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Genome-wide analysis of plastome sequence variation and development of plastidial CAPS markers in common potato and related Solanum species

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Abstract

The plastome sequence of the European cultivated potato, Solanum tuberosum subsp. tuberosum (tbr, GenBank accession no. DQ386163), was compared with that of S. bulbocastanum, a wild potato relative (blb, GenBank accession no. DQ347958), in order to characterize the degree and type of variability in different genomic regions, and develop molecular markers relevant to genetics, breeding and biotechnology of potato. One hundred forty-two and 251 PICs (Potentially Informative Characters) were found in coding and non-coding sequences (NCSs), respectively. Further, while variation in coding regions was almost exclusively due to nucleotide substitutions, 25% of PICs in NCSs of tbr and blb were due to indels, most of them mononucleotide or longer tandem repeats (micro and minisatellites). Four intergenic regions were selected for further analyses in other 16 tuber-bearing Solanum species. The rps16-trnQ UUG gene spacer was found to be the most variable, forty-six PICs in this region distinguishing 18 haplotypes. Analysis of haplotype relationships, based on variability in the four intergenic regions, confirmed that the most primitive species from Central America were the most distant to S. tuberosum. Finally, polymorphic sites in the same regions were used to develop a set of CAPS (Cleaved Amplified Polymorphic Sequences) markers for species/cytoplasm identification in Solanum spp.

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Acknowledgments

Research partially funded by the collaborative grant from the European Union (FP6 Plastomics project LSHG-CT-2003-503228) to TC. The critical review of the manuscript by Dr. A. Nunziata (“Genopom” Genomics Platform, Portici, Italy) and Dr. M.L. Chiusano (University of Naples “Federico II”, Italy) is gratefully acknowledged.

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  1. Daniela Gargano

    Present address: Center for Organelle Research, University of Stavanger, 4036, Stavanger, Norway

Authors and Affiliations

  1. CNR-IGV, Institute of Plant Genetics, Via Università 133, 80055, Portici, Italy

    Daniela Gargano, Nunzia Scotti, Stefania Grillo & Teodoro Cardi

  2. CRIBI Biotechnology Centre and Department of Biology, University of Padova, Via U. Bassi 58/B, 35131, Padova, Italy

    Alessandro Vezzi, Alessandra Bilardi & Giorgio Valle

  3. Department of Structural and Functional Biology, University of Naples “Federico II”, Via Cinthia 26, 80126, Naples, Italy

    Salvatore Cozzolino

  4. CRA-ORT, Research Center for Vegetable Crops, Via dei Cavalleggeri 25, 84098, Pontecagnano (SA), Italy

    Teodoro Cardi

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  1. Daniela Gargano
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  2. Nunzia Scotti
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Correspondence to Teodoro Cardi.

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IGV publication no. 360.

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Gargano, D., Scotti, N., Vezzi, A. et al. Genome-wide analysis of plastome sequence variation and development of plastidial CAPS markers in common potato and related Solanum species. Genet Resour Crop Evol 59, 419–430 (2012). https://doi.org/10.1007/s10722-011-9692-7

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  • DOI: https://doi.org/10.1007/s10722-011-9692-7

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