SNP Mining in Blueberry Using Illumina GAII Sequencing

Genomic tools in blueberry are scarce despite the increased demand for and consumption of these fruits. The overall aim of a recently funded Specialty Crop Research Initiative project, “Generating Genomic Tools for Blueberry Improvement,” is to develop genomic tools for molecular breeding in blueberry. Specific objectives include the development of molecular markers for use in genetic diversity studies and construction of genetic linkage maps in diploid and tetraploid blueberries. Single nucleotide polymorphism (SNP) markers are the most prevalent genetic markers and well-adapted to high throughput variant detection. The advent of next-generation sequencing has dramatically increased the speed while decreasing the cost of DNA sequencing, thus enabling efficient variant discovery in plants with modest genomic resources. The Illumina Genome Analyzer II was used to identify SNPs in four diploid and five tetraploid blueberry lines that included parents of the mapping populations. We generated ~20 Gbp (~33x coverage of the haploid genome) of genomic DNA sequence data from four diploid and five tetraploid blueberry lines. These data were co-assembled into a draft reference genome assembly and the input reads were aligned to this reference to identify putative SNP markers. We plan to use these markers to identify quantitative trait loci associated with cold hardiness, chilling requirement, and fruit quality traits in highbush blueberry (Vaccinium corymbosum).