Understanding and improving the adaptive capacity of agroecosystems through knowledge of genetics and evolution

Project title and acronym: Understanding and improving adaptive capacities of agroecosystems through genetic and evolutionary knowledge - Flagship 2

Date: 2013-2016 (1st phase of LabEx BASC)

Leaders: Stéphane Dupas (EGCE) & Maud Tenaillon (GQE-Le Moulon)

Partners

• academic partners:
  • in BASC: ESE
  • International: Technical University of Munich
• non academic: Edmund Mach Foundation

Context and objectives

This project focuses on understanding the genetic and epigenetic mechanisms behind adaptation of species and how it influences and is influenced by higher organisational levels such as population dynamics, biotic interactions, ecosystem functioning and direct and indirect human intervention on the diverse components of agrobiodiversity. To gain this understanding, we need to know how global change influences natural selection on traits and adaptive genetic variation, but also how agricultural practices and public policy will influence selection and dispersal of adaptative variation through agroecosystems and landscapes.

We will investigate genetic, ecological and societal processes involved in the adaptive evolution and coevolution of a set of model species representing plants, insects and microorganisms. We will develop an integrated (from gene to ecosystem) and interdisciplinary (biological and social sciences) approach that combines mathematical models with controlled laboratory experiments, field observations and field experiments in contrasting land use intensities and in different social and agricultural settings, in particular in intensive European agricultural systems and more extensive agricultural systems in developing countries.

We will investigate processes and patterns of adaptation using three broad approaches:

♦ Modeling: The BASC consortium has expertise in developing and exploring complex models on the genetic basis of trait variation and the evolution of traits under heterogeneous selection regimes using likelihood or approximate Bayesian approaches. We also develop predictive models using multi-agent approaches that integrate individual to population processes (adaptation and species interactions) with human activities.  Multi-agent models will also be used to understand and predict the adaptation of pests and disease vectors to changing patterns of human land use, along with likelihood models to infer adaptation in the context of biological control.

♦ Investigating the heritable and plastic components of adaptive trait variation: Several of our teams work on comparative genomics and transcriptomics of plants, insects, pathogens and other microbes and their interactions. Our aim is to integrate investigations of genetic variation at different scales (genes, networks of genes, species and ecosystems) using data available from new sequencing technologies, to characterize the adaptive component of gene expression variation, and to make the link between genetic/epigenetic and phenotypic variation.

♦ Investigating how natural selection and human practices generate pattern and process of adaptation: Several groups within the BASC consortium study how gene flow among wild, feral and domestic populations facilitates or limits population adaptation to local abiotic and biotic conditions, the latter including species interactions and coevolving hosts, pathogens, herbivores and mutualists. We intend to investigate how changes in agricultural practices, e.g., in response to global change, modify both gene flow, with exchange of adaptive variation among wild and cultivated populations, and the nature/intensity of selection. We will document the changes in agricultural practices and public policies in response to global change and investigate the effect of this on natural and artificial selection regimes experienced by wild and domesticated species and their pests, e.g., to understand the success of particular cultivars and to predict emerging diseases and pests on domesticated and wild species.

Two positions were filled to advance this work:

> Engineer « Caracterisation of structural variation within genomes through re-sequencing » - Yasmine Nooroya – 24 months

> PhD student « Demogenetics and environmental engineering: use of genetics to improve global change responses models » - Arnaud Becheler – 36 months

Results

The project succeeded in strengthening laboratories working on the genetic and epigenetic mechanisms of adaptation, with the main results:

(1) the acquisition and provision of know-how for the detection of structural variants, (2) an understanding of the genetic mechanisms of adaptation of maize to mid-latitudes, complemented by an experimental evolution study that identified determinants of floral transition in this species, (3) in sorghum, a better understanding of a key trait, that of nitrogen use efficiency, (4) in parasitoid insects used in biological control of crop pests, an understanding of the mechanisms of adaptation to new hosts, and (5) finally, in amphibians, the response of the microbiome to changes in habitat.

