Molecular Breeding

, Volume 29, Issue 1, pp 245–260 | Cite as

A genetic map of pineapple (Ananas comosus (L.) Merr.) including SCAR, CAPS, SSR and EST-SSR markers

  • Jorge Dias Carlier
  • Nelson Horta Sousa
  • Tatiana Espírito Santo
  • Geo Coppens d’Eeckenbrugge
  • José Manuel LeitãoEmail author


Despite the paramount importance of pineapple (Ananas comosus L.) in world production and trade of tropical fruits, the genomics of this crop is still lagging behind that of other tropical fruit crops such as banana or papaya. A genetic map of pineapple was constructed using an F2 segregating population obtained from a single selfed F1 plant of a cross A. comosus var. comosus (cv. Rondon, clone BR 50) × A. comosus var. bracteatus (Branco do mato, clone BR 20). Multiple randomly amplified markers (RAPD, ISSR and AFLP) were brought together with SSR and EST-SSR markers identified among sequences uploaded to public databases and with sequence-specific markers (SCAR, SSR and CAPS) derived from random amplified markers. Sixty-three randomly amplified markers (RAPD, ISSR and AFLP) were selected and cloned, resulting in 71 sequences which were used to generate sequence-specific SCAR and CAPS markers. The present map includes 492 DNA markers: 57 RAPD, 22 ISSR, 348 AFLP, 20 SSR, 12 EST-SSR, 25 SCARs, 8 CAPS, and the morphological trait locus “piping”, gathered into 33 linkage groups that integrate markers inherited from both botanical varieties, four linkage groups with markers only from var. comosus and three linkage groups with markers exclusively from var. bracteatus. The relatively higher mapping efficiency of sequence-specific markers derived from randomly amplified markers (50.7%) versus SSR (31.4%) and EST-SSR (28.9%) markers is discussed. Spanning over 80% of the 2,470 cM estimated average length of the genome, the present map constitutes a useful research tool for molecular breeding and genomics projects in pineapple and other Bromeliaceae species.


Pineapple Ananas comosus A. comosus var. bracteatus Genetic map Genomics SCAR CAPS SSR EST-SSR Pineapple genomics 



This research was supported by the project PTDC/AGR-GPL/77398/2006: “Construction of an integrated genetic map of Pineapple”, funded by the Fundação para a Ciência e a Tecnologia (FCT), Portugal. Jorge Dias Carlier is the recipient of the post-doctoral grant SFRH/BPD/41714/2007 awarded by the FCT. Tatiana Espírito Santo and Nelson Horta Sousa were recipients of Research fellowships awarded by the FCT within the framework of the project PTDC/AGR-GPL/77398/2006.

Supplementary material

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Supplementary material 1 (PDF 60 kb)


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Copyright information

© Springer Science+Business Media B.V. 2010

Authors and Affiliations

  • Jorge Dias Carlier
    • 1
  • Nelson Horta Sousa
    • 1
  • Tatiana Espírito Santo
    • 1
  • Geo Coppens d’Eeckenbrugge
    • 2
  • José Manuel Leitão
    • 1
    Email author
  1. 1.BioFIG, FCTUniversidade do AlgarveFaroPortugal
  2. 2.CIRAD, UMR 5175 CEFEMontpellierFrance

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