Genotyping-by-sequencing identifies historical breeding stages of the recently domesticated American cranberry

Authors: DIAZ-GARCIA, LUIS - Instituto Nacional De Investigaciones Forestales Y Agropecuarias (INIFAP); COVARRUBIAS-PAZARAN, GIOVANNY - International Maize & Wheat Improvement Center (CIMMYT); JOHNSON-CICALESE, JENNIFER - Rutgers University; VORSA, NICHOLI - Rutgers University; Zalapa, Juan

Submitted to: Frontiers in Plant Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/20/2020
Publication Date: 12/16/2020
Citation: Diaz-Garcia, L., Covarrubias-Pazaran, G., Johnson-Cicalese, J., Vorsa, N., Zalapa, J.E. 2020. Genotyping-by-sequencing identifies historical breeding stages of the recently domesticated American cranberry. Frontiers in Plant Science. 12. Article 633310. https://doi.org/10.3389/fpls.2020.607770.
DOI: https://doi.org/10.3389/fpls.2020.607770

Interpretive Summary: The American cranberry is a recently domesticated species less than 200 years ago. The USDA began the first breeding program for the species in 1929, but after the first generation of cultivars were released in the 1950s, the program was discontinued. Decades later, renewed efforts for breeding cranberry cultivars at Rutgers University and the University of Wisconsin yielded the first modern cultivars in the 2000’s. Trait data suggests that cultivated cranberries have changed significantly in terms of fruiting habits compared to wild materials. However, due to the few generations of selection and short domestication history of the crop, it is unclear how much they differ genetically. Moreover, the extent that domestication and breeding efforts have shaped cranberry remains mostly obscure. Thus, a historical collection composed of 362 accessions, spanning wild germplasm, first-, second-, and third-generation selection cycles was studied to unravel the breeding and domestication history of cranberry. Genetic analyses showed directional differences among the stages of cranberry domestication and subsequent breeding. Furthermore, genetic analyses revealed a partially defined progressive loss of diversity when transitioning from early domestication stages to current cranberry forms. Breeding cycles differed for total yield and average fruit weight, but not for fruit chemistry traits. Genetic analysis allow us to identify genetic markers associated with average fruit weight and fruit rot, which are two traits of great agronomic relevance and could be further used to accelerate cranberry genetic improvement and benefit growers and consumers.

Technical Abstract: The American cranberry (Vaccinium macrocarpon Ait.) is a recently domesticated species less than 200 years ago. The USDA began the first breeding program for the species in 1929, but after the first generation of cultivars were released in the 1950s, the program was discontinued. Decades later, renewed efforts for breeding cranberry cultivars at Rutgers University and the University of Wisconsin yielded the first modern cultivars in the 2000’s. Phenotypic data suggests that cultivated cranberries have changed significantly in terms of fruiting habits compared to wild materials. However, due to the few generations of selection and short domestication history of the crop, it is unclear how much they differ genetically. Moreover, the extent that domestication and breeding efforts have shaped the genetic and phenotypic variation of cranberry remains mostly obscure. Here, a historical collection composed of 362 accessions, spanning wild germplasm, first-, second-, and third-generation selection cycles was studied to unravel the breeding and domestication history of cranberry. Genome-wide sequence variation at more than 20,000 loci showed directional differences among the stages of cranberry domestication and subsequent breeding. Furthermore, diversity analysis and population structure revealed a partially defined progressive bottleneck when transitioning from early domestication stages to current cranberry forms. Additionally, breeding cycles correlated with phenotypic variation for yield-related traits, but not for fruit metabolites. Particularly, average fruit weight and yield, which were common target traits during early selection attempts, increased dramatically in second and third-generation cultivars, whereas other fruit quality traits such as anthocyanin content, Brix, and acids, showed comparable variation among all breeding stages. Genome-wide association mapping in this diversity panel allowed us to identify marker-trait associations for average fruit weight and fruit rot, which are two traits of great agronomic relevance and could be further exploited to accelerate cranberry genetic improvement. This study constitutes the first genome-wide analysis of cranberry genetic diversity, which explored how the recurrent use of wild germplasm and first-generation selections into cultivar development have shaped the evolutionary history of this crop species.