A high-recovery, high-density targeted genotyping platform for cranberry

The American cranberry (Vaccinium macrocarpon) is a commercially important berry species native to North America. Cranberry is a popular fruit crop with many known health benefits. Thus far, genotyping-by-sequencing (GBS) was the only high-throughput genotyping technique available in cranberry. While GBS is cost efficient, it has the disadvantage of producing variant calls that cannot be easily transferred between populations and across studies. In this study, we report the development of the first targeted high-throughput genotyping platform for cranberry. The Flex-Seq genotyping technology offers repeatable, high-recovery, and high-density single nucleotide polymorphisms as well as concomitant haplotypes. The cranberry Flex-Seq platform contains 17,502 loci, boasting a recovery rate of 99.8% in a diversity panel of 192 cranberry accessions. The level of incompatible marker inheritance in 22 analyzed parent-offspring trios ranged from 1.1% to 13%, with an average of 5.5%. Nine of the 22 crosses had an excess of incompatible markers, indicating inconsistent parentage that could be investigated further. In quantitative trait loci (QTLs) analyses, Flex-Seq identified a greater number of QTLs compared to previously used GBS as well as higher overall logarithm of odds scores for overlapping QTLs. In addition, construction of locus haplotypes resulted in a substantial improvement in resolving the relatedness of cranberry accessions. This platform will aid in utilizing the untapped potential of wild cranberry, mapping key traits with higher precision, and ensuring robust characterization of accessions. The developed genotyping platform will help in the rapid improvement of cranberry cultivars to benefit breeders, growers, and consumers.