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Development of SSR markers and construction of a consensus genetic map for chicory (Cichorium intybus L.)

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Abstract

A consensus genetic map for chicory (2n = 2x = 18) was obtained after the integration of molecular marker data of two industrial chicory progenies (K28K59, Rubis118) and one witloof chicory progeny (BR). As a limited number of co-dominant markers was available at the beginning of this work, three different microsatellite-enriched libraries were produced from genomic DNA, resulting in 420, 719 and 1,251 sequences, respectively. The level of informative Simple Sequence Repeat (SSR) sequences from the three libraries ranged from 28 to 40%, thus defining a set of 730 SSR markers available for polymorphism screening. A subset of 81 Sequence-Tagged Sites (STS) developed from EST, cDNA, genes, and non-coding sequences was screened through Single Strand Conformational Polymorphism (SSCP) analysis, leading to 46 polymorphic loci integrated in the genetic maps. Markers were grouped and ordered on 9 homologous Linkage Groups (LG) for each of the three maps: 274 markers in K28K59, 282 markers in Rubis118, 178 markers in BR. Co-linear regions between maps were identified through 193 ‘bridge’ markers that allowed the integration of the 9 homologous LG in a consensus map containing 472 markers and covering 878 cM. Comparison across maps revealed the presence of 4 conserved regions with significant distorted markers, also defined as Segregation Distortion Regions (SDR), affected by gametic or zygotic selection factors. Marker distribution was not always uniform; 6 LG possessed homologous clustered regions in all maps. The consensus map could be the starting point for the identification and the cloning of major genes and QTL in fundamental and applied genetic areas in chicory.

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Acknowledgments

The present work was financed by a public–private partnership ‘Groupement d’Intérêt Scientifique’ CARTOCHIC involving UMR 1281 SADV, Université de Lille 1, Florimond Desprez Veuve and Fils SAS, Leroux SAS, and SARL Hoquet Endives. We would like to thank Louis Delesalle, Jean-Christophe Lepeltier, Pierre Devaux (Florimond-Desprez) and Pascal Lévêque (Hoquet Endives) who have generated and maintained the Rubis118 and BR populations. We also acknowledge the SREL laboratory of Dr Travis Glenn (Travis Glenn, Cris Hagen, Lucy Dueck, SREL, Aitken, SC, USA) for the training at the first authors in the SSR enrichment protocol, and Aude Darracq (UMR 8016 GEPV, Université de Lille 1) for the development of a program devoted to the identification of unique SSR sequences. Helpful comments and critical reading of the manuscript by Bruno Desprez and Pierre Devaux have also been greatly appreciated.

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  1. GIS CARTOCHIC, USTL, Bât SN2, 3ième étage, 59655, Villeneuve d’Ascq, France

    T. Cadalen, M. Mörchen, C. Blassiau, I. Scheer, J-L. Hilbert, T. Hendriks & M-C. Quillet

  2. UMR USTL/INRA 1281 «Stress Abiotiques et Différenciation des Végétaux Cultivés», ERT 1067, Université de Lille 1, Bât SN2, 3ième étage, 59655, Villeneuve d’Ascq, France

    C. Blassiau, A. Clabaut, J-L. Hilbert, T. Hendriks & M-C. Quillet

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  1. T. Cadalen
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Thierry Cadalen and Monika Mörchen contributed equally to this work.

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Cadalen, T., Mörchen, M., Blassiau, C. et al. Development of SSR markers and construction of a consensus genetic map for chicory (Cichorium intybus L.). Mol Breeding 25, 699–722 (2010). https://doi.org/10.1007/s11032-009-9369-5

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