Theoretical and Applied Genetics

, Volume 125, Issue 2, pp 311–327 | Cite as

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

  • J. M. Bushakra
  • M. J. Stephens
  • A. N. Atmadjaja
  • K. S. Lewers
  • V. V. Symonds
  • J. A. Udall
  • D. Chagné
  • E. J. Buck
  • S. E. Gardiner
Original Paper


The genus Rubus belongs to the Rosaceae and is comprised of 600–800 species distributed world-wide. To date, genetic maps of the genus consist largely of non-transferable markers such as amplified fragment length polymorphisms. 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 markers, and 60 new gene-based markers developed for raspberry. Thirty-four published raspberry simple sequence repeat 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. We used BLAST analysis to align the orthologous sequences used to design primer pairs for Rubus genetic mapping with the genome sequences of Fragaria vesca ‘Hawaii 4’, Malus × domestica ‘Golden Delicious’, and Prunus ‘Lovell’. The alignment of the orthologous markers designed here suggests that the genomes of Rubus and Fragaria have a high degree of synteny and that synteny decreases with phylogenetic distance. Our results give unprecedented insights into the genome evolution of raspberry from the putative ancestral genome of the single ancestor common to Rosaceae.


Simple Sequence Repeat Marker Linkage Group Amplify Fragment Length Polymorphic Black Raspberry Genomic Simple Sequence Repeat 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.



This work was part of a Ph.D. thesis and supported in part by the PFR Excellence Program (JMB), the “New Berries” FRST Programme (CO6XO807) (EJB, MJS), PFR funding (MJS), and USDA-ARS Project 1275-21220-185-00D (KSL). The authors would like to thank Jared C. Price of Brigham Young University, Computer Science Department for his assistance with the Rubus genome; the International Peach Genome Initiative for access to the Prunus genome; Dr Ross Crowhurst and Roy Storey of PFR for bioinformatic support; Tony Corbett of PFR for graphic design of all figures; the Editor and two anonymous reviewers for helpful suggestions on the original manuscript. Mention of trade names or commercial products in this publication is solely for the purpose of providing specific information and does not imply recommendation or endorsement by any of the agencies referenced.

Supplementary material

122_2012_1835_MOESM1_ESM.pdf (210 kb)
Supplemental Fig. 1: Comparison between Rubus idaeus ‘Latham’ genetic map and Fragaria physical map constructed using BLAST analysis. ‘Latham’ map distance is measured in centimorgans (cM); Fragaria map distance is measured in megabase pairs (Mbp). ‘Latham’ LG arranged in proposed order (RLG) with original numbering (OLG) in parentheses. (PDF 210 kb)
122_2012_1835_MOESM2_ESM.pdf (230 kb)
Supplemental Fig. 2: Comparison between Rubus idaeus ‘Latham’ genetic map and Malus physical map constructed using BLAST analysis. ‘Latham’ map distance is measured in cM; Malus map distance is measured in Mbp. ‘Latham’ LG arranged in proposed order (RLG) with original numbering (OLG) in parentheses. (PDF 229 kb)
122_2012_1835_MOESM3_ESM.pdf (201 kb)
Supplemental Fig. 3: Comparison between Rubus idaeus ‘Latham’ genetic map and Prunus physical map constructed using BLAST analysis. ‘Latham’ map distance is measured in cM; Prunus map distance is measured in Mbp. ‘Latham’ LG arranged in proposed order (RLG) with original numbering (OLG) in parentheses. (PDF 201 kb)
122_2012_1835_MOESM4_ESM.pdf (163 kb)
Supplemental Table 1: Redesigned and newly designed primer pair sequences of markers polymorphic in Rubus occidentalis 96395S1 × R. idaeus ‘Latham’ progeny. (PDF 162 kb)
122_2012_1835_MOESM5_ESM.pdf (755 kb)
Supplemental Table 2: Marker design information. Information on origin and type of sequence, locations in strawberry, apple and peach genomes, expected values (E-values), and percent identity for each marker mapped in Rubus occidentalis 96395S1 × R. idaeus ‘Latham’. (PDF 754 kb)


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Copyright information

© Springer-Verlag 2012

Authors and Affiliations

  • J. M. Bushakra
    • 1
    • 2
  • M. J. Stephens
    • 3
  • A. N. Atmadjaja
    • 1
  • K. S. Lewers
    • 4
  • V. V. Symonds
    • 2
  • J. A. Udall
    • 5
  • D. Chagné
    • 1
  • E. J. Buck
    • 1
  • S. E. Gardiner
    • 1
  1. 1.The New Zealand Institute for Plant & Food Research Limited (PFR)Palmerston NorthNew Zealand
  2. 2.Institute of Molecular BiosciencesMassey UniversityPalmerston NorthNew Zealand
  3. 3.PFRMotuekaNew Zealand
  4. 4.USDA-ARS, Genetic Improvement of Fruits and Vegetables LaboratoryBeltsvilleUSA
  5. 5.Plant and Wildlife Science DepartmentBrigham Young UniversityProvoUSA

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