Simple Sequence Repeat (SSR) Markers for Genetic Mapping of Raspberry and Blackberry

Abstract

<jats:p>Interest in molecular markers and genetic maps is growing among researchers developing new cultivars of <jats:italic>Rubus</jats:italic> L. (raspberry and blackberry). Several traits of interest fail to express in seedlings or reliably in some environments and are candidates for marker-assisted selection. A growing number of simple sequence repeat (SSR) molecular markers derived from <jats:italic>Rubus</jats:italic> and <jats:italic>Fragaria</jats:italic> L. (strawberry) are available for use with <jats:italic>Rubus</jats:italic> mapping populations. The objectives of this study were to test 142 of these SSR markers to screen raspberry and blackberry parental genotypes for potential use in existing mapping populations that segregate for traits of interest, determine the extent of inter-species and inter-genera transferability with amplification, and determine the level of polymorphism among the parents. Up to 32 of the SSR primer pairs tested may be useful for genetic mapping in both the blackberry population and at least one of the raspberry populations. The maximum number of SSR primer pairs found useable for mapping was 60 for the raspberry population and 45 for the blackberry population. Acquisition of many more nucleotide sequences from red raspberry, black raspberry, and blackberry are required to develop useful molecular markers and genetic maps for these species. <jats:italic>Rubus</jats:italic>, family Rosaceae, is a highly diverse genus that contains hundreds of heterozygous species. The family is one of the most agronomically important plant families in temperate regions of the world, although they also occur in tropical and arctic regions as well. The most important commercial subgenus of <jats:italic>Rubus</jats:italic> is <jats:italic>Idaeobatus</jats:italic> Focke, the raspberries, which are primarily diploids. This subgenus contains the european red raspberry <jats:italic>R. idaeus</jats:italic> ssp. <jats:italic>idaeus</jats:italic> L., as well as the american black raspberry <jats:italic>R. occidentalis</jats:italic> L. and the american red raspberry <jats:italic>R. idaeus</jats:italic> ssp. <jats:italic>strigosus</jats:italic> Michx. Interspecific hybridization of these, and other raspberry species, has led to greater genetic diversity and allowed for the introgression of superior traits such as large fruit size, fruit firmness and quality, disease resistance, and winter hardiness.</jats:p>

Biology of the European large raspberry aphid (Amphorophora idaei): its role in virus transmission and resistance breakdown in red raspberry

“…It is probable that parasitoids will operate more effectively within the confines of such tunnels, having smaller areas to search for aphid prey and reduced ability to disperse from the tunnel. Second, the development of molecular and genetic tools, including amplified fragment length polymorphism molecular markers and simple sequence repeat microsatellite markers, has recently led to much better understanding of resistance mechanisms in Rubus (Graham et al , 2002; Graham et al , 2004; Stafne et al , 2005; Sargent et al , 2007) and may lead to more durable resistance against A. idaei . If the problem of fruit contamination with aphid mummies can be overcome, these twin approaches of bottom‐up (host plant resistance) and top‐down control (biocontrol agents) might therefore lead to more effective and sustainable control of A. idaei in the future.…”

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

“…The transferability of F. × ananassa loci to Rubus species was moderate: 46.7% in Nordic species, 40% in red raspberry and hybrids, and 33.3% in black raspberry and blackberry (33.3%). Other authors [20,62] reported even a lower transferability from F. × ananassa to diploid red and black raspberries (Idaeobatus subgenus, 8-23%) than to tetraploid blackberry (Rubus subgenus, 26-36%). Only two of the 15 strawberry markers were polymorphic in raspberries (FaFS01 and FaCH01) and five markers if all Rubus species were taken into account.…”

Mapping of A1 conferring resistance to the aphid Amphorophora idaei and dw (dwarfing habit) in red raspberry (Rubus idaeus L.) using AFLP and microsatellite markers

“…AFLPs [14] have become a useful tool for generating maps of large numbers of dominant markers without prior knowledge of DNA sequence [15], although their subsequent application as markers for selection of useful traits is limited to the breeding lines in which they were generated, unless they are first converted to SCARs [16]. Owing to their codominant nature and ease of transferability between germplasm, microsatellite markers (simple sequence repeats; SSRs), have found utility for a variety of purposes including the development of transferable, saturated linkage maps in many rosaceous genera [17-19], and SSRs have recently been developed for Rubus [20-22]. …”