Analysis on Unveiling the Natural Dynamics of Parthenocarpy and Self-Compatibility in Apple Trees

Apple (<i>Malus domestica</i>) is self-incompatible and typically requires cross-pollination for seed and fruit development. Parthenocarpy (fruit development without fertilization) and self-compatibility (fruit set without external pollen) are highly desirable traits in apple breeding, as they ensure consistent fruit production and quality without cross-pollination. However, apple parthenocarpic and self-compatible accessions have not been available for practical breeding. To identify these accessions, we analysed 436 accessions of <i>Malus domestica</i> and 84 accessions of wild <i>Malus</i> species by assessing fruit production. Flowers were bagged before opening to prevent cross-pollination. If fruit developed from the bagged flowers, it indicated the presence of self-compatibility or parthenocarpy, depending on whether the fruit contained seeds. We observed and scored a range of phenotypic expressions among accessions, from weak to strong in both parthenocarpy and potential self-compatibility. Strong parthenocarpy was observed in 5.95% of wild <i>Malus</i> species accessions and 3.44% of <i>M. domestica</i> accessions. Similarly, strong self-compatibility was exhibited in 5.95% of wild <i>Malus</i> species accessions and 2.75% of <i>M. domestica</i> accessions. Although bagged flowers showed lower fruit set rates than open-pollinated (OP) flowers, fruit size, weight, firmness, and soluble sugar and starch content showed no significant differences between fruits produced from bagged and OP flowers. Furthermore, a genome-wide association study (GWAS) was conducted with a high-throughput SNP array. This analysis identified several genes potentially associated with these traits. This research provides parthenocarpic and self-compatible apple accessions for breeding, which can generate novel cultivars that eliminate the need for cross-pollination or produce seedless fruit without pollination.