Leveraging genetic resources and genomic prediction to enhance flavonol content in cranberry fruit

American cranberry fruit (Vaccinium macrocarpon Ait.) are rich in flavonols, a subgroup of flavonoids that contribute to human health and plant stress resilience. Despite their importance, the genetic diversity and potential for improvement of flavonols in cranberry remain underexplored. We analyzed phenotypic and genetic variation for eight flavonol compounds in a genetically diverse germplasm collection (n = 247) over 2 years. Myricetin-3-galactoside, quercetin-3-galactoside, quercetin-3-rhamnoside (Q3Rha), and quercetin-3-arabinofuranoside represented 87% of total flavonol content (TFC) in cranberry fruit, with TFC ranging from 0.17 to 0.75 mg/g FW (where FW is fruit weight). Wild and landrace accessions in the Rutgers cranberry collection exhibited higher genetic variation and breedability for flavonols than the breeding subgroup. We identified a stable locus on Chromosome 3 associated with Q3Rha, explaining 15.8% -19.7% of the genetic variance. Genomic prediction models for TFC exhibited predictive ability varying between 0.12 and 0.26, with combined data from both years yielding the highest values. Although further investigation is needed to improve prediction accuracy, simulated crosses showed similar outcomes between phenotypic and genomic selection. These findings elucidate the genetic architecture of flavonols and show the potential of genomic tools to enhance flavonol content and fruit quality in cranberry breeding programs.