Berberis microphylla, commonly known as calafate, is one of the most promising species of Chilean Patagonia to be domesticated, due to its anthocyanin-rich berries. The main aim of this study was to understand the genetic structure of the wild populations of B. microphylla in the main regions where it grows and its relationship with phenolic secondary metabolite profiles. Ripe berry samples and leaves were collected from the Aysén and Magallanes regions. Genetic analyses were carried out using 18 microsatellite markers. Phenolic compounds were extracted from the ripe fruits and were quantified using high-performance liquid chromatography (HPLC). Their antioxidant capacity was determined according to the Trolox equivalent antioxidant capacity (TEAC) assay. Total phenols were measured as their absorbance at a wavelength of 280 nm. Both the genetic and chemometric data were explored using unsupervised and supervised methods. The genetic markers suggest the existence of three groups, two of them corresponding to the Aysén and Magallanes samples, and the third corresponding to Chile Chico (a district in Aysén), which was the most divergent of the three. Similar results were observed in the phenolic profile obtained with chemometric analysis, with the same samples forming a separate third group. The differentiation achieved using the genetic and chemical data may be the result of intrinsic genetic differences, environmental effects on fruit maturity, or the sum of both factors. These are all points to consider in the domestication of this valuable species by selecting individuals with desirable traits and contrasting phenotypes.

Bunch compactness (BC) is a complex, multi-trait characteristic that has been studied mostly in the context of wine grapes, with table grapes being scarcely considered. As these groups have marked phenotypic and genetic differences, including BC, the study of this trait is reported here using a genetically diverse collection of 116 Vitis vinifera L. cultivars and lines enriched for table grapes over two seasons. For this, 3D scanning-based morphological data were combined with ground measurements of 14 BC-related traits, observing high correlations among both approaches (R² > 0.90–0.97). The multivariate analysis suggests that the attributes ‘berries per bunch’, ‘berry weight and width’, and ‘bunch weight and length’ could be considered as the main descriptors for BC, optimizing evaluation times. Then, GWASs based on a set of 70,335 SNPs revealed that GBS analysis in this same population enabled the detection of several SNPs associated with different sub-traits, with a locus for ‘berries per bunch’ in chromosome (chr) 18 being the most prominent. Enrichment analysis of significant and frequent SNPs found simultaneously in several traits and seasons revealed the over-representation of discrete functions such as alpha-linolenic acid metabolism and glycan degradation. In summary, the utility of 3D automated phenotyping was validated for table grape backgrounds, and new SNPs and candidate genes associated with the BC trait were detected. The latter could eventually become a selection tool for grapevine breeding programs.

Genetic erosion of grapevine is becoming a serious worldwide problem and preserving its germplasm is an urgent task. Chile is not an exception to this scenario, where diverse factors led by the replacement of traditional varieties by renown cultivars have reduced the vineyard diversity. Therefore, discovering and characterizing minor varieties were the main objectives of this study. In addition to the official catalogue of around 100 grapevine varieties used to produce wine, we present here 89 genotypes not previously described as present in Chile, widely dispersed in the main wine valleys, which were retrieved from vineyards, small collections, and city gardens. Strikingly, we found 49 grapevines with allele patterns not described before. Ten of these may be old European varieties; the other 39 have allele patterns similar to Criolla varieties (e.g., descendants from the crossing of European varieties born in America). A parentage analysis performed with 15 SSR markers in these 39 N.N. samples revealed that most of them are descendants of the so-called foundational varieties Listán Prieto and Muscat of Alexandria, plus others in lower proportion such as Mollar Cano and Muscat à petit grains blancs, as well as known Criollas varieties such as Italiona and Moscatel Rosado. The 89 genotypes not described in Chile structured in three distinguishable groups: Criolla varieties, Central European varieties, and a third group enriched in Iberic varieties. The prevalence of each Criolla accession was quite variable, some corresponding to a single or a few vines found at a single place, while others were spread in several vineyards, even in different valleys, suggesting they were positively selected and propagated at some time. All the new Criolla varieties were different than the recently described Criollas found in Argentina. The discovery, rescue, and documentation of this rich heritage of Vitis vinifera L. genotypes found in Chile is the first step of a long-term work that should be continued with the evaluation of their enological characteristics, yield, and optimal management systems, aiming for the diversification of the local wine industry.