The apple cultivar ‘Honeycrisp’ has superior fruit quality traits, cold hardiness, and disease resistance, making it a popular breeding parent. However, it suffers from several physiological disorders, production, and postharvest issues. Despite several available apple genome sequences, understanding of the genetic mechanisms underlying cultivar-specific traits remains lacking. Here, we present a highly contiguous, fully phased, chromosome-level genome of ‘Honeycrisp’ apples, using PacBio HiFi, Omni-C, and Illumina sequencing platforms, with two assembled haplomes of 674 Mbp and 660 Mbp, and contig N50 values of 32.8 Mbp and 31.6 Mbp, respectively. Overall, 47,563 and 48,655 protein-coding genes were annotated from each haplome, capturing 96.8–97.4% complete BUSCOs in the eudicot database. Gene family analysis reveals most ‘Honeycrisp’ genes are assigned into orthogroups shared with other genomes, with 121 ‘Honeycrisp’-specific orthogroups. This resource is valuable for understanding the genetic basis of important traits in apples and related Rosaceae species to enhance breeding efforts.

Genetic resistance is the most recommended measure to control verticillium wilt in olive (VWO), a vascular disease caused by the soil-borne fungus Verticillium dahliae, which has promoted the development of olive breeding programs aimed at obtaining new resistant and highly yielding cultivars in recent years. Screening has been commonly performed under controlled conditions in grow chamber after artificial inoculation during the early stage of breeding programs, but additional evaluation is necessary to confirm previous results as well as to test for additional agronomic traits. During this study, 20 breeding selections initially classified as resistant to the disease have been re-evaluated in artificially infested soils under natural environmental conditions. The maximum disease incidence (52.6%) was reached at 26 months after planting, and the disease intensity index reached the maximum value of 38.5% at 29 months after planting. Nine breeding selections consistently confirmed the previous results regarding resistance to V. dahliae infection; however, contradictory results, compared with those of previous evaluations under controlled conditions in grow chambers, were obtained for the rest of selections tested, thereby underlining the need for long-term experimentation under natural environmental conditions. Additional positive agronomic traits, such as early bearing, were also observed for some of the resistant selections, but plant vigor varied. Some seem highly promising for release as new cultivars when characterization of other important agronomic traits is completed in the future.

Olea europaea subsp. cuspidata has a relatively low commercial value due to the low size and pulp to stone ratio of its drupes compared to commercial olive cultivars. Nevertheless, this subspecies could represent a valid source of useful traits for olive breeding. In the current work, the drupe metabolic composition (secoiridoids, flavonoids, simple phenols, triterpenic acids, etc.) of a progeny of 27 cuspidata genotypes coming from free pollination and their female parent was evaluated by applying a powerful LC-MS method. A total of 62 compounds were detected within the profiles; 60 of them were annotated and 27 quantified. From a quantitative point of view, the genotypes from the progeny of cuspidata showed quite different metabolic profiles to olive common cultivars (“Arbequina”, “Frantoio”, “Koroneiki” and “Picual”) used as controls. Cuspidata drupes were richer in terms of several bioactive compounds such as rutin, hydroxytyrosol glucoside, a few interesting secoiridoids and the compounds of m/z 421 and 363. The relationships among several secondary metabolites determined in the progeny inferred from the results of both PCA and cross-correlation analysis were explained according to metabolic biosynthesis pathways in olive drupes. These outcomes underlined the potential of cuspidata genetic resources as a source of potentially interesting variability in olive breeding programs.

The fruit size of a cultivated olive tree is consistently larger than its corresponding wild relatives because fruit size is one of the main traits associated with olive tree domestication. Additionally, large fruit size is one of the main objectives of modern olive breeding programs. However, as the long juvenile period is one main hindrance in classic breeding approaches, obtaining genetic markers associated with this trait is a highly desirable tool. For this reason, GWAS analysis of both genetic markers and the genes associated with fruit size determination, measured as fruit weight, was herein carried out in 50 genotypes, of which 40 corresponded to cultivated and 10 to wild olive trees. As a result, 113 genetic markers were identified, which showed a very high statistically significant correlation with fruit weight variability, p < 10⁻¹⁰. These genetic markers corresponded to 39 clusters of genes in linkage disequilibrium. The analysis of a segregating progeny of the cross of “Frantoio” and “Picual” cultivars allowed us to confirm 10 of the 18 analyzed clusters. The annotation of the genes in each cluster and the expression pattern of the samples taken throughout fruit development by RNAseq enabled us to suggest that some studied genes are involved in olive fruit weight determination.

Rapid apple decline is a phenomenon characterized by a weakening of young apple trees in high density orchards, often followed by their quick collapse. The nature of this phenomenon remains unclear. In this work, we investigated the root system architecture (RSA) of declining and non-declining apple trees in two orchards in New York State. High-density orchard A consisted of 4-year-old ‘Honeycrisp’ on ‘Malling 9 Nic29’, and conventional orchard B consisted of 8-year-old ‘Fuji’ on ‘Budagovsky 9’. In both orchards, a negative correlation (−0.4–−0.6) was observed between RSA traits and decline symptoms, suggesting that declining trees have weaker root systems. Scion trunk diameter at the graft union, total root length, and the length of fine and coarse roots were significantly (p < 0.05) reduced in declining trees in both orchards. Additionally, internal trunk necrosis at, above, and below the graft union was observed in declining trees in orchard A but not in orchard B. Finally, latent viruses were not associated with decline, as their occurrence was documented in declining and non-declining trees in orchard A, but not in orchard B. Together, these results showed weakened root systems of declining trees, suggesting that these trees may experience deficiencies in water and nutrient uptake, although distinct RSA and trunk health traits between the two orchards were noticeable.