery mildew [6, r1], freshwater snail Physa acuta [7, 8, 21], apple scab [r2], mustards [30]
• Participation to the development of spatio-temporal models describing pathogen dynamics and genetics on an heterogeneous network of fields. Case-studies: phoma stem canker on oilseed rape [9, 14, 15, s3] and barley powdery mildew [3]
• Conceptualisation of the efficiency of disease control on crops in agro-ecosystems, and determinants of its stability. Link between breeding for resistance and epidemiology [v1], efficacy [18] and stability [19] of plant disease control. Links between disciplinary concepts [a1, a2, a3] and conditions suitable to achieve interdisciplinary research [20]

Focus on recent achievements

2008-2019: Picture processing: from a “may be” to a processing chain

Fungal fruiting bodies are essential for the survival during adverse conditions and the transmission of cyclic epidemics from one growing season to the following one. Furthermore, when they are generated by sexual recombination, this process affects the population structure and population adaptation e.g. to host resistance. Quantification of the inoculum produced at the end of phoma stem canker epidemics is thus very desirable. During her PhD, Elise Lô-Pelzer [11] spent hours under the magnifying lens to count pseudothecia. Fortunately, she was able to show that the number of pseudothecia – so tedious to count – is well correlated to the area they occupy on oilseed rape stubble. Since that time, I had in mind that image processing would be of great help. Thus, each year after disease severity scoring at the end of the epidemics, I started collecting stubble, preparing it keeping track of disease severity (drilling and assembling pieces on BBQ skewers with a barcoded label) and incubating stubble over summer and autumn. Once pseudothecia had appeared, I washed stubble and dried it.

At first I took pictures on heterogeneous background, from different height, not paying enough attention to light so stubble had a shadow (later difficult to get rid of). The first attempts of processing pictures with the help of my colleagues Nicolas Parisey, Marcellino Palerme and Melen Leclerc allowed us to identify the key requirements and to optimise the settings. Fortunately dry stubble keeps well in the basement of our building, so I could start again all the pictures.

These pictures provided us with enough images to train algorithms, to statistically evaluate their performance, and thus have an efficient picture processing chain [29]. It was applied to stubble from farmers’ fields, and is being applied to further data sets to test for the effect of host genotype on the production of fruiting bodies [p4].

Publications & Research Reports

Do not hesitate to ask me for the documents mentioned below if you cannot download them using their DOI numbers. Otherwise, the corresponding postprints are available in the INRAE public repository HAL-INRAE.

Academic Publications:

[30] Bousset L, Ermel M, Delourme R (2020). French condiment mustard resistance against Leptosphaeria maculans relies on genes Rlm5 and Rlm6, calling for caution in the deployment of Rlm6 in oilseed rape crops. EJPP 158:799–803. doi:10.1007/s10658-020-02099-2

[29] Bousset L, Palerme M, Leclerc M, Parisey N (2019). Automated image processing framework helps to analyse the density of fruiting bodies of Leptosphaeria maculans on oilseedrape stems. Plant Pathology 68:1749–1760 DOI : 10.1111/ppa.13085

[28] Bousset L, Ermel M, Soglonou B, Husson O (2019). A method to measure redox potential (Eh) and pH in agar media and plants shows that fungal growth is affected by and affects pH and Eh. Fungal Biology 123:117-124 doi: 10.1016/j.funbio.2018.11.008.

[27] Husson O, Audebert A, Benada J, Soglonou B, Tano F, Dieng I, Bousset L, Sarthou JP, Joseph S, Menozzi P, Boulakia S, Futakuchi K (2018). Leaf Eh and pH: A novel indicator of plant stress. Spatial, temporal and genotypic variability in rice (Oryza sativa L.). Agronomy 8, 209; doi:10.3390/agronomy8100209.

[26] Bousset L, Sprague JS, Thrall PH, Barrett LG (2018). Spatio-temporal connectivity and host resistance influence evolutionary and epidemiological dynamics of the canola pathogen Leptosphaeria maculans. Evolutionary Applications 11:1354-1370 doi: 10.1111/eva.12630.

