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ARS Home » Pacific West Area » Corvallis, Oregon » National Clonal Germplasm Repository » Research » Publications at this Location » Publication #318211

Research Project: Management of Temperate-Adapted Fruit, Nut, and Specialty Crop Genetic Resources and Associated Information

Location: National Clonal Germplasm Repository

Title: Development of a multiplexed fingerprinting set in blackberry

Author
item Bassil, Nahla
item Nyberg, April
item Finn, Chad
item Clark, John - University Of Arkansas
item Peace, Cameron - Washington State University
item Iezzoni, Amy - Michigan State University

Submitted to: Acta Horticulturae
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/18/2015
Publication Date: 5/19/2016
Citation: Bassil, N.V., Nyberg, A.M., Finn, C.E., Clark, J.R., Peace, C., Iezzoni, A. 2016. Development of a multiplexed fingerprinting set in blackberry. Acta Horticulturae. 1133:89-96. doi: 10.17660/ActaHortic.2016.1133.14.

Interpretive Summary: The objective of this study was to develop a quick and economical DNA-based method for identifying blackberries and confirming their parentage. We examined the ability of 15 DNA sites to easily distinguish among 13 diverse blackberries and identified 10 that appeared promising. After optimizing the DNA tests, we developed two that can distinguish these blackberries. We plan on evaluating each of these tests for trueness-to-type testing and paternity confirmation of blackberries in the USDA-ARS Corvallis collection and in Eastern and Western US breeding populations.

Technical Abstract: A reliable and fast method for confirming identity and paternity in blackberry is needed. Microsatellite or simple sequence repeat (SSR) markers are ideal for cultivar fingerprinting, paternity testing and identity certification. The objective of this study was to develop a multiplexed fingerprinting set composed of trinucleotide-containing SSRs and to use them to confirm parentage in breeding populations. Fifteen mapped trinucleotide-containing SSRs were used to screen a test panel of 13 diverse blackberry cultivars from the USDA-ARS National Clonal Germplasm Repository (NCGR) blackberry collection. They were first rated for ease of scoring and polymorphism. The ten SSRs that were polymorphic and easy to score were then evaluated for lack of interaction in multiplex PCR after separation of the resulting PCR products by capillary electrophoresis. Each of the SSRs in the resulting two multiplexes generated the same profile in the 13 panel members irrespective of amplification in simplex or multiplex PCR. Both multiplexes differentiated the 13 blackberry cultivars. We plan on evaluating each of these multiplexes for trueness-to-type testing and paternity confirmation of blackberries in the NCGR collection and from Eastern and Western US breeding populations.