BackgroundHighbush blueberry (Vaccinium corymbosum) has long been consumed for its unique flavor and composition of health-promoting phytonutrients. However, breeding efforts to improve fruit quality in blueberry have been greatly hampered by the lack of adequate genomic resources and a limited understanding of the underlying genetics encoding key traits. The genome of highbush blueberry has been particularly challenging to assemble due, in large part, to its polyploid nature and genome size.FindingsHere, we present a chromosome-scale and haplotype-phased genome assembly of the cultivar “Draper,” which has the highest antioxidant levels among a diversity panel of 71 cultivars and 13 wild Vaccinium species. We leveraged this genome, combined with gene expression and metabolite data measured across fruit development, to identify candidate genes involved in the biosynthesis of important phytonutrients among other metabolites associated with superior fruit quality. Genome-wide analyses revealed that both polyploidy and tandem gene duplications modified various pathways involved in the biosynthesis of key phytonutrients. Furthermore, gene expression analyses hint at the presence of a spatial-temporal specific dominantly expressed subgenome including during fruit development.ConclusionsThese findings and the reference genome will serve as a valuable resource to guide future genome-enabled breeding of important agronomic traits in highbush blueberry.

BackgroundAlthough draft genomes are available for most agronomically important plant species, the majority are incomplete, highly fragmented, and often riddled with assembly and scaffolding errors. These assembly issues hinder advances in tool development for functional genomics and systems biology.FindingsHere we utilized a robust, cost-effective approach to produce high-quality reference genomes. We report a near-complete genome of diploid woodland strawberry (Fragaria vesca) using single-molecule real-time sequencing from Pacific Biosciences (PacBio). This assembly has a contig N50 length of ∼7.9 million base pairs (Mb), representing a ∼300-fold improvement of the previous version. The vast majority (>99.8%) of the assembly was anchored to 7 pseudomolecules using 2 sets of optical maps from Bionano Genomics. We obtained ∼24.96 Mb of sequence not present in the previous version of the F. vesca genome and produced an improved annotation that includes 1496 new genes. Comparative syntenic analyses uncovered numerous, large-scale scaffolding errors present in each chromosome in the previously published version of the F. vesca genome.ConclusionsOur results highlight the need to improve existing short-read based reference genomes. Furthermore, we demonstrate how genome quality impacts commonly used analyses for addressing both fundamental and applied biological questions.

The germplasm base of strawberries is restricted. The major cultivated strawberry species, Fragaria ·ananassa, originated ' '250 years ago when South American F. chiloensis subsp. chiloensis forma chiloensis and North American F. virginiana subsp. virginiana accidentally hybridized in European gardens. Since that time, only a handful of native clones have been used by breeders. As a novel way to expand the germplasm base of the strawberry, we preselected native clones of F. virginiana and F. chiloensis for a wide range of horticulturally important characteristics and then reconstructed F. ·ananassa by crossing superior clones of each. Before crossing between species, we undertook one round of selection within species to maximize diversity. Reconstruction appeared to be an effective method of strawberry improvement, because superior families and individuals were identified that had outstanding vigor, high productivity, seed set, fruit color, and firmness. None of the fruit were of commercial size, but one reconstruction family, FVC 11 [(F. virginiana Frederick 9 · LH 50-4) · (F. chiloensis Scotts Creek · 2 MAR 1A)], had individuals with fruit weights of almost 20 g.

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Controlled-atmosphere storage had little effect on the quality of fruit of eight cultivars held under 2 kPa oxygen (O2) and 8 kPa carbon dioxide (CO2) versus ambient air. ‘Elliott’ fruit harvested from bushes with only 30% ripe fruit had significantly better storage quality than fruit picked later; however, there was no significant difference in the storage life of fruit that was stored fully blue versus partially green. Fruit from the first harvest of four cultivars had superior storage quality to that of the second. In one comparison of the long-term storability of nine cultivars, ‘Bluegold’, ‘Brigitta’, and ‘Legacy’ performed the best, storing for 4 to 7 weeks. In another postharvest trial of 17 cultivars, ‘Brigitta’ stored the longest (8 weeks) followed by ‘Aurora’ and ‘Draper’ (7 weeks). The most resistant genotypes to Alternaria spp. were ‘Brigitta’, ‘Aurora’, ‘Elliott’, and ‘Draper’, whereas the most resistant genotypes to Colletotrichum spp. were ‘Elliott’, ‘Brigitta’, ‘Toro’, ‘Draper’, and ‘Bluejay’.