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Chloroplast Genome Diversity in Portuguese Grapevine (Vitis vinifera L.) Cultivars

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Abstract

Grapevine chloroplast (cp) DNA diversity was analysed for the first time through amplification and digestion of fragments of the large single copy (LSC) region by polymerase chain reaction–restriction fragment length polymorphism methodology and also by amplification of three microsatellite loci, previously described as polymorphic in grapevine. Thirty-eight grapevine cultivars collected mainly in the North of Portugal, including some neglected cultivars, four international cultivars (Chasselas, Muscat of Alexandria, Muscat of Hamburg and Pinot) and Vitis riparia and Vitis rupestris, were used in this study with the main goal of finding out their cpDNA diversity and compare the obtained results with previously published data on cultivars from other regions to ascertain their possible origin. Two different alleles were found in each of the three cpSSR loci. Allele variants of the three loci combined in a total of three different haplotypes (A, B and D). The most frequent haplotype, A, was previously reported as the most frequent in Iberian Peninsula and Occidental Europe. Haplotype B was unique to Rabigato, Muscat of Alexandria, V. riparia and V. rupestris. This haplotype was previously proposed to be an ancestral haplotype. Twenty-seven fragments of the LSC region of Vitis vinifera cpDNA were amplified and then digested with HinfI and TaqI restriction enzymes. Polymorphisms were found in the trnT-psbC (TC) and orf184-petA (OA) fragments. In the TC fragment, the polymorphism corresponds to a point mutation in a restriction site of TaqI and is only present in all cultivars with cpSSR haplotype D. In the OA fragment, a short deletion exclusive to the Rabigato cultivar was found. In this case, one sequence tagged site-based marker was developed and will be very useful in future phylogenetic and fingerprinting studies in a broader number of cultivars and in wild grapevine populations. Inference about the progenitors of the Touriga Franca cultivar is done. The present work supports and completes its origin as a descendent of the female and male parents, Marufo and Touriga Nacional.

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Acknowledgments

I. Castro was funded by a predoctoral scholarship from Fundação para a Ciência e a Tecnologia (FCT) (SFRH/BD/22955/2005). The authors acknowledge to the several persons who had the extreme kindness to supply grapevine material.

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Authors and Affiliations

  1. Institute for Biotechnology and Bioengineering, Centre of Genomics and Biotechnology, University of Trás-os-Montes and Alto Douro (IBB/CGB-UTAD), PO BOX 1013, 5001-801, Vila Real, Portugal

    Isaura Castro & Olinda Pinto-Carnide

  2. Department of Plant Biology, E.T.S. Agronomics Engineering, Technical University of Madrid, Ciudad Universitaria s/n, Madrid, Spain

    Jesús María Ortiz & Juan Pedro Martín

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  1. Isaura Castro
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  2. Olinda Pinto-Carnide
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Correspondence to Isaura Castro.

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Castro, I., Pinto-Carnide, O., Ortiz, J.M. et al. Chloroplast Genome Diversity in Portuguese Grapevine (Vitis vinifera L.) Cultivars. Mol Biotechnol 54, 528–540 (2013). https://doi.org/10.1007/s12033-012-9593-9

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