A Functional, Consensus Linkage Map of Blueberry and Cranberry

Blueberry (Vaccinium spp.) is an economically important small fruit crop (564.4 million pounds harvested in the U.S. with a value of $850.9 million in 2012), but relatively few genomic resources are available to researchers and breeders for the purposes of plant improvement. Traditional blueberry breeding is constrained by severe inbreeding depression, the complex nature of the polyploid genome (2n=24, 4n =48 and 6n=72), and the relatively long period of juvenility. With the advent of next-generation sequencing (NGS) and the development of associated informatics tools to interpret this information, blueberry breeding efforts are likely to benefit immensely from these technologies. Toward this end, a genomic scaffolding of 9,170 sequences with an N50 of 275 kb of the diploid blueberry 'W85-20' was created through a combination of NGS sequencing and Sanger BAC end reads. Four genetic linkage maps of blueberry and cranberry (a close relative in the genus Vaccinium) were also constructed for multiple purposes including understanding the genetic basis of important fruit characteristics, cold hardiness and climatic adaptability. These maps have for the most part used unrelated molecular markers and which include RAPDs, ESTs, EST and genomic-derived simple sequence repeats (SSRs), and SNPs. The goal of this research was to create a blueberry/cranberry consensus map of the four individual maps based on the scaffold locations of the associated molecular markers. Multiple software programs were used to predict the genomic location of the markers and to provide alignment (and in some cases, orientation) of genomic scaffolding.  New SSRs markers were also designed for larger scaffolds and for targeting genes in the anthocyanin biosynthesis pathway. Locations of BAC end sequences are highlighted to provide a framework for further refinement of the blueberry sequence assembly. The map is functional in that it represents more than a third of the blueberry genome including several thousand annotated genes. This research provides both an immediate resource to current blueberry researchers and a roadmap for the completion of the sequenced blueberry genome.