Pollen viability, self-incompatibility, and a very singular S-allele structure between the reasons for the limited potential productivity of traditional Basque cider apple varieties

•Some traditional varieties had high pollen quality and might be used as pollinators.•Two varieties showed a certain degree of self-compatibility.•S-allele composition and frequency were unique and S26 frequency was exceptional.•S26 advocates cautious pollinator choice to avoid incompatibility with crabapples.•The presence of an unpublished S-allele, S60, is reported (GenBank OP547868.1). Cider regions conserve a broad diversity of traditional cultivars for which knowledge has hardly evolved. Key aspects of their reproductive biology are barely known, hindering improvement in orchard management and resulting in highly variable yields. In this study, we characterized key aspects of the reproductive biology of some traditional apple cultivars from the Basque-style cider-producing area in northern Spain (Basque Country and Navarre). We tested for pollen quality, self-compatibility, and cross-compatibility (S-genotyping). The pollen quality was good except for Urtebete, Errezila, Reineta Encarnada, and triploid varieties. Self-pollination results confirm the need for pollinators, as only Moko and Txalaka showed certain self-compatibility. Regarding S-genotyping, the population proved very singular, with an atypically high frequency of S26, a frequent allele within crabapples, and the appearance of a novel unpublished allele (S60). The knowledge generated for this variety pool will contribute to a better choice of suitable pollinators, preventing the use of popular crabapple varieties that are demonstrated to be partly incompatible with them, and will lead to an increase in potential yields in the region.