Verifying Parentage and Confirming Identity in Blackberry with a Fingerprinting Set

Authors: Bassil, Nahla; Zurn, Jason; CARTER, KATIE - Oregon State University; YIN, MELINDA - University Of Arkansas; WORTHINGTON, MARGARET - University Of Arkansas; CLARK, JOHN - University Of Arkansas; Finn, Chad; Hummer, Kim

Submitted to: Journal of the American Society for Horticultural Science
Publication Type: Abstract Only
Publication Acceptance Date: 3/15/2018
Publication Date: 9/1/2018
Citation: Bassil, N.V., Zurn, J.D., Carter, K., Yin, M.H., Worthington, M., Clark, J.R., Finn, C.E., Hummer, K.E. 2018. Verifying Parentage and Confirming Identity in Blackberry with a Fingerprinting Set. Abstract for the Journal of the American Society for Horticultural Science; 2018 July 31-August 3; Washington, DC.

Interpretive Summary: Identifying the correct parentage and confirming the identity of blackberries is an important aspect of breeding new varieties and insuring consumers are receiving the correct variety. Trying to establish parentage or identity by visual appearance is extremely difficult. DNA fingerprinting is an excellent solution to quickly establish parentage and identity that is reproducable. A previously developed six marker fingerptinting set was used to evaluate progeny from 12 populations from the University of Arkansas and the USDA-ARS Horticulture Crops Research Unit breeding programs. The six marker fingerprinting set was found to work well for confirming the parents of the populations, however many indiviuals had identical DNA fingerprints. An improved eight marker set was developed which performs better than the six marker set. This improved eight marker set was used to compare 72 accessions in the National Clonal Germplasm Repository blackberry collection. Additionally, this fingerprinting set is currently being used to identify the unknown parentage of the popular blackberry variety 'Boysen'.

Technical Abstract: Parentage and identity confirmation is an important aspect of clonally propagated crops outcrossing. Potential errors resulting misidentification include off-type pollination events, labeling errors, or sports of clones. DNA fingerprinting sets are an excellent solution to quickly identify off-type progeny or confirm clonal identity. A previously developed simple sequence repeat (SSR) fingerprinting set consisting of six primer pairs was used to verify parentage of seedling populations representing important blackberry (Rubus subg. Rubus) accessions from the University of Arkansas (UA) and the USDA-ARS Horticulture Crops Research Unit (HCRU) breeding programs. Six seedling populations from the UA and 12 seedling populations from the USDA-ARS breeding programs were genotyped. Incorrect parentage was detected where alleles that were absent in both parents occurred in seedlings. In the UA breeding program, 16 individuals were off-type while 11 individuals were off-type in the USDA-ARS HCRU program. In one of the USDA-ARS HCRU populations, ORUS 4647, all five individuals were off-type; the male parent was unknown. For parentage confirmation, the 6-SSR fingerprinting set was sufficient, however, 28 groups of individuals had identical DNA fingerprints. To achieve better resolution, 15 SSRs were examined. An improved 8-SSR fingerprinting set was developed by removing one marker from the 6-SSR set and adding three markers that differentiated undifferentiated individuals. The 8-SSR fingerprinting set reduced the number of indistinguishable samples to 10 groups consisting of two progeny per group. Interestingly, these groups consisted of adjacently planted individuals. Sampling errors may have occurred where the plants were inter-grown. The 8-SSR fingerprinting set was also used to evaluate a set of 71 Rubus clones from the USDA-ARS National Clonal Germplasm Repository (NCGR) to compare accessions that may be identical and to establish a library of genotypes for future identity comparison. The 8-SSR fingerprinting set was applied to ‘Boysen’ subclones, its presumed parents, and additional samples from private growers and commercial nurseries. Multiple subclones of this cultivar have been horticulturally recognized since the genotype was introduced in 1935. The results suggested which clone was most likely to be true-to-type, that ‘Lucretia’ was not a parent of ‘Boysen’, and grouped the ‘Boysen’ subclones into two general categories. Continuing work will focus on establishing pedigree or relational links for blackberry and hybrid berry cultivars.