Developing Black Raspberry Genetic and Genomic Resources

This study incorporates field and laboratory components to advance and streamline identification of a variety of traits of economic interest and to develop molecular markers for marker assisted breeding of black raspberry (Rubus occidentalis L.). A lack of adapted, disease resistant cultivars has led to the steady decline of the black raspberry (BR) industry in the United States. Interest in production and breeding new cultivars has been fueled by news regarding the potential health benefits of black raspberry bioactive compounds. To accomplish our goals, we used two related full-sibling populations that were replicated and planted at five production sites (Oregon, Washington, Ohio, North Carolina, and New York). Detailed trait measurements included primocane vigor, flowering and fruiting, disease and aphid tolerance, and plant architecture to assess the influence of environment on genotype (GxE). Initial analysis of GxE on primocane vigor indicated that individual genotypes showed significant variation among sites. We are also developing, and making available, genomic tools including molecular markers for construction of linkage and physical maps, and a draft genome assembly. Markers are being developed by sequencing and analyzing libraries generated by genotyping by sequencing (GBS). Initial analysis through a custom data pipeline identified over 23,000 single nucleotide polymorphic/insertion-deletion (SNP/indel) loci. Preliminary results indicate that GBS is appropriate for SNP detection in this highly-homozygous species. A densely populated genetic linkage map will be used to improve the draft genome assembly, for quantitative trait locus (QTL) mapping, and comparative genomic studies with other Rosaceae species.