[25] Bousset L, Ermel M, Lebreton L (2018). The full life cycle of Leptosphaeria maculans completed on inoculated oilseed rape incubated under controlled conditions. Plant Pathology 67:1321–1328 Doi: 10.1111/ppa.12853

[24] Bousset L, Jumel S, Picault H, Domin C, Lebreton L, Ribule A, Delourme R (2016). An easy, rapid and accurate method to quantify plant disease severity: application to phoma stem canker leaf spots. European Journal of Plant Pathology 145:697-709. DOI

[23] Bousset L, Jumel S, Garetta V, Picault H, Soubeyrand S (2015). Transmission of Leptosphaeria maculans from a cropping season to the following one. Annals of Applied Biology 166:530-543. DOI

[22] Delourme R, Bousset L, Ermel E, Duffé, Besnard AL, Marquer B, Fudal I, Linglin J, Chadœuf J, Brun H (2014). Quantitative resistance affects the speed of frequency increase but not the diversity of the virulent alleles overcoming a major resistance gene toLeptosphaeria maculansin oilseed rape. Infection, Genetics and Evolution 27:490-499. DOI

[21] Bousset L, Pointier JP, David P, Jarne P (2014). Neither variation loss, nor change in selfing rate is associated to the worldwide invasion ofPhysa acutafrom its nativeNorth America. Biological Invasions 16:1769-1783. DOI

[20] Bousset L, Chèvre AM (2013). Stable epidemic control in crops based on evolutionary principles: adjusting the metapopulation concept to agro-ecosystems. Agriculture, Ecosystems and Environment 165:118-129. DOI

[19] Bousset L (in press). Travail d’ébauche interdisciplinaire : peut-on parler simplement d’un processus complexe ?Nature, Sciences, Sociétés. DOI

[18] Bousset L, Chèvre AM (2012). Controlling cyclic epidemics on the crops of the agro-ecosystems: articulate all the dimensions in the formalisation, but look for a local solution. Journal of Botany Article ID 938218, 9p. DOI

[17] Xhaard C, Barrès B, Andrieux A, Bousset L, Halkett F, Frey P (2012). Disentangling the genetic origins of a plant pathogen during disease spread using an original molecular epidemiology approach. Molecular Ecology 21: 2383-98. DOI

[16] Travadon R, Sache I, Dutech C, Stachowiak A, Marquer B, Bousset L (2011). Absence of isolation by distance patterns at the regional scale in the fungal plant pathogenLeptosphaeria maculans. Fungal Biology 115: 649-659. DOI

[15] Lô-Pelzer E, Bousset L, Jeuffroy MH, Salam MU, Pinochet X, Boillot M, Aubertot JN (2010). SIPPOM-WOSR : A simulator for integrated pathogen population management of phoma stem canker on winter oilseed rape. I. Description of the model. Field Crops Research 118: 73-81. DOI

[14] Lô-Pelzer E, Aubertot JN, Bousset L, Salam MU, Jeuffroy MH (2010). SIPPOM-WOSR : A simulator for integrated pathogen population management of phoma stem canker on winter oilseed rape. II. Sensitivity analysis. Field Crops Research 118: 82-93. DOI

[13] Lô-Pelzer E, Aubertot, JN, Bousset L, Pinochet X, Jeuffroy MH (2009). Phoma stem canker (Leptosphaeria maculans/L biglobosa) of oilseed rape (Brassica napus): is the G2 Disease Index a good indicator of the distribution of the observed canker severities? European Journal of Plant Pathology 125: 515-522. DOI

[12] Travadon R, Marquer B, Ribulé A, Sache I, Brun H, Delourme R, Masson JP, Bousset L (2009). Systemic progress of Leptosphaeria maculansfrom cotyledons to hypocotyle in oilseed rape: influence of the number of infection sites, of intraspecific competition and of host polygenic resistance. Plant Pathology 58: 461-469. DOI

[11] Lô-Pelzer E, Aubertot, JN, David O, Jeuffroy MH, Bousset L (2009). Experimental evidence for a relationship between the severity of phoma stem canker (Leptosphaeria maculans/L. biglobosaspecies complex) and subsequent primary inoculum production on oilseed rape stubble. Plant Pathology 58:61-70. DOI

