Development and Validation of 697 Novel Polymorphic Genomic and EST-SSR Markers in the American Cranberry (Vaccinium macrocarpon Ait.)

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.

Informativeness of minisatellite and microsatellite markers for genetic analysis in papaya

“…Similar to the average number of alleles per locus, a lower polymorphism rate and information content were observed for the minisatellite loci. Similar results were observed in cranberry (Vaccinium macrocarpon), in which an average of 2.57 alleles per locus was identified, and the average He and Ho values were 0.45 and 0.66, respectively, when analyzing seven microsatellites with a minimum motif of pentanucleotides (Schlautman et al 2015). These values are lower compared with the analysis of nine di-and tri-nucleotide microsatellites using the same 13 cranberry cultivars, where an average of 4.51 alleles per locus and average He and Ho values of 0.61 and 0.70, respectively, were identified.…”

Development of a high-density cranberry SSR linkage map for comparative genetic analysis and trait detection

“…A comprehensive screen of 881 previously published SSR loci for V. macrocarpon identified 573 SSR markers segregating in the CNJ02-1 population (Bassil et al 2009;Georgi et al 2011;Zhu et al 2012;Georgi et al 2013;Schlautman et al 2015). A complete list of the SSR markers used and their publication origins can be found in Online Resource 1.…”

“…The 573 SSR markers were divided into groups of three primer pairs with non-overlapping allele size ranges for use in subsequent multiplex PCR reactions. PCR reactions and fragment analyses were performed according to Schlautman et al (2015), except the 2.0 ll of ddH 2 O was replaced with 0.5 ll of forward and 0.5 ll of reverse primer from two additional SSR primer pairs so that the final PCR was a 39 multiplex reaction.…”

“…Although the marker density could be considered low for localizing genomic regions linked or associated with the inheritance of traits with continuous distributions, QTL were detected for field fruit rot resistance, sound fruit yield, fruit weight, titratable acidity, and proanthocyanidin content (Georgi et al 2013). More recently, a transcriptome and genome assembly were published , and based on these genetic resources and an additional genome assembly (Fajardo et al 2013;Fajardo et al 2014), 697 polymorphic SSRs were designed and validated using a cranberry diversity panel (Schlautman et al 2015).…”

Genetics and Genomics of Cultivated Eggplants and Wild Relatives

“…Trinucleotide repeat motifs were the most abundant (63.6% and 62.7%), followed by dinucleotide (26.6% and 28.4%) and tetranucleotide (9.8% and 8.9%) repeats. The prevalence of trinucleotide motifs is well documented in literature in eggplant (Stàgel et al, 2008;Barchi et al, 2011) as well as in other crops (Blanca et al, 2011;Schlautman et al, 2015). Metzgar et al (2000) hypothesized that non-triplet SSRs show higher risks of frameshift mutation in coding regions and the selection against these mutations would reduce their chances of fixation.…”