A "mission" to uncover: genomic evidence supports the hybrid origin of Rosa del Peru, a patrimonial grape of the Americas

Abstract This study employed genomic analysis to elucidate the hybrid origin of Rosa del Peru type 2, a significant patrimonial grapevine in the Americas. Twelve accessions from a historical vineyard in Ensenada, Mexico, were characterized using simple sequence repeats (SSR), with three representative samples—Listan Prieto and two Rosa del Peru type 2 accessions—selected for whole-genome resequencing (WGS). SSR profiling revealed a high prevalence of Listan Prieto within the historical vineyard. Neighbor-net analysis, based on 109,529 high-quality single nucleotide polymorphisms (SNPs), clustered Listan Prieto and Rosa del Peru type 2 with Listan Negro and Manai, a Muscat cultivar of Chinese origin. ADMIXTURE analysis (k = 9, 64,175 SNPs) demonstrated that while Listan Prieto shares its genetic profile with Listan Negro, Rosa del Peru type 2 exhibits a hybrid composition derived from Listan Prieto and Manai. Subsequent PhyloNet modeling further supported that Rosa del Peru type 2 originated from a hybridization event between the lineages of Listan Prieto and Manai. Notably, we identified ~ 7,585 SNPs in these patrimonial cultivars not present in their immediate ancestors Listan Negro and Manai, suggesting potential local adaptation, clonal divergence or incomplete lineage sorting. By providing the first WGS datasets for these cultivars, this work offers a high-resolution genomic resource and clarifies the complex historical migration and diversification of New World grapevines.