Low-input breeding in stone pine, a multipurpose forest tree with low genome diversity

Stone pine (Pinus pinea L.) is an emblematic tree species within the Mediterranean basin, with high ecological and economic relevance due to the production of edible nuts. Breeding programmes to improve pine nut production started decades ago in Southern Europe but have been hindered by the near absence of polymorphisms in the species genome and the lack of suitable genomic tools. In this study, we assessed new stone pine’s genomic resources and their utilisation in breeding and sustainable use, by using a commercial SNP-array (5,671 SNPs). Firstly, we confirmed the accurate clonal identification and identity check of 99 clones from the Spanish breeding programme. Secondly, we successfully estimated genomic relationships in clonal collections, an information needed for low-input breeding and genomic prediction. Thirdly, we applied this information to genomic prediction for total number of cones unspoiled by pests and their weight measured in three Spanish clonal tests. Genomic prediction accuracy depends on the trait under consideration and possibly on the number of genotypes included in the test. Predictive ability (ry) was significant for the mean cone weight measured in the three clonal tests, while solely significant for the number of cones in one clonal test. The combination of a new SNP-array together with the phenotyping of relevant commercial traits into genomic prediction models, proved to be very promising to identify superior clones for cone weight. This approach opens new perspectives for early selection.