Agraz (Vaccinium meridionale Swartz) is a shrub native to the Neotropical region of South America, including Colombia, Ecuador, Venezuela, and Peru. Known for its edible fruits valued for their nutritional, nutraceutical, and medicinal properties, the species remains underexplored despite its potential. This research aimed to investigate the genetic diversity and population structure of agraz in Colombia, focusing on native individuals from Santander and commercial individuals from Boyacá and Cundinamarca, providing insights that can support conservation and genetic improvement efforts. Methods: In this study, genotyping by sequencing (GBS) was used to analyze genetic variation and population structure in V. meridionale. The sequencing data were aligned to the V. corymbosum cv. Draper v1.0 reference genome. The obtained single-nucleotide polymorphisms (SNPs) were employed to evaluate genetic diversity, population differentiation, and inbreeding coefficients, with measures such as expected heterozygosity and F-statistics providing insights into population structure and genetic composition across regions. Results: A total of 12,910 SNPs were obtained, and the results revealed moderate genetic diversity within the agraz populations, characterized by an expected heterozygosity (He) of 0.3586. A negative Fis value indicated an excess of heterozygosity and low genetic differentiation among the sampled regions. Population structure analysis identified three distinct subpopulations, with Subpopulation 3 exhibiting the most unique genetic composition. Conclusions: This study provides the first genetic diversity analysis of V. meridionale in Colombia using the GBS approach. The findings contribute to the understanding of the species’ genetic variability and offer valuable information for conservation strategies, genetic improvement and breeding programs to enhance its agricultural potential and ensure the sustainable utilization of agraz resources.

Vaccinium meridionale Swartz represents an underexplored reservoir of nutritional and functional potential. Anthocyanin and nonanthocyanin phenolic compounds in V. meridionale were studied in a control ripe fruit sample, a set of 118 genotypes, a green leaves sample, and a purple leaves sample. The study included the use of reversed-phase ultrahigh-performance liquid chromatography with an diode array detector (RP-UHPLC-DAD) and RP-UHPLC with electrospray ionization, quadrupole-time-of-flight tandem mass spectrometry (ESI-QTOF-MS/MS). A total of 24 compounds were identified, with chlorogenic acid (223.5–2539.8 mg/100 g DW) and cyanidin-3-O-galactoside (86.2–986.0 mg/100 g DW) as the two most abundant phenolic compounds in the fruit collection and caffeoyl arbutin (1204.3 and 3659.5 mg/100 g DW, respectively) followed by chlorogenic acid (628.5 and 1258.6 mg/100 g DW, respectively) as the two most abundant in both the green and purple leaves. To explore the genetic basis underlying this phenolic variation, genome-wide association studies (GWAS) were conducted using 16,709 high-quality SNPs across 69 genotypes. GWAS revealed 40 significant quantitative trait nucleotides (QTNs) associated with seven phenolic compounds, including cyanidin-3-O-galactoside, caffeoyl acetyl arbutin isomer 1, cyanidin feruloyl hexoside, delphinidin-3-O-hexoside, quercetin, quercetin-3-O-glucoside, and quercetin-3-O-rhamnoside. Candidate genes located in linkage disequilibrium with QTNs include key regulators of flavonoid biosynthesis, such as MYB and bHLH transcription factors, WD40 protein, glucosyltransferase, and chalcone isomerase. These findings provide novel insights into the genetic architecture of phenolic compound biosynthesis in V. meridionale, offering molecular targets for breeding programs and biotechnological enhancement of this nutritionally valuable native species.