Genetic architecture of quantitative traits in plant-virus interactions: Consequences for the management of resistant and/or tolerant varieties at the landscape scale. – ArchiV

Studies of plant defense against parasites have focused mainly on qualitative resistance controlled by major-effect genes, which is often compromised by the counter-adaptation of the targeted parasite. Such resistance breakdowns induce heavy economic losses and a waste of genetic resources. The ArchiV project deals with understudied and widespread plant genetic resources to control diseases: quantitative resistance and tolerance.
The project aims (i) to disentangle plant quantitative resistance and tolerance and to map the corresponding quantitative trait loci (QTLs), (ii) to characterize the ‘genetic architecture’ of quantitative pathogenicity traits (virus load, aggressiveness and plant-to-plant transmission capacity) in viruses and (iii) to estimate the durability potential of quantitative resistance/tolerance. We define the ‘genetic architecture’ of viruses as the genetic determinants (QTLs and underlying mutations) of quantitative pathogenicity traits, their phenotypic effect and their interactions with plant resistance/tolerance QTLs. Three different approaches will be followed to map QTLs in viruses, which correspond to different evolution mechanisms and timescales. The virus mutations corresponding to these QTLs will be identified and their phenotypic effect will be quantified in order to characterize the virus genetic architecture.
The biological models consist in two important viruses (Potato virus Y –PVY- and Cucumber mosaic virus –CMV-) and one of their crop host plant: pepper (Capsicum annuum). The contrast between the genome structure and evolutionary mechanisms of these two viruses is expected to have important consequences on the genetic architecture of their pathogenicity traits.
Modelling approaches will explore the consequences of these genetic architectures on virus evolution and on the efficiency of management strategies of cultivars in agricultural landscapes.
Two models will be developed to represent the within-host evolution of viruses. A first approach (phenotype-based model) will exploit the genetic variance-covariance matrices of virus pathogenicity traits, irrespective of the molecular bases of these traits. The second approach (molecular-based model) will exploit (i) the genetic architecture of virus pathogenicity traits together with (ii) the selection coefficients corresponding to the virus variants carrying the different combinations of adaptive mutations and (iii) the effective size of the virus population in different plant genotypes. The latter two parameters will be estimated thanks to a recently-developed Wright-Fisher model dedicated to plant viruses.
These two within-host models will be embedded into between-host models representing virus epidemics in heterogeneous agricultural landscapes. These models will be based on the ‘landsepi’ R package that we recently developed and will be used to test the efficiency and durability of different management strategies of resistance and tolerance QTLs (pyramiding of QTLs in cultivars, rotation or mosaics/mixtures of cultivars carrying different QTLs). We will also estimate the importance of virus reservoir plants. The ‘landsepi’ framework will also allow comparing the optimal strategies to control different plant pathogens (viruses, fungi…).
The project will have impacts both in the scientific fields of virus evolution, plant-pathogen interactions and epidemiological modelling, and for different actors of the horticultural sector. Notably, the methods developed to measure plant tolerance and resistance to viruses in a quantitative manner and data on the durability potential of quantitative resistance and tolerance will be transferred to the breeding industry and to the authorities in charge of the registration of plant cultivars (GEVES). Strategies aiming to the sustainable management of plant resistance and tolerance QTLs at the agricultural landscape scale will be transferred to technical institutes in horticulture (CTIFL) and breeders.