New Anthocyanin and Nonanthocyanin Phenolic Compounds in Wild Bilberry ( Vaccinium meridionale Swartz) and Their Genetic Architecture

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.