[10] Travadon R, Bousset L, Saint-Jean S, Brun H, Sache I (2007). Splash dispersal ofLeptosphaeria maculanspycnidiospores and the spread of blackleg on oilseed rape. Plant Pathology 56: 595-603. DOI

[9] Aubertot JN, West JS, Bousset-Vaslin L, Salam MU, Barbetti MJ, Diggle AJ (2006). Improved resistance management for durable disease control: a case study of phoma stem canker of oilseed rape (Brassica napus). European Journal of Plant Pathology 114: 91-106. DOI

[8] Henry P-Y, Bousset L, Sourrouille P Jarne P (2005) Partial selfing, ecological disturbance and reproductive assurance in an invasive freshwater snail. Heredity 95: 428–436. DOI

[7] Bousset L, Henry P-Y, Sourrouille P, Jarne P (2004) Population biology of the invasive freshwater snailPhysa acutaapproached through genetic markers, ecological characterization and demography. Molecular Ecology 13: 2023-2036. DOI

[6] Bousset L, Pons-Kühnemann J (2003) Effects of acibenzolar-S-methyl and ethirimol on the composition of a laboratory population of barley powdery mildew. Phytopathology 93: 305-315. DOI

[5] Bousset L, de Vallavieille-Pope C (2003). Effect of sexual recombination on pathotype frequencies in barley powdery mildew populations of artificially inoculated field plots. European Journal of Plant Pathology 109: 13-24. DOI

[4] Bousset L, de Vallavieille-Pope C (2003) Barley powdery mildew populations on volunteers and changes in pathotype frequencies during summer on artificially inoculated field plots. European Journal of Plant Pathology 109: 25-33. DOI

[3] Bousset L, Hovmøller MS, Caffier V, de Vallavieille-Pope C, Østergård H (2002) Observed and predicted changes over eight years in frequency of barley powdery mildew avirulent to spring barley in France and Denmark. Plant Pathology 51: 33-44. DOI

[2] Bousset L, Schaeffer B, de Vallavieille-Pope C (2001) Effect of early infection on pathotype frequencies in barley powdery mildew (Blumeria graminis f. sp. hordei) populations in field plots. Plant Pathology 50: 317-324. DOI

[1] Délye C, Bousset L, Corio-Costet MF (1998). PCR cloning and detection of point mutations in the eburicol 14a-déméthylase (CYP51) gene fromErysiphe graminis f. sp. hordei, a "recalcitrant" fungus. Current Genetics 34, 399-403. DOI

Preprints:

[p4] Bousset L, Vallée P, Delourme R, Parisey N, Palerme M, Leclerc M (2020b). Besides stem canker severity, oilseed rape host genotype matters for the production of Leptosphaeria maculans fruiting bodies. BIORXIV-2020. doi : https://doi.org/10.1101/2020.08.06.240168.

[p3] Bousset L, Ermel M, Delourme R (2020a).  A Leptosphaeria maculans set of isolates characterised on all available differentials and used as control to identify virulence frequencies in a current French population. BIORXIV-2020. doi: http://dx.doi.org/10.1101/2020.01.09.900167

[p2] Bousset L, Palerme M, Leclerc M, Parisey N (2018b). Automated image processing to support the analysis of between-year transmission of Leptosphaeria maculans in field conditions. BIORXIV-2018. doi: https://doi.org/10.1101/488890

[p1] Bousset L, Ermel M, Delourme R (2018a). Careful deployment of oilseed rape crops with Rlm6 resistance gene against L. maculans is recommended to prevent the loss of efficacy of this resistance gene in French condiment mustard. BIORXIV-2018. doi: https://doi.org/10.1101/297937

Transfer Publications and Research Reports:

[v1] Bousset L, Brun H, Chèvre AM, Delourme R (2011). Quel lien entre l’épidémiologie, la création variétale et le potentiel de durabilité des résistances ? Illustration chez le phoma du colza.Innovations Agronomiques15:29-43.  www.inra.fr/ciag/content/download/4230/34111

[r3] Bousset L (2014). Epidémies cycliques sur les cultures des agro-écosystèmes : adaptation des champignons aux résistances variétales. Habilitation à diriger des recherches, Université de Rennes 1, 43p. http://tel.archives-ouvertes.fr/tel-00968651

[r2] Bousset L (2000). Evolution saisonnière de populations d'oïdium de l'orge (Blumeria graminis f.sp. hordei) face aux résistances des variétés d'orges d'hiver et de printemps. Thèse de doctorat, INA-PG, 122p.

