An Economical DNA Test for Genetic Identity Confirmation in Blueberry

Authors: BADANI, AMIRA - Faculty Of Sciences Of Gabes; Hummer, Kim; Rowland, Lisa; Bassil, Nahla

Submitted to: Acta Horticulturae International Symposium on Vaccinium Culture
Publication Type: Abstract Only
Publication Acceptance Date: 2/23/2017
Publication Date: N/A
Citation: N/A

Interpretive Summary: Blueberries, originally derived from native North American species during the past century, have become a major global fruit crop. Significant production areas now can be found in North America, South America, Europe, China, Japan, Australia and New Zealand. The United States Department of Agriculture (USDA) National Clonal Germplasm Repository (NCGR) in Corvallis, OR, USA is responsible for preserving genetic diversity of this important fruit crop, and maintains a national collection of > 1750 blueberries representing 71 types from 39 countries. Clonal identity of the plants in this collection must be ensured for scientific, commercial and public needs. Use of an economical DNA-based fingerprinting set can assist in the reduction of plant redundancy and elimination of inaccuracy for efficient conservation. The objective of this study was to develop an efficient and economical fingerprinting set that can be tested in a single reaction and can differentiate genetic variation. We describe the use of this fingerprinting set to confirm identity of 287 accessions, identify incorrectly labeled clones, and explain ways to improve discrimination power of this DNA test.

Technical Abstract: Blueberry (Vaccinium sp.) cultivation began in the early 20th Century in the U.S. Since then it has become a major crop in North America, South America, Europe, China, Japan, Australia and New Zealand. The United States Department of Agriculture (USDA) National Clonal Germplasm Repository (NCGR) in Corvallis, OR, USA preserves genetic diversity of this important genus and maintains a national collection of >1,750 accessions representing 71 species from 39 countries. Reliable identification of the plants in this collection is critical and must be ensured for scientific, commercial and public needs. DNA analysis allows efficient genetic conservation through the reduction of clonal redundancy and can eliminate identification inaccuracies. The objective of this study was to develop an efficient and economical DNA fingerprinting set that consists of reliable primer pairs that can be combined into a single reaction and differentiate genetic variants. Seventeen microsatellite or simple sequence repeat (SSR) primer pairs flanking core repeats of three nucleotides were screened for polymorphism and ease of scoring in seven diverse blueberry cultivars. Five out of these 17 primer pairs were selected to make up a single multiplex set and were evaluated in 287 highly requested blueberry plants preserved at the NCGR. These 287 plants consisted of 126 accessions that exist as replicate clones of the same name in addition to 8 accessions that were present as a single plant, for an expected total of 134 unique genetic profiles. Five of the 126 replicated blueberries had a different genetic profile from other plant(s) with the same name while six pairs of 134 unique accessions could not be differentiated. When 13 additional SSRs were used to confirm genetic similarity among these six pairs, only the closely related ‘Lateblue’ and ‘Berkeley’ were different. We describe the use of this fingerprinting set to confirm identity of these accessions, eliminate incorrectly labeled clones and ways to improve discrimination power of this DNA test.