Comparative diversity analysis of southeastern Rubus germplasm through molecular and pedigree techniques

The North Carolina Rubus germplasm collection contains hundreds of diverse blackberry, raspberry, and black raspberry selections, among which intra- and interspecific crosses were made to achieve breeding goals for expanding commercial production in the southeastern USA. For over 50 years, the breeding program has used wild species from various parts of the world to introgress novel and desired traits. Despite this, it is known that diversity within Rubus is narrow, especially for black raspberries and blackberries, which are mostly selfing or apomictic. Molecular fingerprinting can establish the relatedness in a population and assist in designing crosses, making selections, verifying lineage, and trueness-to-type testing. Within the North Carolina State University Rubus Breeding Program, molecular profiling and diversity analyses of 91 red raspberry (Rubus idaeus L.), black raspberry (Rubus occidentalis L.), and blackberry (Rubus spp.) cultivars was conducted using six simple sequence repeat (SSR) markers. Unique molecular profiles using all alleles were successfully determined for 61 germplasm samples. STRUCTURE software was used to infer population relationships amongst individuals, with seven distinct germplasm groups clustering based on similarity of allele fragment size. These fingerprinted accessions maintained at other institutions as well as in-house duplicates can now be tested for trueness-to-type based on the six-loci profiles. Understanding diversity among and within southeastern Rubus germplasm is critical for the development of molecular breeding technologies, and paves the way for improved cultivar development techniques.