Tree Genetics & Genomes

, Volume 4, Issue 4, pp 897–910 | Cite as

Construction of an intra-specific sweet cherry (Prunus avium L.) genetic linkage map and synteny analysis with the Prunus reference map

  • James W. Olmstead
  • Audrey M. Sebolt
  • Antonio Cabrera
  • Suneth S. Sooriyapathirana
  • Sue Hammar
  • Gloria Iriarte
  • Dechun Wang
  • Charles Y. Chen
  • Esther van der Knaap
  • Amy F. Iezzoni
Original Paper


Linkage maps of the sweet cherry cultivar ‘Emperor Francis’ (EF) and the wild forest cherry ‘New York 54’ (NY) were constructed using primarily simple sequence repeat (SSR) markers and gene-derived markers with known positions on the Prunus reference map. The success rate for identifying SSR markers that could be placed on either the EF or NY maps was only 26% due to two factors: a reduced transferability of other Prunus-species-derived markers and a low level of polymorphism in the mapping parents. To increase marker density, we developed four cleaved amplified polymorphic sequence markers (CAPS), 19 derived CAPS markers, and four insertion–deletion markers for cherry based on 101 Prunus expressed sequence tags. In addition, four gene-derived markers representing orthologs of a tomato vacuolar invertase and fruit size gene and two sour cherry sorbitol transporters were developed. To complete the linkage analysis, 61 amplified fragment length polymorphism and seven sequence-related amplified polymorphism markers were also used for map construction. This analysis resulted in the expected eight linkage groups for both parents. The EF and NY maps were 711.1 cM and 565.8 cM, respectively, with the average distance between markers of 4.94 cM and 6.22 cM. A total of 82 shared markers between the EF and NY maps and the Prunus reference map showed that the majority of the marker orders were the same with the Prunus reference map suggesting that the cherry genome is colinear with that of the other diploid Prunus species.


Prunus Genetic linkage map Synteny analysis Sweet cherry 



This project was supported by the National Research Initiative Competitive Grant 2005-35300-15454 from the US Department of Agriculture Cooperative State Research, Education, and Extension Service.

Supplementary material

11295_2008_161_MOESM1_ESM.doc (29 kb)
Supplemental Table 1 Markers that did not amplify EF or NY DNA arranged by linkage groupa. Markers that identify multiple loci are in bold (DOC 29 kb)
11295_2008_161_MOESM2_ESM.doc (40 kb)
Supplemental Table 2 Markers that were monomorphic for EF and NY arranged by linkage group position. Markers that identify multiple loci are identified in bolda (DOC 40 kb)
11295_2008_161_MOESM3_ESM.doc (26 kb)
Supplemental Table 3 Markers that were “complex” or “difficult.” Bold identifies those SSRs that identified multiple loci (DOC 25.5 kb)


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Copyright information

© Springer-Verlag 2008

Authors and Affiliations

  • James W. Olmstead
    • 1
    • 3
  • Audrey M. Sebolt
    • 1
  • Antonio Cabrera
    • 2
  • Suneth S. Sooriyapathirana
    • 1
  • Sue Hammar
    • 1
  • Gloria Iriarte
    • 2
  • Dechun Wang
    • 1
  • Charles Y. Chen
    • 1
    • 4
  • Esther van der Knaap
    • 2
  • Amy F. Iezzoni
    • 1
    • 5
  1. 1.Michigan State UniversityEast LansingUSA
  2. 2.Ohio Agriculture Research and Development CenterThe Ohio State UniversityWoosterUSA
  3. 3.Washington State UniversityYakimaUSA
  4. 4.USDA/ARS, National Peanut Research LaboratoryDawsonUSA
  5. 5.Department of HorticultureMichigan State UniversityEast LansingUSA

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