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Red-fleshed apple varieties are becoming increasingly popular among fruit consumers. This trait is associated with anthocyanin accumulation, which is known for its beneficial effects on human health. The genetic basis of colour development has been widely characterised, but it does not explain all the variations in intensity and distribution of red pigmentation. New molecular markers are currently needed to increase the selection efficiency of this complex trait.

We developed a multifactorial approach to study red flesh trait in apple by combining image-based phenotyping with the determination of several biochemical traits that influence colour expression: phenolic compound contents, dry matter contents, and pH values. This methodology was applied to decipher the phenotypic diversity in five hybrid families segregating for this trait (450 genotypes). We use image-based phenotyping to evaluate intensity and distribution of red colour in progenies from colour data.

We then defined morphometric descriptors to describe the significant variation of colour patterns in the dataset and to study the inheritance of the colour distribution. Some non-destructive methods are evaluated to predict flesh browning disorder (hyperspectral imaging, sound analysis).

Preliminary study showed important variation in phenolic profile between our hybrid families. We select the ten most discriminating phenolic compounds that could be involved in the expression and stability of red flesh. Targeted analyses were run to quantify these compounds by UPLC-DAD for two years (2021 and 2022). Correlation analyses were performed to assess the robustness of our image analysis pipeline. A model including dry matter, pH, phenolic compounds contents and flesh colour were proposed.

The genetic determinism of red flesh and flesh browning disorder will then be investigated. QTLs associated with genomic regions controlling the observed traits will be identified and will lead to the development of molecular markers applicable in MAS (Molecular marker Assisted Selection).

In parallel, epigenomic studies will be conducted to identify potential epigenetic marks associated with the expression of red flesh character, which expression may vary depending on environmental conditions.