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ARS Home » Pacific West Area » Corvallis, Oregon » National Clonal Germplasm Repository » Research » Publications at this Location » Publication #272405
Title: SSR fingerprinting of black raspberry cultivars shows discrepancies in identification

Author
item DOSSETT, MICHAEL - Oregon State University
item Bassil, Nahla
item Finn, Chad

Submitted to: Acta Horticulturae
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/1/2012
Publication Date: 5/8/2012
Citation: Dossett, M., Bassil, N.V., Finn, C.E. 2012. SSR fingerprinting of black raspberry cultivars shows discrepancies in identification. Acta Horticulturae. 946:49-53.

Interpretive Summary: Black raspberry cultivars are noted for showing very few differences. Genetic fingerprinting using DNA markers called microsatellite, or simple sequence repeat (SSR) markers, is a tool that can be used to reliably identify unique clones and to evaluate diversity in black raspberry cultivars. Twenty-one black raspberry cultivars were sampled from the USDA-ARS National Clonal Germplasm Repository (NCGR) in Corvallis, Oregon. Black raspberry clones were also sampled from nurseries, grower’s fields, and other black raspberry breeding programs for comparison. These genotypes were compared using 18 SSRs. The black raspberry cultivars Bristol, Jewel, and Mac Black had consistent SSR fingerprints between sources. However, plants being sold as ‘Black Hawk’ and ‘Cumberland’ were found to have the same fingerprint as ‘Jewel’. Plants of ‘Bristol’, ‘Cumberland’, ‘Munger’, ‘New Logan’, ‘Plum Farmer’ and ‘Shuttleworth’ in the NCGR collection had identical profiles. Eleven unique SSR fingerprints were found among plants being grown or sold as ‘Munger’, though there was one predominant fingerprint for this cultivar. ‘Allen’ and ‘John Robertson’ were each represented by three different fingerprints from three different sources. Based on SSR analysis, the profiles of ‘Earlysweet’ and ‘Jewel’ do not agree with their reported parentage. While overall genetic diversity in black raspberry cultivars is low, discrepancies in the naming of clones appear to be widespread in commercial and research plantings. Future work in this area should focus on determining the extent of the problem by sampling additional independent sources of plant material and evaluating clones to determine the extent of performance differences. Further SSR development in black raspberry may be needed to fingerprint some unique clones.

Technical Abstract: Breeding progress in black raspberry (Rubus occidentalis L.) has been limited by a lack of genetic diversity in elite germplasm. Black raspberry cultivars are noted for showing very few differences, and seedlings for a lack of segregation for important traits. Genetic fingerprinting using microsatellite, or simple sequence repeat (SSR) markers, is a tool that can be used to reliably identify unique clones and to evaluate diversity in black raspberry cultivars. Twenty-one black raspberry cultivars were sampled from the USDA-ARS National Clonal Germplasm Repository (NCGR) in Corvallis, Oregon. Black raspberry clones were also sampled from nurseries, grower’s fields, and other black raspberry breeding programs for comparison. These genotypes were compared using 18 polymorphic SSR primer pairs. The black raspberry cultivars Bristol, Jewel, and Mac Black had consistent SSR fingerprints between sources. However, plants being sold as ‘Black Hawk’ and ‘Cumberland’ were found to have the same fingerprint as ‘Jewel’. Plants of ‘Bristol’, ‘Cumberland’, ‘Munger’, ‘New Logan’, ‘Plum Farmer’ and ‘Shuttleworth’ in the NCGR collection had identical fingerprints. Eleven unique SSR fingerprints were found among plants being grown or sold as ‘Munger’, though there was one predominant fingerprint for this cultivar. ‘Allen’ and ‘John Robertson’ were each represented by three different fingerprints from three different sources, and ‘Earlysweet’ and ‘Jewel’ had SSR alleles at multiple loci that cannot be explained by their reported pedigrees. While overall genetic diversity in black raspberry cultivars is low, discrepancies in the naming of clones appear to be widespread in commercial and research plantings. Future work in this area should focus on determining the extent of the problem by sampling additional independent sources of plant material and evaluating clones to determine the extent of performance differences. Further SSR development in black raspberry may be needed to fingerprint some unique clones.