[r1] Bousset L (1996) Influence de la stratégie de mélange variétal de pommiers sur une épidémie de tavelure (Venturia inaequalis). DEA, INA-PG, 25p

Working papers

[a1] Bousset L (2011). Point de vue sur l'articulation de concepts disciplinaires : application à la gestion de la maîtrise des épidémies sur les cultures dans les agro-écosystèmes, INRA, Document de travail pp. 76p. – ProdINRA B-1669.

[a2] Bousset L (2012). Maitriser les épidémies dans les agro-écosystèmes : quelques concepts et liens pour la rencontre de disciplines scientifiques, INRA, Document de travail pp. 58p. (ProdINRA 173531).

[a3] Bousset L (2020). Maladie de la plante, Epidémies, Résistance génétique, Adaptation et Tactiques. INRAE, Document de travail. Hal02929934

Supervision of students

[s4] Colonges T (2009). Initiation et caractérisation d’épidémies induites par les ascospores et les conidies deLeptosphaeria maculanssur le colza. Research Master 2, Agrocampus Rennes. Supervisor Bousset L.

[s3] Lô-Pelzer E (2005-2008). Modélisation des effets des systèmes de culture et de leur répartition spatiale sur le phoma du colza et l’adaptation des populations pathogènes responsables de la maladie (Leptosphaeria maculans) aux résistances variétales. PhD, AgroParisTech. Co- Supervisors Aubertot JN, Bousset L, Jeuffroy MH (resp. HDR). Funding INRA EA / CETIOM. http://pastel.paristech.org/3792/

[s2] Travadon R (2005-2008). Facteurs épidémiologiques contribuant à l’adaptation des populations deLeptosphaeria maculansaux résistances spécifiques deBrassica napus: dispersion des pycnidiospores et des ascospores et progression systémique du champignon. PhD, Agrocampus Rennes. Supervisors Bousset L, Sache I, Brun H. Funding INRA SPE / Région Bretagne. http://hal.archives-ouvertes.fr/docs/00/33/34/77/PDF/Final2.pdf

[s1] Travadon R (2005). Etude de la dispersion par la pluie des spores deLeptosphaeria maculansissues de multiplication asexuée ; conséquences potentielles sur la phase initiale du contournement des résistances du colza. Research Master 2, Agrocampus Rennes. Supervisors Bousset L, Sache I, Brun H.

Coordinator of research projects

2005-2008: Cèdre "How to durably exploit plant resistance", interdisciplinary project between biotechnical and social sciences (16 teams) funded by ANR-ADD.

2005-2008: "Adaptation of phoma stem canker populations to oilseed rape resistances: characterisation of partial resistance, biology of populations during the loss of efficacy or resistance and inoculum production at the end of the cropping season" project joining plant pathology, breeding, agronomy and CETIOM (4 teams) funded by CTPS.

Focus on previous achievements:

July 2016 to June 2017, one year on the other side: knowledge on wild plant pathosystems as an inspiration for crops in agroecosystems

My visit to CSIRO in 2016 can be viewed either as the coincidence of the 2014 spatial evolutionary epidemiology workshop where I met Luke Barrett who invited me, or as the 20th anniversary of year 1996 when I first read a paper by the group. Long term dynamics sometimes need a short term shake…

Working in the "Management of Biotic threats in Farming Systems" group in Canberra is for me the opportunity to share and discuss ideas about evolution in fragmented populations under a selective pressure, given the specific settings of the agro ecosystem. Joining forces with researchers in Australia enables us to tackle the challenge of developing reliable means by which landscape scale theoretical models may be field tested [26].

