A black raspberry fingerprinting set identifies seedlings in two families

Authors: Bassil, Nahla; King, Ryan; Peterson, Mary; DOSSETT, MICHAEL - British Columbia Blueberry Council; Hardigan, Michael

Submitted to: Acta Horticulturae
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/9/2023
Publication Date: 2/1/2024
Citation: Bassil, N.V., King, R., Peterson, M.E., Dossett, M., Hardigan, M.A. 2024. A black raspberry fingerprinting set identifies seedlings in two families. Acta Horticulturae. 1388:115-120. https://doi.org/10.17660/ActaHortic.2024.1388.16.
DOI: https://doi.org/10.17660/ActaHortic.2024.1388.16

Interpretive Summary: Black raspberry is a horticultural specialty crop of interest in North America. While the majority of black raspberry acreage is in Oregon and intended for the processing market, fresh market production occurs along the Ohio River Valley and the Great Lakes. The United States Department of Agriculture (USDA) Agricultural Research Service (ARS) National Collection and breeding program are housed in Corvallis, Oregon, at the National Clonal Germplasm Repository (NCGR), and Horticultural Crops Production and Genetic Improvement Research Unit (HCPGIRU), respectively. Seedlings from two breeding families carrying aphid resistance growing in the field had lost their labels. Since these plants were highly productive for over nine years, they may be important sources of resistance to the Raspberry mosaic virus complex including Black raspberry necrosis virus that can cause a shortened life span and small fruit size. The objective of this study was to develop a DNA-based fingerprinting set that could identify the two families to which these 14 field plants belong. A fingerprinting set of six DNA markers was optimized in a single test and identified nine plants that belong to the ORUS 4304 family and five to the ORUS 4305 family. This black raspberry fingerprinting set of six DNA markers is economical, easy to use, and is a new tool for identity confirmation in black raspberry.

Technical Abstract: Black raspberry (Rubus occidentalis L.) is a horticultural specialty crop of interest in North America. While the majority of black raspberry acreage is in Oregon and intended for the processing market, fresh market production occurs along the Ohio River Valley and the Great Lakes. The United States Department of Agriculture (USDA) Agricultural Research Service (ARS) National Collection and breeding program are housed in Corvallis, Oregon, at the National Clonal Germplasm Repository (NCGR), and Horticultural Crops Production and Genetic Improvement Research Unit (HCPGIRU), respectively. Seedlings from two breeding families carrying aphid resistance [ORUS 4304 (ORUS 4158-2 x ORUS 3021-2) or ORUS 4305 (ORUS 3021-2 x ORUS 4153-1)] growing in the field had lost their labels. Since these plants were highly productive for over nine years, they may be important sources of resistance to the Raspberry mosaic virus complex including Black raspberry necrosis virus that can cause a shortened life span and small fruit size. The objective of this study was to develop a long core simple sequence repeat (SSR)-based fingerprinting set that could identify the two families to which these 14 field plants belong. Of 44 SSRs previously screened in the parents of these two families, seven trinucleotide and 16 dinucleotide containing SSRs were polymorphic. A fingerprinting set of six Tri-SSRs was optimized in a multiplexed test and identified nine plants that belong to the ORUS 4304 family and five to the ORUS 4305 family. Two of four additional Di-SSRs tested confirmed this conclusion. Of the 10 SSRs tested, two Tri-SSRs (Ro2173 and Ro20267) and two Di-SSRs (Ro9206 and Ro15590) had parent-specific alleles for each of the two unique parents (ORUS 4158-2 and ORUS 4153-1) and were most informative in these families. This black raspberry fingerprinting set of six SSRs is economical, easy to use, and is a new tool for identity confirmation in black raspberry.