Theoretical and Applied Genetics

, Volume 118, Issue 7, pp 1279–1293 | Cite as

A COSII genetic map of the pepper genome provides a detailed picture of synteny with tomato and new insights into recent chromosome evolution in the genus Capsicum

  • Feinan Wu
  • Nancy T. Eannetta
  • Yimin Xu
  • Richard Durrett
  • Michael Mazourek
  • Molly M. Jahn
  • Steven D. TanksleyEmail author
Original Paper


We report herein the development of a pepper genetic linkage map which comprises 299 orthologous markers between the pepper and tomato genomes (including 263 conserved ortholog set II or COSII markers). The expected position of additional 288 COSII markers was inferred in the pepper map via pepper–tomato synteny, bringing the total orthologous markers in the pepper genome to 587. While pepper maps have been previously reported, this is the first complete map in the sense that all markers could be placed in 12 linkage groups corresponding to the 12 chromosomes. The map presented herein is relevant to the genomes of cultivated C. annuum and wild C. annuum (as well as related Capsicum species) which differ by a reciprocal chromosome translocation. This map is also unique in that it is largely based on COSII markers, which permits the inference of a detailed syntenic relationship between the pepper and tomato genomes—shedding new light on chromosome evolution in the Solanaceae. Since divergence from their last common ancestor is approximately 20 million years ago, the two genomes have become differentiated by a minimum number of 19 inversions and 6 chromosome translocations, as well as numerous putative single gene transpositions. Nevertheless, the two genomes share 35 conserved syntenic segments (CSSs) within which gene/marker order is well preserved. The high resolution COSII synteny map described herein provides a platform for cross-reference of genetic and genomic information (including the tomato genome sequence) between pepper and tomato and therefore will facilitate both applied and basic research in pepper.


Linkage Group Cleave Amplify Polymorphic Sequence Acrocentric Chromosome Tomato Genome Cleave Amplify Polymorphic Sequence Marker 
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.



We highly appreciate the contribution to this project made by the following individuals and groups: Dr. Arnon Ben-Chaim and Dr. Edmund Quirin developed the mapping population and took lead in SSR/RFLP mapping; DNA landmarks Inc. (Québec, Canada) kindly shared their SSR markers; Xiaomin Jia, Eloisa C. Tedeschi, Yaprak Kantoglu and Ingrid S. Phillips carried out COSII mapping; Dr. Christiane Gebhardt (MPI for Plant Breeding Research, Köln, Germany) kindly permitted us to cite an unpublished result; Dr. Silvana Grandillo (CNR-IGV, Institute of Plant Genetics, Portici, Italy) provided helpful discussion. We also thank Dr. Lukas Mueller (Boyce Thompson Institute for Plant Research, Ithaca, NY, USA) and his bioinformatics group for hosting the maps and the marker data in Solanaceae Genomics Network ( This work was supported in part by NSF Plant Genome Award DBI-0421634 (ST), US-BARD IS-3225-01C, BARD Postdoctoral Fellowship Award No. FI-327-2002, USDA IFAFS Plant Genome Award No. 2001-52100-11347, NSF Metabolic Biochemistry Award No. 0412056, NIH Training Grant GM 08500, and the gift support from Syngenta and Seminis (MJ & ST).

Supplementary material

Supplementary material 1 (CPP 5 kb)
122_2009_980_MOESM2_ESM.ppt (1.5 mb)
Supplementary material 2 (PPT 1,579 kb)
122_2009_980_MOESM3_ESM.xls (170 kb)
Supplementary material 3 (XLS 170 kb)


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Copyright information

© Springer-Verlag 2009

Authors and Affiliations

  • Feinan Wu
    • 1
  • Nancy T. Eannetta
    • 1
  • Yimin Xu
    • 1
  • Richard Durrett
    • 2
  • Michael Mazourek
    • 1
  • Molly M. Jahn
    • 1
    • 3
  • Steven D. Tanksley
    • 1
    • 4
    Email author
  1. 1.Department of Plant Breeding and GeneticsCornell UniversityIthacaUSA
  2. 2.Department of MathematicsCornell UniversityIthacaUSA
  3. 3.College of Agriculture and Life SciencesUniversity of WisconsinMadisonUSA
  4. 4.Department of Plant BiologyCornell UniversityIthacaUSA

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