Developing expressed sequence tag libraries and the discovery of simple sequence repeat markers for two species of raspberry (Rubus L.)

Abstract

BackgroundDue to a relatively high level of codominant inheritance and transferability within and among taxonomic groups, simple sequence repeat (SSR) markers are important elements in comparative mapping and delineation of genomic regions associated with traits of economic importance. Expressed sequence tags (ESTs) are a source of SSRs that can be used to develop markers to facilitate plant breeding and for more basic research across genera and higher plant orders.MethodsLeaf and meristem tissue from ‘Heritage’ red raspberry (Rubus idaeus) and ‘Bristol’ black raspberry (R. occidentalis) were utilized for RNA extraction. After conversion to cDNA and library construction, ESTs were sequenced, quality verified, assembled and scanned for SSRs. Primers flanking the SSRs were designed and a subset tested for amplification, polymorphism and transferability across species. ESTs containing SSRs were functionally annotated using the GenBank non-redundant (nr) database and further classified using the gene ontology database.ResultsTo accelerate development of EST-SSRs in the genus Rubus (Rosaceae), 1149 and 2358 cDNA sequences were generated from red raspberry and black raspberry, respectively. The cDNA sequences were screened using rigorous filtering criteria which resulted in the identification of 121 and 257 SSR loci for red and black raspberry, respectively. Primers were designed from the surrounding sequences resulting in 131 and 288 primer pairs, respectively, as some sequences contained more than one SSR locus. Sequence analysis revealed that the SSR-containing genes span a diversity of functions and share more sequence identity with strawberry genes than with other Rosaceous species.ConclusionThis resource of Rubus-specific, gene-derived markers will facilitate the construction of linkage maps composed of transferable markers for studying and manipulating important traits in this economically important genus.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-015-0629-8) contains supplementary material, which is available to authorized users.

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

“…Moreover, a specific feature in the Rubus spp. breeding system is that multiple species are often utilized in breeding programs [7]. Scientific achievements in molecular biology, and use of molecular markers, in particular, can accelerate the selection process, as they will allow for the assessment of the seedlings with valuable traits at a much earlier stage.…”

“…They are very polymorphic with high information content, co-dominant inheritance, locus specificity, extensive genome coverage and simple detection using labelled primers that flank the microsatellite [9,21], and their ability to distinguish even closely related individuals is particularly important for many crop species [21]. Raspberry researchers have noted the benefits of the SSR markers, but very few molecular markers still exist for Rubus [7,22]. It should be also acknowledged that the breeding process can be accelerated using genomic selection (e.g., [23]), an approach under rapid adoption in many species, which is based on multiple marker-trait associations and does not require linkage maps.…”

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

“…A good choice for breeding purposes is a simple sequence repeat (SSR) or microsatellite markers consisting of tandem repeats (1-6 nucleotides). Due to their codominant inheritance, high level of polymorphism, and abundance in genome, they play an important role in identifying genomic regions associated with the traits of economic importance [13]. SSR markers for the Rubus and Fragaria species were first developed in the early 2000s [14,15] and in subsequent years, a number of studies were carried out, including evaluation of marker transferability.…”

“…In raspberry breeding, interspecific hybridization is widely used, and development of molecular genetic markers that can be transferred between different species, especially with different ploidy, becomes an important task. However, very few molecular genetic markers are known for Rubus, and fewer are transferable between species [13]. All strawberry cultivars now available at the market have been produced using traditional breeding methods [3].…”

Identification of Expressed Sequence Tag-simple Sequence Repeat Markers from the De Novo Transcriptome Sequence of Red Raspberry (Rubus idaeus L.)

“…EST-SSRs from Rubus L. are scarce. Overall, 1149 ESTs were obtained from the cDNA library of the red raspberry cultivar Heritage, and 131 SSR-containing sequences were acquired (Bushakra et al, 2015). In this study, in total, 11,158 SSR-containing unigenes and 235 SSR motifs were identified from 59,173 unigenes after transcriptome assembly and SSR search, and 18.67% unigenes included the SSR sequences.…”