Validating blackberry (Rubus L.) seedling pedigrees and developing an improved multiplexed microsatellite fingerprinting set

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

Submitted to: Journal of the American Society for Horticultural Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/9/2018
Publication Date: 9/18/2018
Citation: Zurn, J.D., Carter, K., Yin, M.H., Worthington, M., Clark, J.R., Finn, C.E., Bassil, N.V. 2018. Validating blackberry (Rubus L.) seedling pedigrees and developing an improved multiplexed microsatellite fingerprinting set. Journal of the American Society for Horticultural Science. 143(5):381-390. https://doi:10.21273/JASHS04474-18.
DOI: https://doi.org/10.21273/JASHS04474-18

Interpretive Summary: Determining the parentage or identity of blackberry varieties is extremely difficult when only relying on visual appearance. A solution to this problem, is to use a DNA based test to create a genetic fingerprint of varieties. In this manuscript a DNA fingerprinting test using six markers was used to confirm the parentage of blackberry seedlings from the University of Arkansas and the USDA-ARS horticultural Crops Research Unit breeding programs. In the 18 populations evaluated, 27 seedlings were identified to have different pollen parents than expected. Additionally, 61 individuals divided into 28 sets had identical DNA fingerprint when they should have been different. An improved eight marker DNA fingerprinting test was developed. The 61 individuals with identical fingerprints and 116 additional individuals were evaluated to determine the usefulness of the improved DNA fingerprinting test. The improved test was able to distiguish all samples expected to have unique DNA fingerprints. Additionally, two sets of individauls expected to have the same fingerprint were identified to be different. Additionally, blackberries from the eastern and western United States were shown to be distinctly different groups. Future work will focus on creating a database of DNA fingerprints of blackberry varieties for future identification and to determine pedigree relationships between different varieties.

Technical Abstract: Confirming parentage and clonal identity are important aspects of breeding and managing germplasm collections of clonally propagated, outcrossing crops, like blackberries (Rubus L. subgenus Rubus Watson). DNA fingerprinting sets are used to identify off-type progeny and confirm clonal identity. Previously, a six simple sequence repeat (SSR; 6-SSR) fingerprinting set was developed for blackberry using a small number of samples. The usefulness of the 6-SSR fingerprinting set for pedigree confirmation had not been evaluated. Therefore, it was used in this study to validate parentage for six and 12 biparental populations from the University of Arkansas (UA) and the USDA-ARS Horticultural Crops Research Unit (HCRU) breeding programs, respectively. Twenty-seven of the 489 individuals in these breeding populations were identified as off-type. The 6-SSR fingerprinting set was sufficient for parentage confirmation; however, a total of 61 plants distributed across 28 sets of individuals could not be distinguished from each other. An 8-SSR fingerprinting set with improved resolution was subsequently developed and used to evaluate 177 Rubus accessions from the USDA-ARS National Clonal Germplasm Repository (NCGR), the UA, and the USDA-ARS HCRU programs. The 8-SSR fingerprinting set distinguished all samples expected to have unique genotypes and identified differing DNA fingerprints for two sets of accessions suspected to have identical fingerprints. Cluster analysis grouped the accessions from the eastern and western U.S. breeding programs based on geography and descent. Future work will focus on establishing a database of DNA fingerprints for germplasm identification and for determining pedigree relationships between blackberry accessions.