A bigger lock, partly overcome by the project, was the strengthening and structuring of adaptation research in BASC at the interface with other sciences, social and environmental. The main results at the interfaces were:

(1) the development of a model to optimise seed management within an exchange network, (2) the development of a statistical methodology to identify wheat varieties that are sustainable in terms of resistance to yellow rust, (3) the characterisation of genetic diversity in millet in relation to climate and language barriers around Lake Chad, (4) in apple trees, demonstration of a dysfunction in the conservation strategies of wild apple trees, and concrete proposals for strategies to improve this conservation, (5) finally, at the interface with the environmental sciences, the implementation of a generic tool that aims to exploit multidisciplinary data sets to infer Bayesian models on the scenarios of biodiversity response to global changes

Among the benefits of FP2 are the establishment of long-term collaborations between teams, a better cohesion of communities at the interface between ecology, evolution and social sciences, the obtaining of funding as a result of the projects initiated, and an important participation in the training of students and researchers.

===> Find the powerpoint presentation of the results of the flagship project 2 (LabEx days 2017)

Publications

International journals

> Naino Jika, A., Dussert, Y., Raimond, C. et al. Unexpected pattern of pearl millet genetic diversity among ethno-linguistic groups in the Lake Chad Basin. Heredity 118, 491–502 (2017). https://doi.org/10.1038/hdy.2016.128

> Lilioso M., Folly-Ramos E., Rocha F., Rabinovich J., Capdevielle-Dulac C., Harry M., Marcet P., Costa J., Almeida C., 2017. High Triatoma brasiliensis densities and Trypanosoma cruzi prevalence in domestic and peri-domestic habitats in the state of Rio Grande do Norte, Brazil: the source for Chagas disease outbreaks? The American Journal of Tropical Medicine and Hygiene. https://doi.org/10.4269/ajtmh.16-0823 ===>

> Feurtey A., Cornille A., Shykoff J.A., Snirc A., Giraud T., 2016. Crop-to-wild gene flow and its fitness consequences on a wild fruit tree: towards a comprehensive conservation strategy of the wild apple in Europe. Evol. App. 10(2):180-188. https://doi.org/10.1111/eva.12441

> Brandenburg J-T., Mary-Huard T., Rigaill G., Hearne S., Corti H., Joets J., Vitte C., Charcosset A., Nicolas S., Tenaillon M.I., 2017. Independent introductions and admixtures have contributed to adaptation of European maize and its American counterparts. PLOS Genetics. https://doi.org/10.1371/journal.pgen.1006666

> Marchant A., Mougel F., Jacquin-Joly E., Costa J., Almeida C. E., M. Harry., 2016. Under expression of chemosensory genes in domiciliary bugs of the Chagas disease vector Triatoma brasiliensis. Plos Neglected disease, 10(10), e0005067. https://doi.org/10.1371/journal.pntd.0005067

> Leforestier D., Ravon E., Muranty H., Cornille A., Lemaire C., Giraud T., Durel C.E., Branca A., 2015. Genomic basis of the differences between cider and dessert apple varieties. Evol. App. 8(7):650-61.https://doi.org/10.1111/eva.12270

> Cornille A., Feurtey A., Gélin U., Misvanderbrugge K., Gladieux P., Ropars J., Giraud T., 2015. Anthropogenic and natural drivers of gene flow in a temperate wild fruit tree: a basis for conservation and breeding programs in apples. Evol App. 8: 373–384. https://doi.org/10.1111/eva.12250

Theses

> Arnaud Becheler, Thèse doctorat. "Environmental demogenetic model". Dirigée par Stéphane Dupas, (financement BASC), soutenue en mai 2018, Université Paris-Saclay

> Fatima Awada, Thèse doctorat. "Assessment of sorghum response to nitrogen availability". Dirigée par N. Takvorian (ESE), soutenue en septembre 2016, Université d’Orsay.

