Since its domestication 200 years ago, breeding of the American cranberry (Vaccinium macrocarpon) has relied on phenotypic selection because applicable resources for molecular improvement strategies such as marker-assisted selection (MAS) remain limited. To enable MAS in cranberry, the first high-density SSR linkage map with 541 markers representing all 12 cranberry chromosomes was constructed for the CNJ02-1 progeny from a cross of elite cultivars, CNJ97-105-4 and NJ98-23. The population was phenotyped for a 3-year period for total yield (TY), mean fruit weight (MFW), and biennial bearing index (BBI), and data were analyzed using mixed models and best linear unbiased predictors (BLUPs). Significant differences between genotypes were observed for all traits. Quantitative trait loci (QTL) analyses using BLUPs identified four MFW QTL on three linkage groups (LGs), three TY QTL on three LGs, and one BBI QTL which colocalized with a TY QTL. Local BLAST of a cranberry nuclear genome assembly identified homologous sequences for the mapped SSRs which were then anchored to 12 pseudo-chromosomes using the linkage map information. Analyses comparing coding regions (CDS) anchored in the cranberry linkage map with grape, kiwifruit, and tomato genomes were Electronic supplementary material The online version of this article (

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.

American cranberry (Vaccinium macrocarpon) is a perennial, woody plant species, native to North American bogs and wetlands. Cranberries represent one of the few agriculturally important native plants in which wild gene pools are still readily available within the undeveloped wetlands of the northern US and Canada. Earlier studies have reported low genetic variation in V. macrocarpon at the species and population level. However, in this study, we characterised 229 individuals of wild V. macrocarpon and V. oxycoccos (small cranberry) from Wisconsin and 22 accessions using microsatellite markers and observed substantial genetic variation and differentiation within and among populations and species. While V. macrocarpon was analysed using 108 alleles from 11 microsatellite loci revealing 42 unique genotypes, V. oxycoccos was analysed using 156 alleles from eight loci revealing 28 unique genotypes. There were a total of 182 alleles found in both species combined with 156 of those alleles present in V. oxycoccos and 84 alleles found in V. macrocarpon. All eight loci possessed species-specific alleles with V. oxycoccos possessing 98 private alleles versus 26 private alleles found V. macrocarpon, and 58 alleles were found in common between both species. Our data will be valuable not only for future wild cranberry diversity and population genetics research, but for other cranberry breeding and genetics studies.

Sugarbeet is a major source of refined sucrose and increasingly grown for biofuel production. Demand for higher productivity for this crop requires greater knowledge of sugarbeet physiology, pathology, and genetics, which can be advanced by the development of new genomic resources. Towards this end, a sugarbeet transcriptome of expressed genes from leaf and root tissues at varying stages of development and production, and after elicitation with jasmonic acid (JA) or salicylic acid (SA), was constructed and used to generate simple sequence repeat (SSR) markers. The transcriptome was generated via paired-end RNA sequencing and contains 82,404 unigenes. A total of 37,207 unigenes were annotated, of which 9480 were functionally classified using clusters of orthologous groups (COG) annotations, 17,191 were classified into biological process, molecular function, or cellular component using gene ontology (GO) terms, and 17,409 were assigned to 126 metabolic pathways using Kyoto Encyclopedia of Genes and Genomes (KEGG) identifiers. A SSR search of the transcriptome identified 7680 SSRs, including 6577 perfect SSRs, of which 3834 were located in unigenes with ungapped sequence. Primer-pairs were designed for 288 SSR loci, and 72 of these primer-pairs were tested for their ability to detect polymorphisms. Forty-three primer-pairs detected single polymorphic loci and effectively distinguished diversity among eight B. vulgaris genotypes. The transcriptome and SSR markers provide additional, public domain genomic resources for an important crop plant and can be used to increase understanding of the functional elements of the sugarbeet genome, aid in discovery of novel genes, facilitate RNA-sequencing based expression research, and provide new tools for sugarbeet genetic research and selective breeding. Sugarbeet (Beta vulgaris L.) is an herbaceous dicotyledon and member of the Amaranthaceae family. Grown primarily for the production of refined sucrose, sugarbeet provides approximately 22% of the world's sugar (Südzucker, 2013). It is also the source of two highenergy animal feeds (beet molasses and beet pulp), and is increasingly grown for biofuel production (Harland et al., 2006;Panella, 2010). Sugarbeet is grown in 42 countries on five continents, with Europe and North America producing more than 60% of the crop. Other economically important members of the species include table beet, chard, and fodder beet. Sugarbeet production is challenged by an array of abiotic and biotic stresses that reduce biomass and sucrose content. Insufficient water, excessively hot or cold temperatures, and saline soils prevent the crop from reaching its full genetic potential and can reduce yield by as much as 50% (Boyer, 1982;Ober and Rajabi, 2010). Insects, including the sugarbeet root maggot (Tetanops myopaeformis von Röder) and root aphid (Pemphigus betae Doane),