Cranberry microsatellite marker development from assembled next-generation genomic sequence

The large-fruited cranberry (Vaccinium macrocarpon Ait.) is a native North American fruit that is a rich source of dietary phytochemicals with demonstrated and potential benefits for human health. Cranberry is a perennial, self-fertile 2n = 2x = 24 diploid, with a haploid genome size of about 570 Mbp. Present commercial cultivars are only a few breeding and selection cycles removed from their wild progenitors. With an irreducible minimum of 2 years per generation, and significant space and time requirements for phenotypic selection of traits of horticultural interest, genetic enhancement of cranberry could be facilitated by marker-assisted selection (MAS); however, the necessary resources, such as transcript or genomic sequences, molecular genetic markers, and genetic linkage maps, are not yet available. We have begun to generate these resources, starting with next-generation [sequencing by oligonucleotide ligation and detection (SOLiD) mate-paired] sequencing of an inbred cranberry clone, assembling the reads, and developing microsatellite markers from the assembled sequence. Evaluation of the resulting cranberry genomic microsatellite primers has provided a test of the accuracy of the sequence assembly and supplied much-needed molecular markers for a genetic linkage map of cranberry. Mapping these markers will permit sequence scaffolds to be anchored on the genetic map.