The apple REFPOP – a reference population for genomics-assisted breeding in apple

The apple REFPOP is composed of diverse old and modern apple germplasm and current European breeding material planted in six copies across various European environments and forms a backbone of apple breeding improvement in Europe. To increase selection efficiency, genomic and phenotypic information collected from this population can be utilized for genomics-assisted breeding. For this purpose, a high-density SNP marker dataset of the apple REFPOP genotypes was assembled via cost-effective marker imputation and phenotypes of two well-studied phenological traits were measured. The rediscovery of marker-trait associations in previously identified genomic regions and moderate to high predictive abilities supported the applicability of the apple REFPOP for the development and application of genome-wide association studies (GWAS) and genomic prediction in apple. Furthermore, the study emphasized the positive effects of high marker density on GWAS and the role of trait architecture in both GWAS and genomic prediction. In the future, this population will become a unique resource for multi-environment, multi-trait and multi-management modelling of many phenotypic traits with horticultural importance leading to the ultimate improvement of the apple breeding efficiency.

This study is another outcome of the successful collaboration between Agroscope and the Molecular Plant Breeding group of ETH Zurich, embedded in a European consortium with a long-standing history of collaboration.

Citation:
Jung M, Roth M, Aranzana MJ, Auwerkerken A, Bink M, Denancé C, Dujak C, Durel C, Font i Forcada C, Cantin CM, Guerra W, Howard NP, Keller B, Lewandowski M, Ordidge M, Rymenants M, Sanin N, Studer B, Zurawicz E, Laurens F, Patocchi A, Muranty H (2020) The apple REFPOP—a reference population for genomics-assisted breeding in apple. Horticulture Research 7:189
external page https://doi.org/10.1038/s41438-020-00408-8