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Characterization of wheat DArT markers: genetic and functional features

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Abstract

Diversity array technology (DArT) markers are largely used for mapping, genetic diversity, and association mapping studies. For years, they have been used as anonymous genomic markers, as their sequences were not known. As the sequences of 2,000 wheat DArT clones are now available, this study was designed to analyze these sequences with bioinformatic approaches, and to study the genetic features of a subset of 291 markers positioned on the A and B genomes in three durum wheat genetic maps. A set of 1,757 non-redundant sequences was identified, and used as queries for similarity searches. Analysis of the genetic positions of markers corresponding to nearly identical sequences indicates that redundancy of sequences is one of the factors that explains the clustering of these markers in specific genomic regions. Of a total of 1,124 DArT clones (64 %) that represent putatively expressed sequences, putative functions are proposed for more than 700 of them. Of note, many clones correspond to genes that are related to disease resistance, as characterized by leucine-rich repeat domains, and 40 of these clones are positioned in the three genetic maps presented in this study. Finally, DArT markers have been used to find syntenic regions in the Brachypodium and rice genomes. In conclusion, the analyses herein presented contribute to explain the main features of DArT markers observed in genetic maps, as clustering in short chromosome regions. Moreover, the attribution of putative gene functions for more than 700 sequences makes these markers an optimal tool for collinearity studies or for the identification of candidate genes.

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Acknowledgments

This study was supported by the Italian Ministry of Agriculture (MiPAAF), with the special grants AGRONANOTECH and ESPLORA, and by the Ministry of Education, Universities and Research (MIUR), with the special grant AGROGEN. We are grateful to Andrzej Kilian and Eric Huttner for assistance in DArT marker handling and for providing clone sequences. We are also grateful to Valentina Giovanniello and Pina Ferragonio for their technical support in the construction of the three genetic maps, and to Christopher Berrie for scientific English language editorial assistance.

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Authors and Affiliations

  1. CRA, Cereal Research Centre, SS16 km 675, 71122, Foggia, Italy

    Daniela Marone, Giosuè Panio, Donatella B. M. Ficco, Maria A. Russo, Pasquale De Vita, Roberto Papa, Luigi Cattivelli & Anna M. Mastrangelo

  2. Institute for Sustainable Agriculture, National Scientific Research Council (CSIC), Apdo. 4084, 14080, Córdoba, Spain

    Diego Rubiales

  3. CRA, Genomics Research Centre, Via S. Protaso, 302, 29017, Fiorenzuola d’Arda (PC), Italy

    Luigi Cattivelli

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  1. Daniela Marone
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  2. Giosuè Panio
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  3. Donatella B. M. Ficco
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  4. Maria A. Russo
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  5. Pasquale De Vita
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  6. Roberto Papa
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  7. Diego Rubiales
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  8. Luigi Cattivelli
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  9. Anna M. Mastrangelo
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Correspondence to Anna M. Mastrangelo.

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Communicated by R. Waugh.

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Marone, D., Panio, G., Ficco, D.B.M. et al. Characterization of wheat DArT markers: genetic and functional features. Mol Genet Genomics 287, 741–753 (2012). https://doi.org/10.1007/s00438-012-0714-8

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