|COLT, KELLY - Salk Institute|
|HARTWICK, NOLAN - Salk Institute|
|ABRAMSON, BRADLEY - Salk Institute|
|VORSA, NICHOLI - Rutgers University|
|MICHAEL, TODD - Salk Institute|
Submitted to: PLOS ONE
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/19/2022
Publication Date: 3/7/2022
Citation: Kawash, J.K., Colt, K., Hartwick, N.T., Abramson, B.W., Vorsa, N., Polashock, J.J., Michael, T.P. 2022. Contrasting a reference cranberry genome to a crop wild relative provides insights into adaptation, domestication, and breeding. PLoS ONE. 17(3):e0264966. https://doi.org/10.1371/journal.pone.0264966.
Interpretive Summary: Cranberry (Vaccinium macrocarpon) is a low-growing woody perennial native to North America that is both economically important and has significant health benefits. Breeding in cranberry is a slow process and the current gene pool is limited. To speed the breeding program and expand the gene pool, we generated a chromosome-resolved V. macrocarpon reference genome and a high-quality draft genome of V. oxycoccos, a wild relative of cultivated cranberry. We identified genomic regions in both species that are targets of improvement. The regions identified include environmental response and plant architecture genes, the characterization of which will be important for future breeding in cranberry. The sequence data have been made publicly available and serve as an important resource for improvement of cranberry and related crops, such as blueberry.
Technical Abstract: Cranberry (Vaccinium macrocarpon) is a member of the Heath family (Ericaceae) and is a temperate low-growing woody perennial native to North America that is both economically important and has significant health benefits. While some native varieties are still grown today, breeding programs over the past 50 years have made significant contributions to improving disease resistance, fruit quality and yield. An initial genome sequence of an inbred line of the wild selection ‘Ben Lear,’ which is parent to multiple breeding programs, provided insight into the gene repertoire as well as a platform for molecular breeding. Recent breeding efforts have focused on leveraging the circumboreal V. oxycoccos, which forms interspecific hybrids with V. macrocarpon, offering to bring in novel fruit chemistry and other desirable traits. Here we present an updated, chromosome-resolved V. macrocarpon reference genome, and compare it to a high-quality draft genome of V. oxycoccos. Leveraging the chromosome resolved cranberry reference genome, we confirmed that the Ericaceae has undergone two whole genome duplications that are shared with blueberry and rhododendron. Leveraging resequencing data for ‘Ben Lear’ inbred lines, as well as several wild and elite selections, we identified common regions that are targets of improvement. These same syntenic regions in V. oxycoccos, were identified and represent environmental response and plant architecture genes. These data provide insight into early genomic selection in the domestication of a native North American berry crop.