A blackberry (Rubus L.) expressed sequence tag library for the development of simple sequence repeat markers

Abstract

Background: The recent development of novel repeat-fruiting types of blackberry (Rubus L.) cultivars, combined with a long history of morphological marker-assisted selection for thornlessness by blackberry breeders, has given rise to increased interest in using molecular markers to facilitate blackberry breeding. Yet no genetic maps, molecular markers, or even sequences exist specifically for cultivated blackberry. The purpose of this study is to begin development of these tools by generating and annotating the first blackberry expressed sequence tag (EST) library, designing primers from the ESTs to amplify regions containing simple sequence repeats (SSR), and testing the usefulness of a subset of the EST-SSRs with two blackberry cultivars.

Identification of SSR markers using soybean (Glycine max) ESTs from globular stage embryos

“…The occurrence of SSRs in ESTs provides an opportunity to use currently available ESTs in databases for SSR development (Qiu et al 2000). This strategy has been used successfully in plant species such as grape (Vitis vinifera L.) (Scott et al 2000), wheat (Triticum aestivum L.) (Hackauf and Wehling, 2002;Peng and Lapitan, 2005), barley (Hordeum vulgare L.) (Thiel et al 2003), strawberry (Fragaria x ananassa) (Folta et al 2005), orange (Citrus sinensis osbeck) (Jiang et al 2006), foxtail millet (Setaria italica) (Jia et al 2007), ryegrass (Lolium perenne) (Asp et al 2007), blackberry (Rubus L) (Lewers et al 2008). …”

RuGT1, A New Candidate Proanthocyanidin-related Glycosyltransferase?

“…It was 796 bp in length, containing an 84 bp intron, encoding 238 amino acids. Further screening of other blackberry cDNA libraries (Lewers et al, 2008) did not came up with any EST sequences with significant similarities. Blast analysis revealed the relationship between RuGT1 and other GTs as well as biochemically characterized plant glycosyltransferases.…”

“…qPCR primers qGT-F: 5'-GGA GCT GAA GAA AAG ACT CCA GAA-3' and QGT-R: 5'-ACT GGC CGG ACC AGA TGT AG-3' were picked out in primer express 3.0 avoiding cross homology to other sequences in the blackberry EST library (Lewers et al, 2008). Expression analysis of the RuGT was done by real-time qPCR, using SYBR green method on a CFX96 real-time cycler (BIO-RAD).…”

Identification of Four New Est-Based Markers on the Apple (MALUS ⋉ DOMESTICA) Genetic Map

“…Transfer of markers became useful and reliable for comparative mapping and colinearity assessment (Pierantoni et al 2004). However, the efficiency of markers transferability is dependent on the genotype (Lewers et al 2005, Varshney et al 2005) and can be quite unsuccessful between distant genera (Gasic et al 2009). It means that application of markers for other populations than originally described as a marker source always needs validation (Liebhard & Gessler 2000).…”

“…Among them many sequences were linked to economically important traits such as plant resistance to pests and diseases, plant growth habit, fruit colour, acidity and sweet taste (Korban & Tartarini 2009). The conserved character of certain markers and their transferability between botanical taxa (Lewers et al 2005, Sargent et al 2007, Gasic et al 2009) contributed to the progress in apple mapping (Gianfranceschi et al 1998). …”