A public mid-density genotyping platform for cultivated cranberry (Vaccinium macrocarpon Aiton)

Cranberry (Vaccinium macrocarpon Aiton), a native North American fruit crop, has gained global popularity due to its unique flavor and health benefits. As the market expands for new cranberry products, the requirements to produce varieties that meet new standards have increased. DNA-assisted breeding in cranberry has been limited due to the lack of cost-effective genotyping tools. To address this gap, Breeding Insight developed and validated a 3K DArTag panel. Target loci were strategically selected from 507K single-nucleotide polymorphisms (SNPs), generated from resequencing 53 diverse cultivated cranberry accessions. Selection criteria prioritized even genomic distribution, genic regions, maximum genetic diversity among North American breeding germplasm, and markers associated with known quantitative trait loci. The cranberry 3K DArTag panel was validated using a diverse collection of cranberry accessions, interspecific hybrids, and two F₁ populations. The panel, optimized for cultivated V. macrocarpon, demonstrated a high average amplification rate (83.4%) and robust performance in its close relatives, Vaccinium microcarpum and Vaccinium oxycoccos, as well as somewhat lower but acceptable performance in interspecific hybrids. However, transferability to the more distant blueberry was limited. The panel successfully revealed expected ploidy levels and population structure among the tested materials. Two individual linkage maps and one consensus map were constructed for the mapping populations, with an average marker density of 0.68 markers per centimorgan. This cost-effective (∼$15/sample), rapid genotyping platform offers valuable capabilities for public and private breeding programs. Its open-access nature enables genetic datasets generated from the marker panel to be compared and integrated across projects and geographical boundaries.