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Title: Development and validation of 697 novel polymorphic genomic and EST-SSR Markers in the American cranberry (Vaccinium macrocarpon Ait.)

item SCHLAUTMAN, BRANDON - University Of Wisconsin
item FAJARDO, DIEGO - University Of Wisconsin
item BOUGIE, TIERNEY - University Of Wisconsin
item Wiesman, Eric
item Polashock, James
item VORSA, NICHOLI - Rutgers University
item Steffan, Shawn
item Zalapa, Juan

Submitted to: Molecules
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/26/2015
Publication Date: 1/27/2015
Publication URL:
Citation: Schlautman, B., Fajardo, D., Bougie, T., Wiesman, E., Polashock, J., Vorsa, N., Steffan, S., Zalapa, J. 2015. Development and validation of 697 novel polymorphic genomic and EST-SSR Markers in the American cranberry (Vaccinium macrocarpon Ait.). Molecules. 20(2):2001-2013.

Interpretive Summary: The growing importance of cranberries due of the potential health benefits provided by their array of phytochemical constituents has created a demand for new cultivars which meet the economic, social, and environmental demands of cranberry growers, processors, and consumers. The industry currently relies on only a handful of cultivars with a narrow genetic base. Cranberry improvement through classical breeding approaches has been limited but successful; however, most commercial varieties are separated from their wild brethren by only a few breeding and selection cycles. Because of the increased demand for new cranberry cultivars, many recent investigations have aimed to increase the genetic resources available for cranberry molecular crop improvement. Multiple sets of microsatellite or short sequence repeat (SSR) markers have been developed in blueberry and transferred to cranberry or have been developed by mining cranberry next generation sequencing data. However, despite these efforts to develop genetic resources, fewer than 200 molecular markers have been tested and validated, and only 136 markers have been added to a cranberry genetic linkage map. Abundant genome-wide molecular markers are a prerequisite for initiating a marker-assisted selection (MAS) program. Therefore, the primary intent of this study was to increase the number of markers available for genetic research in cranberry by testing and validating polymorphic SSR loci in a set of genotypes of diverse, but known origins. The SSR loci developed herein will allow for the identification of quantitative trait loci (QTL) and candidate genes of agronomic importance. This information will be essential for the development of innovative plant breeding systems and MAS programs aimed at generating and releasing new cultivars adapted to meet the current and future challenges of the cranberry industry. Broader implications may follow by adapting these markers for use in comparative genomic and evolutionary studies within the genus Vaccinium and the family Ericaceae.

Technical Abstract: The American cranberry, Vaccinium macrocarpon Ait., is an economically important North American fruit crop that is consumed because of its unique flavor and potential health benefits. However, a lack of abundant, genome-wide molecular markers has limited the adoption of modern molecular assisted selection approaches in cranberry breeding programs. To increase the number of available markers in the species, this study identified, tested, and validated microsatellite markers from existing nuclear and transcriptome sequencing data. In total, new primers were designed, synthesized, and tested for 979 SSR loci; 697 of the markers amplified allele patterns consistent with single locus segregation in a diploid organism and were considered polymorphic. Of the 697 polymorphic loci, 507 were selected for additional genetic diversity and segregation analyses in 29 cranberry genotypes. More than 95% of the 507 loci did not display segregation distortion at the p < 0.05 level and contained moderate to high levels of polymorphism with a polymorphic information content > 0.25. This comprehensive collection of developed and validated microsatellite loci represents a substantial addition to the molecular tools available for geneticists, genomicists, and breeders in cranberry and Vaccinium.