Development of a high-density cranberry SSR linkage map for comparative genetic analysis and trait detection

Since its domestication 200 years ago, breeding of the American cranberry (Vaccinium macrocarpon) has relied on phenotypic selection because applicable resources for molecular improvement strategies such as marker-assisted selection (MAS) remain limited. To enable MAS in cranberry, the first high-density SSR linkage map with 541 markers representing all 12 cranberry chromosomes was constructed for the CNJ02-1 progeny from a cross of elite cultivars, CNJ97-105-4 and NJ98-23. The population was phenotyped for a 3-year period for total yield (TY), mean fruit weight (MFW), and biennial bearing index (BBI), and data were analyzed using mixed models and best linear unbiased predictors (BLUPs). Significant differences between genotypes were observed for all traits. Quantitative trait loci (QTL) analyses using BLUPs identified four MFW QTL on three linkage groups (LGs), three TY QTL on three LGs, and one BBI QTL which co-localized with a TY QTL. Local BLAST of a cranberry nuclear genome assembly identified homologous sequences for the mapped SSRs which were then anchored to 12 pseudo-chromosomes using the linkage map information. Analyses comparing coding regions (CDS) anchored in the cranberry linkage map with grape, kiwifruit, and tomato genomes were performed. Moderate micro-synteny between the cranberry and kiwifruit genomes was detected, although none of the regions overlapped with the QTL identified in this study. The linkage map, QTL, and elite genotypic constitutions identified herein may be applied in subsequent cranberry MAS programs for the development of new cultivars, and potential marker transferability should allow for comparative genomic studies within economically important Vaccinium species.