The Haplotype-Resolved And Chromosome-Scale Genome Of Vaccinium Stamineum: A New Source Of Genetic Variability For Blueberry Breeding

The Vaccinium genus comprises several commercially important fruit crops, such as blueberry, lingonberry, bilberry, and cranberry. However, past breeding efforts have primarily focused on a limited number of wild relatives as sources of genetic variability, leaving a vast genetic reservoir untapped. In this study, we present the first haplotype-phased reference genome for V. stamineum, a blueberry wild relative with potential for de novo domestication and introgression into breeding programs. V. stamineum is particularly notable for several agronomic traits of interest, such as high soluble sugars, unique flavor profile, and its unique anthocyanin accumulation in fruit pulp, a trait absent in cultivated blueberries.Our assemblies revealed 12 pseudomolecules corresponding to the base chromosome number of Vaccinium species, with a genome size of 529.16 Mb and 493.82 Mb for primary and secondary haplotypes, respectively. Despite a slightly smaller genome than other Vaccinium species, V. stamineum exhibited a higher number of predicted protein-coding genes, while the repetitive elements comprised 39.77% and 42.38% of the primary and secondary haplotypes, respectively. BUSCO analysis indicated 97% transcriptome completeness, supporting the accuracy of gene annotation. Genome-wide alignments showed that V. stamineum haplotypes were highly collinear to each other, as well as to V. corymbosum. However, further validation is required to resolve a putative translocation in chromosome 1 of the primary haplotype. Altogether, this study established a genomic framework that will facilitate the introgression of traits of interest into blueberry breeding programs and support the potential domestication of V. stamineum as a novel fruit crop.