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 two 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. 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.