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Genetic diversity of cultivated flax (Linum usitatissimum L.) germplasm assessed by retrotransposon-based markers

Abstract

Retrotransposon segments were characterized and inter-retrotransposon amplified polymorphism (IRAP) markers developed for cultivated flax (Linum usitatissimum L.) and the Linum genus. Over 75 distinct long terminal repeat retrotransposon segments were cloned, the first set for Linum, and specific primers designed for them. IRAP was then used to evaluate genetic diversity among 708 accessions of cultivated flax comprising 143 landraces, 387 varieties, and 178 breeding lines. These included both traditional and modern, oil (86), fiber (351), and combined-use (271) accessions, originating from 36 countries, and 10 wild Linum species. The set of 10 most polymorphic primers yielded 141 reproducible informative data points per accession, with 52% polymorphism and a 0.34 Shannon diversity index. The maximal genetic diversity was detected among wild Linum species (100% IRAP polymorphism and 0.57 Jaccard similarity), while diversity within cultivated germplasm decreased from landraces (58%, 0.63) to breeding lines (48%, 0.85) and cultivars (50%, 0.81). Application of Bayesian methods for clustering resulted in the robust identification of 20 clusters of accessions, which were unstratified according to origin or user type. This indicates an overlap in genetic diversity despite disruptive selection for fiber versus oil types. Nevertheless, eight clusters contained high proportions (70–100%) of commercial cultivars, whereas two clusters were rich (60%) in landraces. These findings provide a basis for better flax germplasm management, core collection establishment, and exploration of diversity in breeding, as well as for exploration of the role of retrotransposons in flax genome dynamics.

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Acknowledgments

This work was financially supported by the Ministry of Education of Czech Republic research project MSMT 2678424601. The technical support of Mrs. L. Vítámvásová and E. Fialová, as well as the laboratory support of Anne-Mari Narvanto and Ursula Lönnqvist of the Institute of Biotechnology, University of Helsinki, are gratefully acknowledged. P.S. acknowledges the OECD fellowship AGR/PR(2006)1-JA00035882, within which flax LTR sequences and IRAP primers were generated in the Schulman laboratory.

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Correspondence to P. Smýkal.

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Gene Bank accessions

DQ767972, GU735096–GU735098, GU929874–GU929878, GU980587–GU980590

Communicated by A. Graner.

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Smýkal, P., Bačová-Kerteszová, N., Kalendar, R. et al. Genetic diversity of cultivated flax (Linum usitatissimum L.) germplasm assessed by retrotransposon-based markers. Theor Appl Genet 122, 1385–1397 (2011). https://doi.org/10.1007/s00122-011-1539-2

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Keywords

  • Amplify Fragment Length Polymorphism
  • Long Terminal Repeat
  • Breeding Line
  • Fiber Flax
  • Primer Binding Site