Novel microsatellite markers acquired from Rubus coreanus Miq. and cross-amplification in other Rubus species.

Gi-An Lee,Young-Ah Jeon,Jung-Ro Lee,Kyung-Ho Ma,Heh-Ran Choi,Jae Song,Jong-Wook Chung,Myung-Chul Lee

doi:10.3390/molecules20046432

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.

Highlights

The Rubus genus in the Rosaceae family consists of more than 600 species grouped in12 subgenera
A total of 358 kb sequences were acquired in 684 clones, and 646 singleton sequences were used to search for simple sequence repeats (SSRs) motifs
Microsatellite analyses of R. coreanus and the genetic relatedness among seven Rubus species based on SSR profiles were not previously reported, whereas several studies have focused on cultivated Rubus species such as red raspberry [10,25]

Summary

Introduction

The Rubus genus in the Rosaceae family consists of more than 600 species grouped in. 12 subgenera. A few of these species, including raspberries, blackberries, dewberries, arctic fruits, and flowering raspberries, have been domesticated and are the focus of breeding programs [1] Both cultivated and wild Rubus species have the potential to interact with other species belonging to different Rubus subgenera. Cross-fertilization within the Rubus genus implies that wild populations could be useful resources to improve domesticated species [2,3,4]. For this reason, Rubus coreanus, which is distributed throughout Southeast Asia, could be a valuable resource for breeding programs and the biotech industry [5,6]. New microsatellite markers with polymorphisms and transferability across species might be valuable tools to evaluate genetic variability and identify genes controlling agronomic traits in the Rubus genus

Results and Discussion

Plant Materials and Genomic DNA Extraction

Construction of an SSR-Enriched Library and Primer Design

PCR Amplification and Genotyping

Conclusions