Patterns of simple sequence repeats in cultivated blueberries (Vaccinium section Cyanococcus spp.) and their use in revealing genetic diversity and population structure

Blueberry (Vaccinium section Cyanococcus) is an important small fruit crop native to North America. Relationships among the primary species known as ‘blueberry’ has been a source of speculation due to the out-breeding nature of the crop, the use of intra-specific hybridization and open-pollinated selection in breeding programs, and the lack of genomic resources to adequately address the issue. The objectives of this study were to characterize simple sequence repeats (SSRs) from an emerging genomic draft sequence, develop useful molecular markers and provide an in-depth analysis of genetic diversity and population structure in blueberry using a broad range of cultivated blueberry accessions representing multiple species, ploidy levels and sources of origin. Genomic scaffolding was assembled from the whole-genome sequencing of a diploid V. corymbosum accession ‘W8520.’ From the assembled 358 Mb sequence, a total number of 43,594 SSRs were identified (122 per Mb). Among genomic regions, SSRs were longest and occurred most frequently in predicted 5′ untranslated regions (5′ UTR), while SSRs were shortest and least common in the predicted coding sequences. AG/CT and AAG/CTT were the most frequent motifs while CG/CG and CCG/CGG motifs were the rarest di- and trinucleotide motifs, respectively. For analysis of genetic diversity and population structure, 42 genomic SSR and EST–SSR markers with an average of 14.2 alleles and 56.0 allele phenotypes per locus were used to genotype a diverse blueberry population of 150 accessions. Cluster analysis grouped the 150 accessions in a manner consistent with known information regarding species, ploidy levels and pedigree. The analysis of population structure among blueberry accessions revealed inter- and intra-specific levels of stratification. Rabbiteye blueberry (V. virgatum) represents a genetically distinct subgroup within Cyanococcus. Three additional subpopulations were detected among highbush varieties that are largely attributable to distinctions between northern and southern highbush and founder effects of a single cultivar (‘Weymouth’). The identification of substructure that correlates with known pedigree information, and the availability of new genomic molecular markers will facilitate future evolutionary and genetic studies in blueberry.