Developing a single sequence repeat (SSR) fingerprinting set to characterize the NCGR Ribes Collection

Authors: Bushakra, Jill; ALVAREZ, ANTONIO - Oregon State University; King, Ryan; GREEN, JAIMIE - Oregon State University; Nyberg, April; Bassil, Nahla

Submitted to: Acta Horticulturae
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/9/2023
Publication Date: 2/1/2024
Citation: Bushakra, J., Alvarez, A., King, R., Green, J., Nyberg, A.M., Bassil, N.V. 2024. Developing a single sequence repeat (SSR) fingerprinting set to characterize the NCGR Ribes Collection. Acta Horticulturae. 1388:107-114. https://doi.org/10.17660/ActaHortic.2024.1388.15.
DOI: https://doi.org/10.17660/ActaHortic.2024.1388.15

Interpretive Summary: The US Department of Agriculture (USDA), National Clonal Germplasm Repository (NCGR) in Corvallis, Oregon, preserves a diverse collection of currants and gooseberries of more than 1,100 accessions from 41 countries. The collection consists of 371 cultivars and advanced selections of 44 species and 8 subspecies. Currants and gooseberries are maintained as field-grown plants, in pots in screenhouses, and as seeds of wild relatives. The objective of this study was to develop a DNA-based fingerprinting set to develop baseline genetic profiles for the collection. A 7-marker fingerprinting set was used to genotype 69 plants representing 53 accessions from the NCGR collection. The results identified two potential synonyms and 13 cultivated genotypes with the same name from different sources; five cultivars with the same name but with different alleles; two genotypes with different names but the same fingerprint; two unknown accessions; and differences among suspected synonyms. This fingerprinting set accurately separated species and will provide another tool to better manage the botanical and horticultural identity of currant and gooseberry collections.

Technical Abstract: The US Department of Agriculture (USDA), National Clonal Germplasm Repository (NCGR) in Corvallis, Oregon, preserves a diverse Ribes (currants and gooseberries) germplasm collection of more than 1,100 accessions from 41 countries. The collection consists of 371 cultivars and advanced selections of 44 species and 8 subspecies. Ribes accessions are maintained as field-grown plants, in pots in screenhouses, and as seeds of wild relatives. The objective of this study was to develop a multiplexed Ribes single sequence repeat (SSR) fingerprinting set of long-core repeats to develop baseline genetic profiles for the Ribes collection. Thirteen published SSRs that appeared polymorphic in at least two Ribes species were evaluated in a testing panel of 12 accessions representing R. aureum, R. nigrum, R. uva-crispa, R. spicatum, R. petraeum, and R. × nidigrolaria. Seven primer pairs that amplified and were polymorphic across the tested species were multiplexed and their concentration optimized in a single polymerase chain reaction (PCR). This 7-SSR fingerprinting set was used to genotype 69 plants representing 53 accessions from the NCGR collection. The results identified two potential synonyms and 13 cultivated genotypes with the same name from different sources; five cultivars with the same name but with different alleles at one or more SSR locus; two genotypes with different names but the same fingerprint; two unknown accessions; and differences among suspected synonyms. This fingerprinting set accurately separated species and will provide another tool to better manage the botanical and horticultural identity of Ribes germplasm collections.