Targeted population genomics uncovers demographic history and genetic divergence in North American wild cranberry

Authors: JIMENEZ, NICOLAS - Rutgers University; TORRES-MERAZ, MARIA ALEJANDRA - University Of Wisconsin; Neyhart, Jeffrey; Zalapa, Juan; SIDELI, GINA - Rutgers University

Submitted to: Horticulture Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/21/2026
Publication Date: 4/21/2026
Citation: Jimenez, N., Torres-Meraz, M., Neyhart, J.L., Zalapa, J.E., Sideli, G. 2026. Targeted population genomics uncovers demographic history and genetic divergence in North American wild cranberry. Horticulture Research. https://doi.org/10.1093/hr/uhag161.
DOI: https://doi.org/10.1093/hr/uhag161

Interpretive Summary: To ensure the future of farmed cranberries, breeders need to find wild genes that help plants resist pests and survive extreme weather, but scientists were unsure how much genetic variety was left or where to find it. By analyzing the DNA of 179 wild cranberries from the Midwest and East Coast and reconstructing their history since the last ice age, researchers discovered two distinct genetic groups: a Midwest population and an East Coast population. These groups were separated thousands of years ago, evolving unique genes to survive their specific local climates. Critically, the study revealed that current breeding programs have almost exclusively used genes from the East Coast group, meaning an entire "genetic toolbox" from the Midwest cranberries—which may hold key traits for toughness—has been completely overlooked. This finding underscores the urgent need to conserve and study both wild populations to find the unique genes needed to protect the cranberry industry.

Technical Abstract: Wild populations of North American cranberry (Vaccinium macrocarpon Aiton) are reservoirs of genetic variation that may contribute to the improvement of breeding-relevant traits. However, the extent to which wild genetic variation is geographically structured and represented in elite germplasm remains unclear. We analyzed 179 wild cranberry accessions from the upper Midwest and Eastern North America to estimate nucleotide diversity (p), population structure, and loci associated with genetic differentiation and environmental variables using a genome-informed targeted genotyping panel. Additionally, 14 demographic scenarios were evaluated using site-frequency-spectrum–based inference to identify historical events that could explain current genetic diversity. We observed extremely low nucleotide diversity within the targeted panel (p = 5 × 10-6). Rare allele distributions strongly influenced p and Tajima’s D values, suggesting constrained diversity in the genomic regions assayed that is not captured by heterozygosity-based estimates alone. However, we interpreted these results as conservative lower bounds on genome-wide neutral diversity because the targeted panel is enriched for genic and conserved regions. A clear separation between the Midwest and East populations was observed, with inbreeding coefficients ranging from -0.13 to 0.15. Furthermore, site frequency spectrum inference from the targeted panel supported a demographic scenario consistent with a significant population reduction ˜15-14 thousand years ago (kya), followed by a divergence between the two regions ˜12 kya, and an asymmetric gene flow ˜1.3 kya. We detected 254 candidate loci showing regional allele-frequency differentiation. Several of these loci colocalized with candidate genes linked to stress response, development, and metabolic processes. To evaluate the representation of geographically differentiated wild alleles in a breeding context, we analyzed Rutgers breeding materials (n = 484) and found that this panel is enriched for common alleles in Eastern wild populations. These findings indicate regionally structured allele-frequency variation in wild cranberry, with potential relevance to environmental response and breeding. This study extends prior wild cranberry population-genetic research by providing targeted-panel estimates of diversity, comparisons of demographic models, and breeding insights on geographically differentiated alleles, while highlighting the importance of conserving wild cranberry germplasm for use in modern breeding programs.