Whole genome scan reveals high level of clonal differentiation in the Primitivo cultivar (Vitis vinifera L.)

Apulia is a prominent wine-growing region in Europe, covering 95,000 hectares and producing 1,202,860 tonnes of grapes in 2023. The region's diverse geography, historical plant migrations, and long-lasting winegrape traditional cultivation have contributed to substantial intra- and inter-varietal diversity within its grapevine germplasm. A key factor in this rich agrobiodiversity is the occurrence of spontaneous somatic mutations, leading to the development of ‘clones' with promising traits associated with grape quality and plant resilience. This study investigated 35 Primitivo clones selected, or also certified clones propagated at CRSFA-Centro Ricerca, Sperimentazione e Formazione in Agricoltura 'Basile Caramia', Locorotondo (Bari) over several years. PRIMITIVO clones were collected from different sites of Apulia. Whole genome scan performed by Genotyping-by-sequencing (GBS) was used to assess intra- genetic variability within and between Primitivo clones. Based on a large panel of 77,613 SNPs, pairwise identical-by-state (IBS) analysis revealed no duplicate clones, highlighting the high level of variability among the samples. Genetic diversity analysis revealed the presence of distinct clusters in Primitivo clones, that reflect the geographical cultivation of grape. Based on groups identified by population structure, fixation index (FST) detected numerous loci associated with renowned genes involved in grapevine phenotypic adaptability and environmental responsiveness. This study enriches our understanding of the inherent genetic diversity in these esteemed traditional grape varieties, emphasizing the imperative to conserve and characterize these invaluable genetic reservoirs. Preserving their intra-varietal richness is crucial for facilitating future advances in grapevine selection, cultivation and addressing breeding challenges.