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United States Department of Agriculture

Agricultural Research Service

Research Project: MANAGEMENT OF TEMPERATE FRUIT NUT AND SPECIALTY CROP GENETIC RESOURCES

Location: National Clonal Germplasm Repository (Corvallis, Oregon)

Title: A universal fingerprinting set for red raspberry

Authors
item Bassil, Nahla
item Nyberg, April
item Hummer, Kim
item Graham, Julie -
item Dossett, Michael -
item Finn, Chad

Submitted to: International Rubus Ribes Symposium
Publication Type: Abstract Only
Publication Acceptance Date: May 1, 2011
Publication Date: N/A

Interpretive Summary: Red raspberry is an economically important fruit crop in the Pacific Northwestern United States. Other major world production occurs in Europe, South and North America including central highlands of Mexico, California and British Columbia (Canada). The USDA-ARS National Clonal Germplasm Repository (Corvallis, Ore.), is responsible for preserving a collection of that includes 370 red raspberry genotypes originating from 26 countries. The red raspberry clones are maintained in pots in screenhouses. DNA-based ‘markers’ called ‘microsatellite markers’ can be used for rapid identity verification. The objective of this study was to develop a universal fingerprinting set for establishing DNA-based profiles for red raspberries and enabling comparison of foundation plants between national and international collections. We tested 24 of these DNA ‘markers’ for ease of use and ability to distinguish 36 red raspberry genotypes in common between the NCGR and Scottish Crop Research Institute (SCRI) collections. Six of these markers were easy to use and were used to compare fingerprints from eight red raspberries in common between the two collections for use as reference cultivars. This fingerprinting set differentiated between the unique plants included in the study and will be a useful tool for identity confirmation.

Technical Abstract: Red raspberry, Rubus idaeus L., is the most economically important fruit crop in the highly diverse Rubus subgenus Idaeobatus, which also includes black raspberry R. occidentalis L. Major world production occurs in Europe, South and North America including central highlands of Mexico, California (U.S.), the Pacific Northwestern U.S., and British Columbia (Canada). The USDA-ARS National Clonal Germplasm Repository (Corvallis, Ore.), is responsible for preserving a Rubus collection of 1940 accessions that includes 370 red raspberry genotypes originating from 26 countries. The red raspberry clones are maintained in pots in screenhouses. Microsatellite or Simple Sequence Repeat (SSR) markers can be used for rapid identity verification. The objective of this study was to develop a universal SSR fingerprinting set for establishing genetic profiles for red raspberry accessions and enabling comparison of genotypes across collections. We tested 24 SSRs for ease of scoring and polymorphism in 36 red raspberry accessions in common between the NCGR and Scottish Crop Research Institute (SCRI) collections. Additional accessions included four blackberry cultivars (Rubus subsp. Rubus), nine black raspberry genotypes and one representative each of wild red raspberry species R. biflorus Buch.-Ham. ex Sm. and R. niveus Thunb. Six SSRs were easy to score, polymorphic, and mapped to five of the seven red raspberry linkage groups. They were amplified in two multiplexes and used to compare fingerprints from eight red raspberry accessions in common between the two collections for use as reference cultivars. This fingerprinting set differentiated between the unique accessions included in the study and will be a useful tool for identity verification across collections.

Last Modified: 7/22/2014