Jung M., Roth M., Aranzana M.-J., Auwerkerken A., Bink M., Denancé C., Dujak C., Durel C.-E., Font i Forcada C., Cantin C., Guerra W., Howard N., Keller B., Lewandowski M., Ordidge M., Rymenants M., Sanin N., Studer B., Zurawicz E., Laurens F., Patocchi A., Muranty H.
The apple REFPOP—a reference population for genomics-assisted breeding in apple.
Breeding of apple is a long-term and costly process due to the time and space requirements for screening selection
candidates. Genomics-assisted breeding utilizes genomic and phenotypic information to increase the selection
efficiency in breeding programs, and measurements of phenotypes in different environments can facilitate the
application of the approach under various climatic conditions. Here we present an apple reference population: the
apple REFPOP, a large collection formed of 534 genotypes planted in six European countries, as a unique tool to
accelerate apple breeding. The population consisted of 269 accessions and 265 progeny from 27 parental
combinations, representing the diversity in cultivated apple and current European breeding material, respectively. A
high-density genome-wide dataset of 303,239 SNPs was produced as a combined output of two SNP arrays of
different densities using marker imputation with an imputation accuracy of 0.95. Based on the genotypic data, linkage
disequilibrium was low and population structure was weak. Two well-studied phenological traits of horticultural
importance were measured. We found marker–trait associations in several previously identified genomic regions and
maximum predictive abilities of 0.57 and 0.75 for floral emergence and harvest date, respectively. With decreasing SNP
density, the detection of significant marker–trait associations varied depending on trait architecture. Regardless of the
trait, 10,000 SNPs sufficed to maximize genomic prediction ability. We confirm the suitability of the apple REFPOP
design for genomics-assisted breeding, especially for breeding programs using related germplasm, and emphasize the
advantages of a coordinated and multinational effort for customizing apple breeding methods in the genomics era.