Novel Microsatellite Markers Acquired from Rubus coreanus Miq. and Cross-Amplification in Other Rubus Species

Abstract

The Rubus genus consists of more than 600 species that are distributed globally. Only a few Rubus species, including raspberries and blueberries, have been domesticated. Genetic diversity within and between Rubus species is an important resource for breeding programs. We developed genomic microsatellite markers using an SSR-enriched R. coreanus library to study the diversity of the Rubus species. Microsatellite motifs were discovered in 546 of 646 unique clones, and a dinucleotide repeat was the most frequent (75.3%) type of repeat. From 97 microsatellite loci with reproducible amplicons, we acquired 29 polymorphic microsatellite markers in the Rubus coreanus collection. The transferability values ranged from 59.8% to 84% across six Rubus species, and Rubus parvifolius had the highest transferability value (84%). The average number of alleles and the polymorphism information content were 5.7 and 0.541, respectively, in the R. coreanus collection. The diversity index of R. coreanus was similar to the values reported for other Rubus species. A phylogenetic dendrogram based on SSR profiles revealed that seven Rubus species could be allocated to three groups, and that R. coreanus was genetically close to Rubus crataegifolius (mountain berry). These new microsatellite markers might prove useful in studies of the genetic diversity, population structure, and evolutionary relationships among Rubus species.

Transferability and Polymorphism of SSR Markers Located in Flavonoid Pathway Genes in Fragaria and Rubus Species

“…A total of 118 SSR loci were identifies in 21 genes, and pentanucleotide motifs were the most abundant. Our result is in contrast to previous findings identifying trinucleotide [21,37] as the most frequent genic repeats in Rosaceae plant species, unlike dinucleotide motifs that were the most frequent among non-genic random genomic repeats [36,48,49]. The difference can be also explained, at least partly, by less stringent search parameters that were used in our study compared to those that are typically used in searches for random genomic SSRs, but they were similar with those that are usually used for the search of SSRs in coding regions.…”

“…In our study, the mean values of H o , H e , and PIC were 0.23, 0.51, and 0.46, respectively. These values were lower than those observed in R. idaeus [28] and R. coreanus [49]. This may be because the gene sequences, from which our SSR markers are derived, are more conserved compared to random genomic SSRs used in these published reports.…”

Assessment of Genetic Diversity in Differently Colored Raspberry Cultivars Using SSR Markers Located in Flavonoid Biosynthesis Genes

“…There are several studies that used random genomic SSR markers to assess genetic diversity in cultivars within [8,28] and between [29] different species. However, we are unaware of studies in which genetic diversity would be assessed using markers located in genes of any metabolic pathway and the biosynthesis of flavonoids, in particular.…”

ANÁLISIS DE LA DIVERSIDAD GENÉTICA DE LA MORA(Rubus spp.)EN EL DEPARTAMENTO DE BOYACÁ

“…[18], desarrollaron nuevos marcadores microsatélites a partir de de Rubus coreanus y probaron su transferibilidad a otras especies de Rubus, encontrando valores promedios de heterocigosidad observada y esperada de 0,56 y 0,54. los anteriores estudios ponen de manifiesto la gran diversidad genética del género Rubus lo cual se refleja por su gran plasticidad fenotípica y molecular.…”