In the past, the Silk Road was a vital trade route that spanned Eurasia, connecting East Asia to the Mediterranean Sea. The genus Prunus, belonging to the Rosaceae family and encompassing plums, peaches, apricots, cherries, and almonds, thrived as human travel along the Silk Road increased. The majority of fruits within this genus, whether wild or cultivated, are naturally sweet and easily preserved by drying for storage and transport. The interaction along the Silk Road between wild populations and diverse varieties of Prunus fruits led to the development of various hybrids. This article provides a summary of archaeological findings related to prominent Prunus fruits such as peaches, apricots, plums, cherries, and almonds, shedding light on their evolutionary history, genetic diversity, population structure, and historical dynamics crucial for species conservation. The origins of biodiversity may involve factors like migration of pre-adapted lineages, in situ variation, or the persistence of ancestral lineages. Furthermore, climate change is affecting spatial genetic patterns and potentially further threatening rare Prunus species. Evaluating the scope and composition of genetic diversity within germplasm collections is essential for enhancing plant breeding initiatives and preserving genetic resources in this changing context. From a molecular point of view, techniques such as genome-wide association studies (GWASs) and the identification of quantitative trait loci (QTLs) and genes responsible for phenotypic changes in cultivars and germplasm collections should be of great interest in these breeding programs, while genomic estimated breeding values (GEBVs) derived from genome-wide DNA polymorphism information can facilitate the selection of superior genotypes.

Cultivated species of the Prunus genus are of great economic importance worldwide and can be severely affected by viral diseases that compromise both yield and fruit quality. Among the most significant is Potyvirus plumpoxi (PPV), the causal agent of sharka disease, which has a direct and severe impact on stone fruit production. In this study, high-throughput RNA sequencing was employed to detect and characterize viruses present in commercial peach and apricot orchards located in different regions of Spain. After processing five samples, a total of ten viruses were identified, with PPV being the predominant virus in all analyzed samples, specifically the Marcus strain (PPV-M), which is described as one of the most aggressive PPV strains. In addition, other viruses were detected with high sequencing depth, including Luteovirus nucipersicae (nectarine stem pitting associated virus, NSPaV) and Peach-associated luteovirus (PaLV). Single-nucleotide variation (SNV) analysis of PPV-M populations revealed specific mutations distributed across the viral genome. Furthermore, phylogenetic analyses indicated the presence of multiple infection sources of European origin. These results highlight the presence of PPV-M in Spain, providing evidence of different routes of exchange of infected plant material. These findings underscore the need to strengthen monitoring programs, certification of planting material, and phytosanitary control measures to limit the dissemination of viruses and minimize their impact on stone fruit production.