> Alice Feurtey, Thèse doctorat. « Hybridations inter-spécifiques chez le pommier et co-évolution hôte pathogène ». Dirigée par T. Giraud (ESE), soutenue en septembre 2016, Université Paris-Saclay.

> Kader Neino-jikka, Thèse doctorat. « Flux de gènes et évolution des ressources génétiques du mil (Pennisetum glaucum) dans le Bassin du Lac Tchad : rôle de la diversité socio-culturelle ». Dirigée par T. Robert (ESE), soutenue en juillet 2016, Université Paris-Saclay.

Communications at scientific events

> Becheler et al. Modèle de démogénétique environnementale : étude des processsus d’invasion biologique. Empirisme et théorie en écologie et évolution, Gif-sur-Yvette, France, 2015. Com. Orale ===>

> Marchant A., Coppé R., Bourret J., Petit E., Mougel F., Mendonça V., Béranger J-M, Blanchet D., Jacquin-Joly,E. da Rosa,A., Filée, F. Harry M. 2015. Répertoire des gènes chimiosensoriels (OBP, CSP) chez les espèces du genre Rhodnius vectrices de la malade de Chagas et processus de domiciliation: 3ème colloque de génomique environnementale, Montpellier, 26-28 octobre 2015.

> Feurtey et al. Crop-to-wild gene flow influenced by human activities: insights from the cultivated apple and its wild European relative. CONFÉRENCE SMBE, 2015 (Vienne, Autriche). Poster.

> Cornille et al. Flux de gènes du pommier cultivé vers le pommier sauvage: vers une mise en place d’une stratégie de conservation du pommier sauvage. Empirisme et théorie en écologie et évolution, Gif-sur- Yvette, France, 2015.

> Cornille. Processes of divergence in fruit trees with an emphasis on apples, 2015. Conférence invitée, Académie des sciences de Shanghaï (Chine).

> Perronne et al. Structure spatio-temporelle de la diversité cultivée du blé tendre et de ses déterminants potentiels: étude de cas en France. PETIT POIS DÉRIDÉ – 37ème édition, Amiens, France, 2016. Com. Orale ===>

> Becheler et al. Modèle de démogénétique environnementale : étude des processsus d’invasion biologique. Rencontres doctorales Lebesgue, Angers, France, 2016. Com. Orale.

> Brandenburg J-T. et al. Independent introductions and admixtures have contributed to adaptation of European maize and its American counterparts. Maize Genetic Conference 59th, 2017 (Saint Louis, Missouri, USA). Com. orale.

> Brandenburg J-T. Histoire, diversité et adaptation des maïs européens. GDR AIEM, 2016 (Montpellier, France). Com. orale.

> Walker et al. (2016). Invited talk. Population structure and host specialization in Botrytis cinerea. In XVII International Botrytis symposium (Santa Cruz, Chile).

> Modelling and seed organization. I Goldringer, A Miramon, M Thomas. 2nd annual meeting Diversifood. 21-23 february 2017, Campus Living Bononia, Bologna, Italy. Com. Orale

> Enjalbert et al. Monitoring the commercial life cycle of varieties and screening disease resistances in on- farm managed genetic resources to improve crop resilience to pathogens. Eucarpia Crop diversification in a changing world - Mobilizing the green gold of plant genetic resources Montpellier, 8-11 may 2017. Poster

> Perronne et al. Relative influence of agricultural systems, pathogen pressures and socio-economic drivers on spatio-temporal changes of cultivated bread wheat diversity over recent decades in France. Eucarpia Crop diversification in a changing world - Mobilizing the green gold of plant genetic resources Montpellier, 8-11 may 2017. Com. Orale.

Outreach

> Giraud H, Cornille A, Giraud T ,2016. « Pommiers sauvage et cultivé : ce que la génétique nous apprend de leurs liens passés et présents sur leurs conservation et réimplantation futures »; Forêt Entreprise 229:26-29 ===>

> Giraud T et Branca A, 2015. « Quand l'homme perfectionne les espèces végétales ». Les échos.