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Over the last 75 years, the black raspberry industry in the United States has steadily declined due to lack of adapted and disease resistant cultivars. The high anthocyanin content of black raspberry and associated health benefits have revived interest in production and breeding new cultivars. The United States Department of Agriculture (USDA) Agricultural Research Service, National Clonal Germplasm Repository manages black raspberry germplasm and maintains a collection of over 175 accessions. Wild black raspberries collected in their native range from more than 130 locations across 27 US states and two Canadian provinces were recently added to this collection. Evaluation of this wild germplasm led to the identification of four sources of aphid resistance, two of which were introgressed into the elite breeding pool in two mapping populations. A major focus of this project is to develop, and make available, genomic tools including linkage and physical maps, a draft genome assembly, ESTs, SNP and SSR markers for use in black and red raspberry breeding. We will study genotype by environment interactions in this black raspberry germplasm in four different production regions across North America and apply the genomic tools to identify QTL important for breeding objectives. These tools will facilitate informed decisions regarding germplasm value and usage, crossing, and selection through marker-assisted breeding, and will be useful for breeding programs across the US. Here, we present the current status of global genetic resources and genomic research in black raspberry.

Lack of variation among black raspberry cultivars is thought to be a limiting factor in fruit production and in breeding improved cultivars. An assessment of the available diversity in black raspberry is needed to effectively develop improved cultivars. Such an assessment was done to estimate the genetic similarities for RAPD markers in 16 black raspberry genotypes and to determine the genetic diversity among these genotypes based on these markers. In addition, the ability to distinguish between the black raspberry genotypes, two red raspberry cultivars (Rubus idaeus L.), and a blackberry cultivar (Rubus hybrid) was determined. A similarity matrix from 379 RAPD markers was calculated, and a phylogenetic tree was constructed using the PHYLIP suite of phylogeny software, which revealed the relationship among the genotypes. An average of 81% similarity was calculated among 16 black raspberry genotypes with a maximum similarity of 98% and a minimum of 70%. The average similarity between black raspberry and red raspberry was 41% and was 26% between black raspberry and blackberry. Combined marker profiles from six RAPD primers could be used to distinguish between the 16 black raspberry genotypes. Red raspberry and blackberry could be distinguished from black raspberry by 27 and 29 of 30 RAPD primers tested, respectively. Genetic diversity was most prominent in genotypes from the extremes of the black raspberry indigenous range. Diversifying the germplasm pool for black raspberry cultivar improvement can be achieved through utilizing genotypes from the extremes of the black raspberry range and through interspecific hybridization.