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.

Implementation of genomic tools is desirable to increase the efficiency of apple breeding. Recently, the multi-environment apple reference population (apple REFPOP) proved useful for rediscovering loci, estimating genomic predictive ability, and studying genotype by environment interactions (G × E). So far, only two phenological traits were investigated using the apple REFPOP, although the population may be valuable when dissecting genetic architecture and reporting predictive abilities for additional key traits in apple breeding. Here we show contrasting genetic architecture and genomic predictive abilities for 30 quantitative traits across up to six European locations using the apple REFPOP. A total of 59 stable and 277 location-specific associations were found using GWAS, 69.2% of which are novel when compared with 41 reviewed publications. Average genomic predictive abilities of 0.18–0.88 were estimated using main-effect univariate, main-effect multivariate, multi-environment univariate, and multi-environment multivariate models. The G × E accounted for up to 24% of the phenotypic variability. This most comprehensive genomic study in apple in terms of trait-environment combinations provided knowledge of trait biology and prediction models that can be readily applied for marker-assisted or genomic selection, thus facilitating increased breeding efficiency.

Apple is widely cultivated in temperate regions. The beneficial properties of apple for preventing several illnesses are widely known. Nevertheless, qualitative variables such as sweetness or sourness may influence consumer satisfaction; they are critical factors for fruit consumption and essential in plant breeding. In the present work, 155 apple accessions were assessed during five consecutive years (2014–2018). Four individual sugars and seven organic acids were analysed by HPLC. A mixed-effects model was fitted with accessions and the years’ climatic features as independent variables. A cluster analysis was applied on the mixed-effects model coefficients. Four groups were considered as optimum. Genetics seemed to have the strongest effect and showed clear differences between accession groups, while climate effects were strong only for certain compounds and had a more horizontal behaviour equally affecting the different accession groups. In fact, non-Spanish cultivars tended to concentrate, while autochthone accessions had a much wider spread. Individual sugars and acids concentrations correlated negatively with precipitation and positively with temperature range and solar radiation in all accession groups. The geographic region where the orchard is grown is thus very important in the resulting metabolites profiles. Moreover, apple genetics would also play a decisive role as highlighted in the cluster analysis.

Japanese plums are classified as climacteric; however, some economically important cultivars selected in California produce very little ethylene and require long ripening both ‘on’ and ‘off’ the tree to reach eating-ripe firmness. To unravel the ripening behavior of different Japanese plum cultivars, ripening was examined in the absence (air) or in the presence of ethylene or propylene (an ethylene analogue) following a treatment or not with 1-methylcyclopropene (1-MCP, an ethylene action inhibitor). Detailed physiological studies revealed for the first time three distinct ripening types in plum fruit: climacteric, suppressed-climacteric and non-climacteric. Responding to exogenous ethylene or propylene, the slow-softening supressed-climacteric cultivars produced detectable amounts of ethylene, in contrast to the novel non-climacteric cultivar that produced no ethylene and softened extremely slowly. Genetic analysis using microsatellite markers produced identical DNA profiles for the climacteric cultivars ‘Santa Rosa’ and ‘July Santa Rosa’, the suppressed-climacteric cultivars ‘Late Santa Rosa’, ‘Casselman’ and ‘Roysum’ and the novel non-climacteric ‘Sweet Miriam’, as expected since historic records present most of these cultivars as bud-sport mutations derived initially from ‘Santa Rosa’. This present study provides a novel fruit system to address the molecular basis of ripening and to develop markers that assist breeders in providing high-quality stone fruit cultivars that can remain ‘on-tree’, increasing fruit flavor, saving harvesting costs, and potentially reducing the need for low-temperature storage during postharvest handling.