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.

Since there are many different factors which affect peach orchard profitability, it is necessary to conduct long-term studies to find the best scion/rootstock combination within the constraints imposed by local climate and economic conditions. The influence of six peach-almond hybrids (“Adafuel”, “Adarcias”, Garnem”, “GF 677”, “PADAC 9902-01” and “Rootpac 70”); one P. persica × P. davidiana hybrid: “Cadaman”; five hexaploid plums (“Adesoto 101”, “PM 44 AD”, “PM 105 AD”, “PM 150 AD”, and “Penta”); three plum × peach-almond hybrids (“PADAC 04-01”, “PADAC 04-03” and “PADAC 99-05”), and one plum x almond hybrid (“Rootpac R”) on agronomic, basic fruit quality parameters, and flower and leaf mineral nutrients of the “Big Top” nectarine was tested. The highest vigor was induced by “Adafuel”, while the lowest vigor was exhibited by “PM 105 AD”, although the latter did not differ from the rest of the rootstocks. Yield efficiency was higher for “Adesoto 101” and lower for “Adafuel”. Regarding the soluble solids content (SSC), “PADAC 04-01” rootstock induced the highest average content, although it did not differ from “Adarcias”, “Adesoto 101”, “PADAC 99-05”, “PM 105 AD”, and “Rootpac R”. In addition, significant effect of rootstock was found on the flower and leaf mineral analysis traits evaluated. The medium (“Adarcias”, “Adesoto 101”, “PM 105 AD”) to high vigorous plum based hybrid rootstocks (“PADAC 04-01”, “PADAC 99-05” and “Rootpac R”) showed the tendency to induce a better fruit quality, based on higher concentration of SSC, and other yield attributes, demonstrating their commercial interest as new rootstocks for peaches. Considering its overall performance, “PADAC 04-01” appears as a new promising rootstock alternative to peach-almond hybrids on heavy and calcareous textured soils.

A basic knowledge of linkage disequilibrium and population structure is necessary in order to determine the genetic control and identify significant associations with agronomical and phytochemical compounds in apple (Malus × domestica Borkh). In this study, 186 apple accessions (Pop1), representing both Spanish native accessions (94) and non-Spanish cultivars (92) from the EEAD-CSIC apple core collection, were assessed using 23 SSRs markers. Four populations were considered: Pop1, Pop2, Pop3, and Pop4. The initial Pop1 was divided into 150 diploid (Pop2) and 36 triploid accessions (Pop3), while for the inter-chromosomal linkage disequilibrium and the association mapping analysis, 118 phenotype diploid accessions were considered Pop4. Thus, the average number of alleles per locus and observed heterozygosity for the overall sample set (Pop1) were 15.65 and 0.75, respectively. The population structure analysis identified two subpopulations in the diploid accessions (Pop2 and Pop4) and four in the triploids (Pop3). Regarding the Pop4, the population structure with K = 2 subpopulations segregation was in agreement with the UPGMA cluster analysis according to the genetic pairwise distances. Moreover, the accessions seemed to be segregated by their origin (Spanish/non-Spanish) in the clustering analysis. One of the two subpopulations encountered was quite-exclusively formed by non-Spanish accessions (30 out of 33). Furthermore, agronomical and basic fruit quality parameters, antioxidant traits, individual sugars, and organic acids were assessed for the association mapping analysis. A high level of biodiversity was exhibited in the phenotypic characterization of Pop4, and a total of 126 significant associations were found between the 23 SSR markers and the 21 phenotypic traits evaluated. This study also identified many new marker-locus trait associations for the first time, such as in the antioxidant traits or in sugars and organic acids, which may be useful for predictions and for a better understanding of the apple genome.