Publication Overview
Abstract The advent of next-generation, or massively parallel sequencing technologies has been a boon to the cost-effective
development of molecular markers, particularly in nonmodel species. Here, we demonstrate the efficiency of microsatellite
or simple sequence repeat (SSR) marker development from short-read sequences in black and red raspberry (Rubus
occidentalis L. and R. idaeus L., respectively), compare transferability of markers across species, and test whether the rate of
polymorphism in the recovered markers can be improved upon by how marker sequences are chosen. From 28,536,412
black raspberry reads and 27,430,159 reads in red raspberry, we identified more than 6000 SSR sequences in each species
and selected 288 of these (144 from each species), for testing in black and red raspberry. A total of 166 SSR primer pairs
were identified with informative polymorphism in one or both species. SSRs selected based on different percentages (90% to
97% as compared with ‡98%) of read cluster similarity did not differ in polymorphism rates from each other or from those
originating from singletons. Efficiency of polymorphic SSR recovery was nearly twice as high in black raspberry from black
raspberry-derived sequences as from red raspberry-derived sequences, while efficiency of polymorphic SSR recovery in red
raspberry was unaffected by the source of the primer sequences. Development of SSR markers that are transferable
between red and black raspberry for marker-assisted selection, evaluation of genome collinearity and to facilitate comparative
studies in Rubus L. will be more efficient using SSR markers developed from black raspberry sequences.
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