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Title: Development and transferability of black and red raspberry microsatellite markers from short-read sequences

item DOSSETT, MICHAEL - Pacific Agri-Food Research Center
item Bushakra, Jill
item Gilmore, Barbara
item KOCH, CAROL - Pacific Agri-Food Research Center
item KEMPLAR, CHAIM - Pacific Agri-Food Research Center
item Finn, Chad
item Bassil, Nahla

Submitted to: Journal of the American Society for Horticultural Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/18/2015
Publication Date: 5/1/2015
Citation: Dossett, M., Bushakra, J., Gilmore, B.S., Koch, C., Kemplar, C., Finn, C.E., Bassil, N.V. 2015. Development and transferability of black and red raspberry microsatellite markers from short-read sequences. Journal of the American Society for Horticultural Science. 140(3):243–252.

Interpretive Summary: Technical advances and decreased costs associated with DNA sequencing is opening doors for research into specialty crops such as red and black raspberry. Here we examine the ability to share DNA tools between these related crops using new DNA sequencing technologies. We found that we can use tools developed in black raspberry in red raspberry and this allows us an opportunity to compare the DNA sequences between these two crops.

Technical Abstract: The advent of next-generation sequencing technologies has been a boon to the cost-effective development of molecular markers, particularly in non-model species. Here, we demonstrate the efficiency of microsatellite or simple sequence repeat (SSR) marker development from short-read sequences using the Illumina® platform in red and black raspberry (Rubus idaeus L. and R. occidentalis 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. More than 5,000 markers were identified from sequences in each species, with 144 markers chosen from each species and tested in both. Markers selected based on different percentages (90-97 % as compared to = 98 %) of microread cluster identity did not differ in polymorphism rates from each other or from those originating from singletons. Efficiency of polymorphic locus recovery was nearly twice as high in black raspberry from black raspberry-derived sequences as from red raspberry-derived sequences, while efficiency of polymorphic locus recovery in red raspberry was not affected by the source of the primer sequences. Development of transferable SSR markers for red and black raspberry for evaluation of genome colinearity and to facilitate comparative studies in Rubus will be more efficient using SSR markers developed from black raspberry sequences.