Microsatellite markers confirm identity of blueberry plants in the USDA-ARS National Clonal Germplasm Repository collection

Authors: Bassil, Nahla; BIDANI, AMIRA - Ecole Nationale Supérieure D’Hydraulique De Blida; Nyberg, April; Hummer, Kim; Rowland, Lisa

Submitted to: Genetic Resources and Crop Evolution
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/24/2019
Publication Date: 1/4/2020
Citation: Bassil, N.V., Bidani, A., Nyberg, A.M., Hummer, K.E., Rowland, L.J. 2020. Microsatellite markers confirm identity of blueberry plants in the USDA-ARS National Clonal Germplasm Repository collection. Genetic Resources and Crop Evolution. 67:393-409. https://doi.org/10.1007/s10722-019-00873-8.
DOI: https://doi.org/10.1007/s10722-019-00873-8

Interpretive Summary: The United States Department of Agriculture (USDA)-Agricultural Research Service (ARS)-National Clonal Germplasm Repository (NCGR) in Corvallis Oregon preserves blueberry and its wild relatives. The identity of the blueberry cultivars in the NCGR collections is critical to management and operations of this valuable resource. Previously, identity confirmation was determined through the morphology of key traits, but molecular tools have been developed for more thorough “fingerprinting.” In this study, we used a DNA test to: compare fingerprints of all plants representing the most requested blueberry cultivars in the screenhouse and field collections of the NCGR; conduct parentage analysis to confirm identity; establish reference fingerprints for these cultivars; and expand the fingerprinting set with additional DNA sequences. Fingerprinting 367 samples with this DNA test and parentage analysis where possible detected 54 true-to-type (TTT) cultivars, 13 sets of plants with the same name but different fignerprints (homonyms) and ten groups of synonyms. Parentage analysis identified five of the TTT cultivars among the homonyms (‘Bluecrop’, FL 4B, ‘Nelson’ and ‘Clara’) and ‘Elizabeth’ among the synonym sets. A public database of these reference genetic profiles is available on GRIN-Global. We plan to continue adding to this public database and eliminate redundant genotypes for more efficient management of blueberry diversity.

Technical Abstract: The United States Department of Agriculture (USDA)-Agricultural Research Service (ARS)-National Clonal Germplasm Repository (NCGR) in Corvallis Oregon preserves genetic resources of fruit crops. This genebank contains more than 1800 Vaccinium accessions from 34 countries. The genotypic identity of the blueberry cultivars in the NCGR collections is critical to genebank management and operations. Previously, identity confirmation was determined through the morphology of key taxonomic traits, but simple sequence repeat (SSR)-based molecular tools have been developed for more thorough “fingerprinting.” We had previously developed a 5-SSR fingerprinting set of tri-nucleotide-containing SSRs in blueberry. The objectives of this study were to use this 5-SSR blueberry test to compare fingerprints of all plants representing the most requested blueberry cultivars in the screenhouse and field collections of the NCGR; conduct parentage analysis to confirm identity; establish reference fingerprints for these cultivars; and expand the fingerprinting set with additional long core repeats, if needed. The SSR-set distinguished all but ‘Lateblue’ and ‘Berkeley’ and was supplemented with five additional SSRs with long core repeats to generate a 10-SSR fingerprinting set. Genotyping 367 samples with one or both of these SSR sets and parentage analysis where possible detected 54 true-to-type (TTT) cultivars, 13 sets of homonyms and ten groups of synonyms. Parentage analysis identified five of the TTT cultivars among the homonyms (‘Bluecrop’, FL 4B, ‘Nelson’ and ‘Clara’) and ‘Elizabeth’ among the synonym sets. A public database of these reference genetic profiles is available on GRIN-Global. We plan to continue adding to this database and eliminate redundant genotypes for more efficient management of blueberry diversity. Confirmed blueberry genotypes will benefit the germplasm community for use in continued breeding and genetic studies.