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

Authors: JIMENEZ, NICOLAS - Rutgers University; FONG, STEPHANIE - Rutgers University; Neyhart, Jeffrey; JOHNSON-CICALESE, JENNIFER - Rutgers University; SIDELI, GINA - Rutgers University

Submitted to: The Plant Genome
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/1/2025
Publication Date: N/A
Citation: N/A

Interpretive Summary: Cranberry fruit contains flavonols, plant compounds that benefit human health and help plants tolerate stress. However, the genetic diversity influencing cranberry fruit's flavonol content is poorly understood. In this study, we analyzed a genetically diverse collection of cranberry plants to identify natural variations in flavonol content. We discovered wild and traditional cranberries have more genetic diversity for flavonol content than cultivated varieties. A key DNA genetic region was strongly linked to one flavonol, quercetin-3-rhamnoside, explaining nearly 20% of the variation. We also used genomic prediction models to simulate breeding strategies, showing that selecting plants based on their DNA could accelerate the development of cranberries with higher flavonol content. These findings highlight the value of plant genetic resources for improving fruit quality and suggest that modern genetic tools can make cranberry breeding more efficient.

Technical Abstract: American cranberry fruits (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. Myricetin-3-galactoside, quercetin-3-galactoside, quercetin-3-rhamnoside, 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 quercetin-3-rhamnoside, explaining 15.8-19.7% of the genetic variance. The locus harbors a MYB transcription factor implicated in flavonoid biosynthesis under abiotic stress. 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.