Associating chemical analysis to molecular markers for the valorization of <Emphasis Type="Italic">Citrus aurantium</Emphasis> leaves: a useful starting point for marker-assisted selection

Variation in metabolite composition and content is often observed in citrus, however, it is poorly understood to what extent this variation has a genetic basis. C. aurantium genotypes originating from Tunisia were evaluated to detect genomic (SSR markers) and chemotypic polymorphisms and to discover possible associations between them. A total of fifteen highly polymorphic SSR markers were selected to screen the genetic variability of the most widespread sour orange genotypes. Targeted secondary metabolite profiling analysis generated twenty-one compounds differentially accumulated in the leaves of sour orange genotypes. PCA analysis revealed that genomic and chemotypic data generated similar pattern of clustering, highlighting the intra-specific variability in C. aurantium species. Both data were integrated, leading to the identification of associated SSR alleles with secondary metabolites. Based on results, a relatively high correlation (r = 0.381; p < 0.0001) between chemotypic patterns and genetic markers was identified. Associations between traits of interest for phenolic compounds and genetic markers were tested using statistical methods including three linear model approaches. These results consolidate the presence of a chemical fingerprint that may be suitable for assessing identity and quality of a particular genotype which will be very useful for citrus breeding programs.