Location: Vegetable Crops ResearchTitle: Cranberry SSR multiplexing panels for DNA horticultural fingerprinting and genetic studies Author
Submitted to: Scientia Horticulturae
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/1/2017
Publication Date: 3/24/2017
Publication URL: https://handle.nal.usda.gov/10113/5645825
Citation: Schlautman, B., Bolivar-Medina, J., Hodapp, S., Zalapa, J. 2017. Cranberry SSR multiplexing panels for DNA horticultural fingerprinting and genetic studies. Scientia Horticulturae. 219:280-286. doi. 10.1016/j.scienta.2017.03.005. Interpretive Summary: Cranberry is in need of inexpensive high-throughput DNA fingerprinting methods for genetic research and germplasm purity testing for agricultural purposes. This study developed sixteen molecular marker panels, which can be used for high-throughput DNA fingerprinting in cranberry. The panels contained a total of 61 molecular markers which easily separated important commercial cranberry cultivars. In addition, a subset of these panels were used to genotype (characterize with molecular markers) seedlings extracted from fruits in a cranberry bed planted to the cultivar Stevens. The seedlings were determined to be either self-pollinated or cross-pollinated using presence/absence of Stevens inherited molecular markers. We provided the first quantitative evidence that the majority of seeds in commercial cranberries are self-pollinated. Therefore, the efficient and powerful DNA fingerprinting made possible by the presented molecular marker panels represents an important and applicable resource in the cranberry industry for assessing the purity of grower and licensed propagator cranberry vines, protecting intellectual property rights, assisting grower’s in determining genetic purity of existing beds, and for enabling genetic research and analysis of genetic diversity in cultivated, breeding and wild cranberry germplasm.
Technical Abstract: 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 3 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.