Ice age split left wild cranberry with two distinct genetic toolkits — and breeders have been using only one

Wild cranberries across North America carry two distinct genetic toolkits shaped by Ice Age climate shifts—and modern breeding programs have been drawing almost exclusively from one of them, according to new research. The study reveals that wild cranberry populations in the Midwest and Eastern North America diverged around 12,000 years ago, evolving unique genetic adaptations to their local environments. These regionspecific alleles, many linked to stress response and environmental tolerance, remain largely untapped in commercial breeding, pointing to an urgent need to broaden the genetic base of cultivated cranberry.

Cranberry is a highvalue U.S. crop, with 37,000 acres harvested in 2024 and a production value of nearly $340 million. Yet growers face mounting challenges: fruit rot caused by multiple pathogens, the reemergence of falseblossom disease, and increasing climate pressures. Over roughly 200 years of breeding, cultivars have improved in berry size and yield, but many economically important traits—including stress tolerance and disease resistance—have shown minimal progress. Wild relatives are known reservoirs of beneficial alleles, but the extent to which wild genetic variation is geographically structured and already represented in elite germplasm has remained unclear. Based on these challenges, a comprehensive populationgenomic investigation of wild cranberry across its native range was needed.

Now, a team of researchers from Rutgers University, the University of Wisconsin–Madison, and the U.S. Department of Agriculture’s Agricultural Research Service has published the first populationgenomic analysis of wild cranberry using markers derived from the Vaccinium pangenome. The findings appear (DOI: 10.1093/hr/uhag161) April 21 in Horticulture Research. The team analyzed 179 wild accessions from nine U.S. states and one Canadian province, using a highdensity targeted genotyping platform to measure nucleotide diversity, population structure, and allelefrequency patterns linked to environmental variation.

The study uncovered a striking genetic divide: Midwest populations (Minnesota, Wisconsin, and Michigan) formed a distinct cluster, separate from Eastern populations stretching from Delaware to New Brunswick. Demographic modeling traced this split to approximately 12,000 years ago, following a severe population bottleneck between roughly 15,000 and 14,000 years ago—a period coinciding with the retreat of the Laurentide Ice Sheet and rapid climatic warming. The Eastern population retained an effective population size nearly four times larger than the Midwest, and asymmetric gene flow over the past 1,300 years has moved predominantly from East to West. The team identified 254 candidate loci showing regional allelefrequency differentiation, several of which colocalized with genes linked to stress response, development, and metabolic processes. Notably, nucleotide diversity within the targeted panel was extremely low (π = 5 × 10⁻⁶)—two to four orders of magnitude lower than values seen in other outcrossing fruit crops—underscoring how tightly genetic variation is constrained in functional genomic regions.

The authors said the findings highlight a major gap in how cranberry breeders source genetic material. “We found that current breeding materials are heavily enriched for alleles from Eastern wild populations, while Midwestern alleles—which may hold key traits for stress tolerance and climate adaptation—have been largely overlooked,” they explained. “This means an entire 'genetic toolbox' from the Midwest has been sitting untapped. If we want to build a cranberry industry that can withstand climate change and emerging diseases, we need to start looking west.”

The implications extend beyond cranberry breeding. The study demonstrates how targeted genotyping approaches can illuminate the demographic history of a crop wild relative and pinpoint regionally adapted alleles with breeding relevance. The Rutgers breeding panel, comprising 484 genotypes from controlled crosses, showed that some pedigreedefined families carry Midwestern allele frequencies at specific loci—suggesting that targeted introgression from wild sources is both feasible and urgently needed. The research also underscores the conservation value of wild cranberry populations, particularly in the upper Midwest, which harbor private alleles not found in Eastern populations or elite germplasm. As climate pressures intensify and diseases like false blossom reemerge, broadening the genetic base of cultivated cranberry may be essential for the crop’s longterm resilience.

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References

DOI

10.1093/hr/uhag161

Original Source URL

https://doi.org/10.1093/hr/uhag161

Funding information

This project was supported by USDA-ARS (#5090-21220-007- 00-D); UW-USDA NIFA (#2019-51181-30015; VacciniumCAP).

About Horticulture Research

Horticulture Research is an open access journal of Nanjing Agricultural University and ranked number one in the Horticulture category of the Journal Citation Reports ™ from Clarivate, 2023. The journal is committed to publishing original research articles, reviews, perspectives, comments, correspondence articles and letters to the editor related to all major horticultural plants and disciplines, including biotechnology, breeding, cellular and molecular biology, evolution, genetics, inter-species interactions, physiology, and the origination and domestication of crops.