ARS | Publication request: Microsatellite Markers Identify Raspberries and Blackberries

Submitted to: Plant and Animal Genome
Publication Type: Abstract Only
Publication Acceptance Date: January 20, 2007
Publication Date: February 20, 2007
Citation: Castillo, N., Bassil, N.V., Reed, B.M. 2007. Microsatellite Markers Identify Raspberries and Blackberries. Plant and Animal Genome. p. 134.

Interpretive Summary: The United States Department of Agriculture (USDA) - Agricultural Research Service (ARS) - National Clonal Germplasm Repository (NCGR) in Corvallis, Oregon, preserves 2094 blackberries, raspberries and relatives. This collection represents 193 species originating from 64 countries. In this study, 13 molecular markers were developed and generated a unique fingerprint for 96 types of blackberry, raspberry, hybrids and unusual species relatives chosen from the collection. These markers will be used to fingerprint additional blackberry and raspberry relatives and will assist genebank managers, nurserymen and growers in verifying the identity of questionable types.

Technical Abstract: Twelve genomic SSRs and one Expressed Sequence Tag- (EST)-simple sequence repeats (SSR) designed from an (AT)6-containingred raspberry, R. idaeus sequence from Genbank were used for fingerprinting 48 raspberry and 48 blackberry (Rubus L. subgenus Rubus)cultivars stored at the United States Department of Agriculture (USDA) - Agricultural Research Service (ARS) - National Clonal Germplasm Repository (NCGR) in Corvallis, Oregon. The SSR markers developed in Rubus were highly polymorphic. In raspberries, the 12 SSRs generated 3 to 16 alleles per locus, with an average of 8 and a total of 96 alleles. In blackberries, the 12 primer pairs amplified 6 to 31 alleles per locus, with an average of 15 and a total of 177 alleles. These markers distinguished between the raspberries and blackberries except in the blackberry x raspberry hybrid berries, R. hybrid ‘Logan’ and ‘Boysen’ clones. Neighbor joining cluster analysis based on the proportion of shared alleles distance using 13 SSRs separated the cultivars into two main groups: the raspberries and the blackberries and blackberry x raspberry hybrids. Cultivars with uncommon ancestry grouped separately. The raspberry and blackberry groups were further divided according to their pedigrees.