Apricots, scientifically known asPrunus armeniacaL, are drupes that resemble and are closely related to peaches or plums. As one of the top consumed fruits, apricots are widely grown worldwide except in Antarctica. A high-quality reference genome for apricot is still unavailable, which has become a handicap that has dramatically limited the elucidation of the associations of phenotypes with the genetic background, evolutionary diversity, and population diversity in apricot. DNA fromP. armeniacawas used to generate a standard, size-selected library with an average DNA fragment size of ~20 kb. The library was run on Sequel SMRT Cells, generating a total of 16.54 Gb of PacBio subreads (N50 = 13.55 kb). The high-qualityP. armeniacareference genome presented here was assembled using long-read single-molecule sequencing at approximately 70× coverage and 171× Illumina reads (40.46 Gb), combined with a genetic map for chromosome scaffolding. The assembled genome size was 221.9 Mb, with a contig NG50 size of 1.02 Mb. Scaffolds covering 92.88% of the assembled genome were anchored on eight chromosomes. Benchmarking Universal Single-Copy Orthologs analysis showed 98.0% complete genes. We predicted 30,436 protein-coding genes, and 38.28% of the genome was predicted to be repetitive. We found 981 contracted gene families, 1324 expanded gene families and 2300 apricot-specific genes. The differentially expressed gene (DEG) analysis indicated that a change in the expression of the 9-cis-epoxycarotenoid dioxygenase (NCED) gene but not lycopene beta-cyclase (LcyB) gene results in a low β-carotenoid content in the white cultivar “Dabaixing”. This complete and highly contiguousP. armeniacareference genome will be of help for future studies of resistance toplum pox virus(PPV) and the identification and characterization of important agronomic genes and breeding strategies in apricot.

Stone fruits (Prunus spp.) occupy a pivotal position in global fruit production due to their significant nutritional profile and distinctive organoleptic characteristics. Contemporary orchard systems are undergoing transformation through innovative cultivation approaches, notably high-density dwarfing systems, greenhouse cultivation, agri-tech integration, and simplified management. As a crucial agronomic component in modern stone fruit cultivation, rootstock systems confer multi-benefits including enhanced environmental resilience, improved scion productivity, superior fruit quality, controlled vigor, and dwarfing capacity. While the majority of European apple orchards have transitioned to dwarfing rootstock systems, achieving substantial gains in productivity and profitability, stone fruit cultivation lags significantly due to the key gaps in prunus rootstock development, including genetic complexity, extended evaluation cycles, clonal propagation barriers, and limited research programs. Urgent innovation is required to address these challenges in rootstock breeding to meet the demand of sustainable stone fruit production. This review systematically examines strategic breeding objectives and innovative molecular methodologies in prunus rootstock development, with particular emphasis on marker-assisted selection and genomic prediction technologies. We provide a comprehensive synthesis of breeding achievements across major commercial rootstock cultivars, while proposing forward-looking research strategies incorporating CRISPR-based genome editing and multi-omics approaches. The synthesized insights establish a theoretical pathway for advancing rootstock genetic improvement and sustainable orchard management practices in stone fruit cultivation systems.

Stone fruits (Prunus spp.) occupy a pivotal position in global fruit production due to their significant nutritional profile and distinctive organoleptic characteristics. Contemporary orchard systems are undergoing transformation through innovative cultivation approaches, notably high-density dwarfing systems, greenhouse cultivation, agri-tech integration, and simplified management. As a crucial agronomic component in modern stone fruit cultivation, rootstock systems confer multi-benefits including enhanced environmental resilience, improved scion productivity, superior fruit quality, controlled vigor and dwarfing capacity. While the majority of european apple orchards have transitioned to dwarfing rootstock systems, achieving substantial gains in productivity and profitability, stone fruits cultivation lag significantly due to the key gaps in prunus rootstock development include genetic complexity, extended evaluation cycles, clonal propagation barriers and limited research programs. Urgent innovation is required to address these challenges in rootstock breeding to meet the demand of sustainable stone fruits production. This review systematically examines strategic breeding objectives and innovative molecular methodologies in Prunus rootstock development, with particular emphasis on marker-assisted selection and genomic prediction technologies. We provide a comprehensive synthesis of breeding achievements across major commercial rootstock cultivars, while proposing forward-looking research strategies incorporating CRISPR-based genome editing and multi-omics approaches. The synthesized insights establish a theoretical pathway for advancing rootstock genetic improvement and sustainable orchard management practices in stone fruit cultivation systems.

Storage of ripe apricot (Prunus armeniaca) fruit at low temperatures results in the loss of volatile aroma compounds. Here, we analyzed volatile compounds in fruit from the apricot cultivars ‘Chuanzhihong’ and ‘Mituoluo’ during ripening and identified esters as key contributors to fruit aroma. The cultivars accumulated different profiles of volatiles during ripening. Transcriptome analysis identified more than 20,000 genes that were differentially expressed during fruit development and a cluster of genes that were enriched in KEGG pathways associated with fatty acid–derived ester biosynthesis. The key ester biosynthetic genes LOX and AAT were upregulated during fruit ripening but suppressed at low temperatures. Volatile emissions dropped below 10 °C and partially recovered at 25 °C, but LOX and AAT enzymatic activities failed to recover, leading to diminished aroma. Storage at 0–5 °C caused a strong and largely irreversible suppression of ester accumulation, even after rewarming.