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United States Department of Agriculture

Agricultural Research Service


Location: Genetic Improvement for Fruits & Vegetables Laboratory

Title: Construction of black (Rubus occidentalis) and red (R. idaeus) raspberry linkage maps and their comparison to the genomes of strawberry, apple, and peach

item Bushakra, J
item Stephens, J
item Atmadjaja, A
item Lewers, Kimberly
item Symonds, V
item Udall, J
item Chagne, D
item Buck, E
item Gardiner, S

Submitted to: Theoretical and Applied Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/15/2012
Publication Date: 2/26/2012
Publication URL:
Citation: Bushakra, J.M., Stephens, J., Atmadjaja, A.N., Lewers, K.S., Symonds, V.V., Udall, J.A., Chagne, D., Buck, E.J., Gardiner, S.E. 2012. Construction of black (Rubus occidentalis) and red (R. idaeus) raspberry linkage maps and their comparison to the genomes of strawberry, apple, and peach. Theoretical and Applied Genetics. 125(2):311-327.

Interpretive Summary: Black raspberry variety development could be more efficient with the use of modern molecular resources available for many other crops. This research reports the development of the most useful of these molecular resources, a genetic “map” of the black raspberry genome which provides the location within the genome of genetic markers and genes of known function. The map was compared with those from close relatives, such as red raspberry, blackberry, wild strawberry, peach, apple, and pear. The black raspberry map was found to be extremely similar to the red raspberry and the wild strawberry maps. These findings will be useful to raspberry breeders and to geneticists who study raspberry and its close relatives.

Technical Abstract: The genus Rubus belongs to the Rosaceae and is comprised of 600-800 species distributed worldwide. To date, genetic maps of the genus consist largely of non-transferable markers such as amplified fragment length polymorphisms (AFLP). An F1 population developed from a cross between an advanced breeding selection of Rubus occidentalis (96395S1) and R. idaeus ‘Latham’ was used to construct a new genetic map consisting of DNA sequence-based markers. The genetic linkage maps presented here are constructed of 131 markers on at least one of the two parental maps. The majority of the markers are orthologous, including 14 Rosaceae conserved orthologous set (RosCOS) markers, and 60 new gene-based markers developed for raspberry. Thirty-four published raspberry simple sequence repeat (SSR) markers were used to align the new maps to published raspberry maps. The 96395S1 genetic map consists of six linkage groups (LG) and covers 309 cM with an average of 10 cM between markers; the ‘Latham’ genetic map consists of seven LG and covers 561 cM with an average of 5 cM between markers. The use of orthologous genetic markers allows this raspberry genetic linkage map to be compared with the sequenced genomes of other Rosaceae members such as strawberry, apple and peach. Our results suggest a high degree of synteny between the raspberry and strawberry genomes and gives unprecedented insights into the genome evolution of raspberry from the putative ancestral genome of the single ancestor common to Rosaceae.

Last Modified: 06/28/2017
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