PLANT-PLANT INTERACTIONS THROUGH THE LENS OF GENOMICS – APPLICATION TO THE DESIGN OF EFFICIENT VARIETAL MIXTURES FOR A PESTICIDE-FREE AGRICULTURE

Offer description
Varietal mixtures have been proposed as a way to take better advantage of biological processes naturally occurring in agroecosystem, allowing the development of more sustainable agricultural systems with reduced chemical inputs (e.g. Litrico & Violle 2015, Barot et al 2017). Meta-analyses indeed show that variety mixture can improve pathogen control and increase yield. Yet, mixing effects can be highly variable and even negative, making it difficult to guide the choice of component mixtures. Ecological mechanisms that trigger positive mixing effects are well described in the literature (e.g. niche complementarity : MacArthur & Levins 1967, facilitation : Callaway et al 2002, see Barot et al 2017 for a review on variety mixtures). In contrast, mechanisms that underlie negative mixing effects are still poorly known. Using durum wheat as a model species, our team is interested in the application of evolutionary biology concepts, namely the kin selection theory (Hamilton 1964a), to understand the relative contribution of evolutionary and ecological mechanisms to mixture performance and adaptive dynamics of genetically diverse crop populations (Fréville et al 2019, Montazeaud et al 2020a, Montazeaud et al 2020b, Montazeaud et al 2022). Recent advances in genotyping technologies have opened up exciting opportunities to decipher the mechanisms that drive plant-plant interactions (Wuest & Niklaus 2018, Colombo et al 2022). Using a genome-level approach, we recently identified one locus at which allelic differences between mixture components were associated with a decrease in grain yield and an increase in disease incidence (Montazeaud et al, 2022). The effect of having two different alleles at this locus in a mixture was larger in magnitude than the effect of having two different varieties in the mixture. This suggests that positive effects emerging from varietal diversity might be reversed by unfavorable allelic plant-plant interaction at this locus. Moreover, the reproductive output of each allelic copy in the mixture was larger when grown in interaction with an identical allelic copy, a pattern consistent with a green beard effect described in evolutionary biology (Hamilton 1964b). Greenbeard genes have been reported in microbes (Queller et al., 2003) and insects (Keller & Ross, 1998). Investigating plant-plant interactions at the genomic level offers new opportunities to test for such greenbeard effects in plants, and most particularly in crops. Using durum wheat and Septoria tritici blotch, a major leaf disease, as a model system, the PhD student will tackle plant-plant interactions at the genomic level to (i) identify genomic regions for which allelic combinations in the mixture affect disease resistance and yield, (ii) disentangle the underlying mechanisms, and (iii) assess the impact of domestication and varietal improvement on the evolution of plant-plant-pathogen interactions. To do so, he/she will build up on already available data and additional experiments in the field. He/she will use a set of genetic analyses including quantitative genetics modeling to assess how the plant phenotype is affected by its genotype and the genotype of its neighbors.

Hosting environment
● The PhD student will be part of the large pluridisciplinary MOBIDIV consortium (https://www6.inrae.fr/cultiver-proteger-autrement/Les-Projets/MOBIDIV)
● The PhD student will be hosted by the team GE2pop, UMR AGAP (https://umr-agap.cirad.fr/en). He/she will be supervised by Hélène Fréville (evolutionary biologist, INRAE, https://sites.google.com/site/evolbiolhelenefreville/) and Jacques David (quantitative and population geneticist, Institut Agro Montpellier), both strongly involved in national and international projects dealing with the mobilization of within species diversity in agriculture. He/she will benefit from strong interactions with UMR PHIM in Montpellier (E Balllini, JB Morel), which has a recognized expertise in phytopathology.
● Montpellier has one of the largest communities of crop geneticists and evolutionary biologists in Europe, and a large student community, and provides a very stimulating scientific environment.
● The PhD student will be hired by INRAE. Salary and functioning costs will be covered by the MOBIDIV grant.

Applicant’s profile
● Strong expertise in either (or combined) evolutionary biology, quantitative genetics, genomics, and data analysis.

Eligibility and application procedure
● Applicants from all countries are eligible, provided that they have a MSc. Degree
● The deadline for applications is May 27th 2022. Please provide : (i) a motivation letter with a statement of your research interests, skills and experience relevant to the position, (ii) a CV, and (iii) contact details for two referees. All materials should be emailed as a single PDF file to Helene.freville@inrae.fr and Jacques.david@supagro.fr).
● The position can start from October 2022 onwards.

Recent relevant references of the GE2pop team
Fréville H et al (2019) Preferential helping to relatives: a potential mechanism responsible for lower yield of crop variety mixtures? Evolutionary Applications 12, 1837–1849. https://doi.org/10.1111/eva.12842.
Montazeaud G et al (2017) Crop mixtures: does niche complementarity hold for belowground resources? An experimental test using rice genotypic pairs. Plant and Soil, 1-16. https://doi.org/10.1007/s11104-017-3496-2
Montazeaud G et al (2020a) Multifacted functional diversity for multifaceted crop yield: towards ecological assembly rules for varietal mixtures. Journal of Applied Ecology. https://doi.org/10.1111/1365-2664.13735.
Montazeaud G et al (2020b) Farming plant cooperation in crops. Proceedings of the Royal Society B 287, 20191290. http://dx.doi.org/10.1098/rspb.2019.1290.
Montazeaud G et al (2022) From cultivar mixtures to allelic mixtures: opposite effects of allelic richness between genotypes and genotype richness in wheat. New Phytologist 233, 2573–2584. http://doi.org/10.1111/nph.17915.
Colombo M et al (2022) A genome-wide analysis suggests pleiotropic effects of Green Revolution genes on shade avoidance in wheat. Evolutionary Applications. https://doi.org/10.1111/eva.13349.

Cited references outside the host team
Barot S et al (2017) Designing mixtures of varieties for multifunctional agriculture with the help of ecology. A review. Agronomy for Sustainable Development 37: 13.
Callaway R et al (2002) Positive interactions among alpine plants increase with stress. Nature 417: 844–848.
Hamilton W (1964a) The genetical evolution of social behaviour. I. Journal of Theoretical Biology, 7(1), 1–16.
Hamilton W (1964b) The genetical evolution of social behaviour. II. Journal of Theoretical Biology, 7(1), 17–52.
conceptual framework. Trends in Plant Science 20: 604–613.
Keller L, Ross K (1998) Selfish genes: a green beard in the red fire ant. Nature 394: 573–575.
Macarthur R, Levins R (1967) The limiting similarity, convergence, and divergence of coexisting species. The American Naturalist 101: 377–385.
Queller et al (2003) Single-gene greenbeard effects in the social amoeba Dictyostelium discoideum. Science 299: 105–106.
Wuest S, Niklaus P (2018) A plant biodiversity effect resolved to a single chromosomal region. Nature Ecology & Evolution 2: 1933–1939.

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