Contributing to sustainable production systems involves selecting planting material that is resistant to, or tolerant of, pests and diseases (Citrus greening, or Huanglongbing –HLB– in particular) and is adapted to restrictive environments (tolerance of water deficits, saline and nutritional stress). Improving the nutritional and sensory qualities of fruits, along with staggered production, are also major objectives for assuring the economic sustainability of the supply chains. Research is centred on the different phases of the complete breeding process, from managing genetic resources to selecting novel material.

Preserving, characterizing and making optimum use of genetic resources

CRB Agrumes (INRA-CIRAD, https://citrus.corse.inra.fr/), which is an ex situ certified biological resource centre (BRC) managed in Corsica by the Citrus experimental unit (INRA), fuels the research and development projects implemented by SEAPAG. The team contributes to the different BRC processes and carries out cryopreservation work. These collections serve for studies on phenotypic and genotypic diversity and form the basis of all our varietal improvement schemes.

Analysing the structures of genomes and species complexes

Vegetative propagation greatly affects the evolution of plant species by making it possible to fix genomic structures arising from rare events, such as interspecific or sub-specific crosses, or polyploidization. The work undertaken focuses on (i) analysing the phylogenetic structuring of species complexes, (ii) deciphering genomic structures of interspecific or sub-specific origin, based on NGS data and the development of reference sequences for the different ancestral taxa.

Understanding the dynamics of complex genomes

The complex genomic structures of cultivated Citrus affect segregations and sexual recombination. Studying meiotic functioning is thus a strong component of the SEAPAG project. In a context where varietal innovation is mostly sought at the triploid and tetraploid levels, we study unreduced gamete formation mechanisms, the meiotic functioning of tetraploids and their implication in the genotypic structures of hybrid populations. Eventually, there are plans to study how the epigenetic component and transposable elements are involved in the phenotypic variability of horticultural groups having evolved asexually (e.g. orange trees).

Understanding trait architecture, genome functioning and phenotype elaboration 

Interspecificity and polyploidy make it complicated to analyse the determinants of phenotypic variability and of its genetic architecture. The initial differentiation between species or sub-species from which the cultivated forms arose is a major component of the phenotypic variance of cultivars and how it is structured. For instance, a large share of functional allelic diversity is linked to phylogeny. The studies undertaken by SEAPAG also show greater plasticity in polyploids (versus diploids), whose physiological and molecular bases largely remain to be discovered. This biological context raises some original research questions, on (i) the implication of interspecificity and ploidy in genome and phenotype expression, (ii) phenotype modelling incorporating the allelic doses in diploids and tetraploids, and (iii) association genomics approaches based on phylogenomics. These issues are studied for targeted traits, in order to take up the challenges of sustainable Citrus growing: tolerance of Citrus greening, resistance to Phytophthora, to Alternaria brown spot of mandarins, anthracnose of limes, adaptation to abiotic stress (water and saline stress, iron chlorosis) and product quality (primary metabolites –sugars and acids– and secondary metabolites –aromas, essential oils, carotenoids, polyphenols– in particular).

Integrating research results to optimize varietal creation

The work mainly involves optimized use of the diversity of species complexes (the true Citrus) by (i) taking on board new knowledge, (ii) taking pre-breeding approaches to improve parental populations, (iii) using in vitro tools (embryo rescue, somatic hybridization) to create novel material, (iv) establishing selection criteria and indexes based on biological and environmental stresses and the expectations of consumer supply chains (ideotypes), (v) developing fine phenotyping methods, and (vi) using early selection tools (marker-assisted selection with a view to genomic selection).

Creating and selecting novel planting material

Modern citrus fruit cultivation is based on orchards of grafted plants. It is thus partly possible to split selection objectives between varieties and rootstocks. For varieties, fruit quality (of which seedless fruits is an essential criterion for the fresh fruit market), staggered production and resistance to certain diseases (Alternaria brown rot of mandarins, anthracnose of limes, etc.) are the main targets. For rootstocks, selection focuses on a better performance in relation to Citrus greening, along with adaptation to the abiotic stresses of the main production basins, incorporating resistance to Phytophthora and to the Tristeza virus, which are essential for any rootstock. Varieties are selected and validated in partnership with stakeholders from research-development and the supply chains.