Supplementary data from: Targeted population genomics uncovers demographic history and genetic divergence in North American wild cranberry

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 (π),
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 (π = 5x10-6). Rare allele
distributions strongly influenced π 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.