INRA supports this visit as a long term mission, and we have been granted a 12 months Sir Frederick McMaster fellowship for the project « Impact of inoculum carry-over on landscape dynamics of the blackleg canola pathogen ». The overall aim of the project is to share knowledge and collaboratively advance the science underlying resistance durability strategies in agriculture. The research component of the project will focus on building synergy between the French INRA IGEPP knowledge on field recurrent selection experiments, with the Australian CSIRO knowledge on ecological and evolutionary dynamics in spatially separated populations (i.e. metapopulations).

2014: HDR "Cyclic epidemics on the crops of the agro-ecosystems: adaptation of fungi to varietal resistances / Epidémies cycliques sur les cultures des agro-écosystèmes : adaptation des champignons aux résistances variétales." (http://tel.archives-ouvertes.fr/tel-00968651)

Why to defend HDR? Scientific approach leans on the continuous re-evaluation of hypotheses and theories, on the light of experimental results. Training tomorrow’s researchers to question our own today’s certainties, allows renewing the current ways of thinking, it is allowing them to explore the current topics in a different manner, or to explore different ones.

 I conclude my HDR manuscript by referring to the physician Carlo Rovelli:

"Au cœur de la force de la pensée scientifique est la remise en question continuelle des hypothèses et des résultats antérieurs ; remise en question qui, néanmoins, repose avant tout sur la reconnaissance profonde de la valeur de connaissance contenue dans ces mêmes résultats. " (Rovelli 2009. Anaximandre de Milet ou la naissance de l’esprit scientifique p83)

that I translate as "At the heart of the strength of the scientific thinking is the continuous questioning of hypotheses and previous results; questioning that nevertheless rests on the deep acknowledgement for the knowledge contained in these results. " (Rovelli 2009. Anaximandre de Milet ou la naissance de l’esprit scientifique p83).

 This leads him to write a little further

"(…) follow and extend the master’s path, while criticising the master (…)".

appreciate this sentence for several reasons. On the one hand, it marks the way for our production of knowledge: pushing further the limits of knowledge, in continuation to the ones before us. On the other hand, it tells what we have to pass to and teach our students: daring tomorrow doubting of what we today consider as the most firmly based certainty, as the most appropriate method, as the most appropriate formalisation. It lies in our hand to teach those who will come after us, so that this questioning always keeps going.

The only addition I will make to this sentence is that following and intermingling several points of view greatly enrich the reflexion. It is thus numerous masters that one should listen to!

 The manuscript is available in French (http://tel.archives-ouvertes.fr/tel-00968651). For the purpose of evaluation, I have produced an English version of the French manuscript, as accurate as my limited skills allow me to. I take the responsibility for the potential translation mistakes, and encourage – whenever possible – the readers to refer to the French manuscript.

2012-2013: Conceptualisation of efficacy and stability of disease control strategies in agro-ecosystems

In agro-ecosystems, human actions exacerbate homogeneities alternating with sharp discontinuities on scales of time and space. The dynamics of cyclic epidemics takes discontinuities into account. We have formalised cyclic epidemics, which development depends on interaction in space and in time between host plants, pathogens, environment and human actions. This allows decomposing control at the field and at the landscape scales into goals to reach, corresponding to the components of the pluriannual dynamics of epidemics. Articulating disciplinary concepts opens the prospect of optimization by identification of one’s potential contributions. We propose that cyclic epidemics could be controlled by looking for a local solution, in a decentralized manner. [18]

At present, the pathogen agro-metapopulation adapts to its host and the other way around does not occur. We have proposed ways to adjust the geographic mosaic of coevolution theory between hosts and pathogens to agro-ecosystems, rendering possible to link ecological and evolutionary concepts at the landscape scale, as achieved for natural ecosystems. This opens the prospect to optimize the stabilisation of disease control efficacy by designing management strategies to selectively apply evolutionary costs in order to maintain the pathogen agro-metapopulation locally non-adapted to the host agro-metapopulation. [20]