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United States Department of Agriculture

Agricultural Research Service

Research Project: MANAGEMENT OF TEMPERATE FRUIT NUT AND SPECIALTY CROP GENETIC RESOURCES

Location: National Clonal Germplasm Repository (Corvallis, Oregon)

Title: Microsatellite Markers for Raspberries and Blackberries

Authors
item Flores, Nina -
item REED, BARBARA
item Graham, Julie -
item Fernandez-Fernandez, Feli -
item BASSIL, NAHLA

Submitted to: Journal of the American Society for Horticultural Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: April 14, 2010
Publication Date: May 1, 2010
Citation: Flores, N.R., Reed, B.M., Graham, J., Fernandez-Fernandez, F., Bassil, N.V. 2010. Microsatellite Markers for Raspberries and Blackberries. Journal of the American Society for Horticultural Science. 135(3):271-278.

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 were placed on two red raspberry genetic maps. They 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 microsatellites were isolated from SSR-enriched genomic libraries of Rubus idaeus L.‘Meeker’ red raspberry (diploid) and R. loganobaccus L. H. Bailey ‘Marion’ blackberry-raspberry hybrid (hexaploid). These primer pairs, with the addition of one developed from a GenBank R. idaeus sequence, were evaluated in 48 raspberry and 48 blackberry genotypes. RhM031 failed in raspberries while RiG001 failed in blackberries and their hybrids. The number of alleles per locus in the 12 SSRs that successfully amplified was higher in blackberry and their hybrids than in raspberry, ranging from three to 29 in blackberries (average 14.4) and from one to 15 in red raspberries (average 7.5). Diversity estimates were determined for 10 of 12 SSRs that amplified up to two products in 44 red raspberry genotypes. The best SSR loci based on high observed (Ho) and expected heterozygosities (He), high polymorphic information index (PIC) and low inbreeding coefficient (F) were RiM019, RhM003 and RhM011 and could differentiate between each of the genotypes identified with the 12 SSRs in each crop type. They also mapped to three different linkage groups (5, 2 and 7) in the red raspberry reference population ‘Glen Moy’ × ‘Latham’, as well as in the ‘Autumn Bliss’ × ‘Malling Jewel’ mapping progeny. These three SSRs will be tested further across laboratories and platforms to provide a subset of a robust fingerprinting panel for red raspberry and blackberry.

Last Modified: 7/25/2014
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