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Genetic structure and linkage disequilibrium in landrace populations of barley in Sardinia

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Abstract

Multilocus digenic linkage disequilibria (LD) and their population structure were investigated in eleven landrace populations of barley (Hordeum vulgare ssp. vulgare L.) in Sardinia, using 134 dominant simple-sequence amplified polymorphism markers. The analysis of molecular variance for these markers indicated that the populations were partially differentiated (F ST = 0.18), and clustered into three geographic areas. Consistent with this population pattern, STRUCTURE analysis allocated individuals from a bulk of all populations into four genetic groups, and these groups also showed geographic patterns. In agreement with other molecular studies in barley, the general level of LD was low (13 % of locus pairs, with P < 0.01) in the bulk of 337 lines, and decayed steeply with map distance between markers. The partitioning of multilocus associations into various components indicated that genetic drift and founder effects played a major role in determining the overall genetic makeup of the diversity in these landrace populations, but that epistatic homogenising or diversifying selection was also present. Notably, the variance of the disequilibrium component was relatively high, which implies caution in the pooling of barley lines for association studies. Finally, we compared the analyses of multilocus structure in barley landrace populations with parallel analyses in both composite crosses of barley on the one hand and in natural populations of wild barley on the other. Neither of these serves as suitable mimics of landraces in barley, which require their own study. Overall, the results suggest that these populations can be exploited for LD mapping if population structure is controlled.

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Acknowledgments

MR performed the experiments under the supervision of DOS and analysed the data; MR and DR interpreted the data and wrote the manuscript; AHDB contributed ideas and co-wrote the manuscript; DOS, RP and GA contributed ideas and commented on the manuscript. RP and GA conceived and designed the study. Molecular analyses were carried out by the first author during the 2003 at NIAB (Cambridge, UK) while supported from the EC by a Marie-Curie Training Site Fellowship. This work was also supported by the Sardinian Region (Master and Back Program). The reviewers of the manuscript are thanked for helpful comments.

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Authors and Affiliations

  1. Centro per la Conservazione e Valorizzazione della Biodiversità Vegetale, Università degli Studi di Sassari, Via E. de Nicola, 07100, Sassari, Italy

    Monica Rodriguez & Giovanna Attene

  2. Sezione di Agronomia, Coltivazioni Erbacee e Genetica (SACEG), Dipartimento di Agraria, Università degli Studi di Sassari, Via E. de Nicola, 07100, Sassari, Italy

    Domenico Rau & Giovanna Attene

  3. John Bingham Laboratory, National Institute of Agricultural Botany, Huntington Road, Cambridge, CB3 0LE, UK

    Donal O’Sullivan

  4. Centre for Australian National Biodiversity Research CSIRO Plant Industry, GPO Box 1600, Canberra, ACT 260, Australia

    Anthony H. D. Brown

  5. Dipartimento di Scienze Agrarie, Alimentari ed Ambientali, Università Politecnica delle Marche, Via Brecce Bianche, 60131, Ancona, Italy

    Roberto Papa

  6. Cereal Research Centre, CRA-CER Agricultural Research Council (CRA), S.S. 16, km 675, 71122, Foggia, Italy

    Roberto Papa

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  1. Monica Rodriguez
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  2. Domenico Rau
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Correspondence to Monica Rodriguez.

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Communicated by A. Graner.

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Rodriguez, M., Rau, D., O’Sullivan, D. et al. Genetic structure and linkage disequilibrium in landrace populations of barley in Sardinia. Theor Appl Genet 125, 171–184 (2012). https://doi.org/10.1007/s00122-012-1824-8

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