Cranberry SSR multiplexing panels for DNA horticultural fingerprinting and genetic studies

•16 simple sequence repeat (SSR) multiplexing panels were developed for cranberry.•The panels consist of 61 SSRs randomly distributed on the 12 cranberry chromosomes.•Panels were tested and validated using 18 cranberry cultivars.•174 Stevens seedlings were genotyped and determined to be self- or cross-pollinated.•First evidence that commercial cranberries contain mainly self-pollinated seeds.

Cranberry (Vaccinium macrocarpon) is in need of inexpensive high-throughput DNA fingerprinting methods for genetic research and germplasm purity testing for agricultural purposes. Therefore, we designed and validated 16-multiplexing panels containing 61 evenly distributed simple sequence (SSR) markers, with non-overlapping allele ranges, throughout the 12 cranberry linkage groups. Several important cranberry cultivars and selections (n = 18) and a diploid accession of V. oxycoccos were genotyped with the multiplexing panels and separated through principal component analysis (PCA) to demonstrate their effectiveness for DNA fingerprinting and genetic diversity analysis. A subset of three multiplexing panels containing 12 SSR markers was used to genotype 174 seedlings from fruits collected in a commercial cranberry bed of the cultivar Stevens, and identification of intra-cultivar heterogeneity was investigated in the bed to validate the use of the markers in such future applications. Furthermore, determining the likelihood that each seedling was self- or cross-pollinated provided the first quantitative evidence (p < 0.0001) that the majority of seeds within commercial cranberry beds are self-pollinated. These multiplexing panels represent an important, applicable resource for cranberry researchers and farmers of the North American industry. These markers can be used to assess the genetic homogeneity of grower and licensed propagators’ cranberry beds, to protect the intellectual property rights of plant breeders, and to enable cranberry researchers to monitor the genetic identity of genotypes within their breeding programs and genetic studies.