Breeding efforts in the American cranberry (Vaccinium macrocarpon Ait.), a North American perennial fruit crop of great importance, have been hampered by the limited genetic and phenotypic variability observed among cultivars and experimental materials. Most of the cultivars commercially used by cranberry growers today were derived from a few wild accessions bred in the 1950s. In different crops, wild germplasm has been used as an important genetic resource to incorporate novel traits and increase the phenotypic diversity of breeding materials. Vaccinium microcarpum (Turcz. ex Rupr.) Schmalh. and V. oxycoccos L., two closely related species, may be cross-compatible with the American cranberry, and could be useful to improve fruit quality such as phytochemical content. Furthermore, given their northern distribution, they could also help develop cold hardy cultivars. Although these species have previously been analyzed in diversity studies, genomic characterization and comparative studies are still lacking. In this study, we sequenced and assembled the organelle genomes of the cultivated American cranberry and its wild relative, V. microcarpum. PacBio sequencing technology allowed us to assemble both mitochondrial and plastid genomes at very high coverage and in a single circular scaffold. A comparative analysis revealed that the mitochondrial genome sequences were identical between both species and that the plastids presented only two synonymous single nucleotide polymorphisms (SNPs). Moreover, the Illumina resequencing of additional accessions of V. microcarpum and V. oxycoccos revealed high genetic variation in both species. Based on these results, we provided a hypothesis involving the extension and dynamics of the last glaciation period in North America, and how this could have shaped the distribution and dispersal of V. microcarpum. Finally, we provided important data regarding the polyploid origin of V. oxycoccos.

Knowledge of the genetic diversity in populations of crop wild relatives (CWR) can inform effective strategies for their conservation and facilitate utilization to solve agricultural challenges. Two crop wild relatives of the cultivated cranberry are widely distributed in the US. We studied 21 populations of Vaccinium macrocarpon Aiton and 24 populations of Vaccinium oxycoccos L. across much of their native ranges in the US using 32 simple sequence repeat (SSR) markers. We observed high levels of heterozygosity for both species across populations with private alleles ranging from 0 to 26. For V. macrocarpon, we found a total of 613 alleles and high levels of heterozygosity (H_O = 0.99, H_T = 0.75). We also observed high numbers of alleles (881) and levels of heterozygosity (H_O = 0.71, H_T = 0.80) in V. oxycoccos (4x). Our genetic analyses confirmed the field identification of a native population of V. macrocarpon on the Okanogan-Wenatchee National Forest in the state of Washington, far outside the previously reported range for the species. Our results will help to inform efforts of the United States Department of Agriculture Agricultural Research Service (USDA-ARS) and the United States Forest Service (USFS) to conserve the most diverse and unique wild cranberry populations through ex situ preservation of germplasm and in situ conservation in designated sites on National Forests.

Plant breeding continuously evolves to satisfy the needs of the growing population, but in many crops, it has resulted in a decline in the genetic diversity available. Therefore, increasing knowledge of the range, genetic relationships, and diversity among crop wild relatives (CWR) is essential for the efficient use of available germplasm in breeding programs. In cranberries (Vaccinium macrocarpon Ait.), most cultivars share the same genetic background based on only a few wild selections. This limits the breeding pool for selection to support the cranberry industry. Therefore, we studied 36 wild populations of V. macrocarpon and V. oxycoccos L. across Wisconsin and Minnesota using 32 simple sequence repeat (SSR) markers. We found high levels of heterozygosity in both species, despite previous molecular markers studies revealing low genetic variation. In V. macrocarpon, a total of 294 alleles and moderate to high levels of heterozygosity (observed [H_O] = 0.51, total [H_T] = 0.66) were found. As expected for outcrossed polyploid species (4x), higher levels of heterozygosity (H_O = 0.81, H_T = 0.83) were found in V. oxycoccos than in V. macrocarpon. A comparison between wild V. macrocarpon with a group of cultivated and experimental hybrids found a distinct separation between both groups, suggesting there is diversity in the wild that needs to be explored and incorporated into breeding programs. The results of our studies are the first to explore in depth the genetic diversity of wild cranberry populations in the upper midwestern United States and provide novel information to support in situ conservation efforts to protect CWR of one of the few North American native crops.