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Development and analysis of EST-SSRs for flax (Linum usitatissimum L.)

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Abstract

A set of 146,611 expressed sequence tags (ESTs) were generated from 10 flax cDNA libraries. After assembly, a total of 11,166 contigs and 11,896 singletons were mined for the presence of putative simple sequence repeats (SSRs) and yielded 806 (3.5%) non-redundant sequences which contained 851 putative SSRs. This is equivalent to one EST-SSR per 16.5 kb of sequence. Trinucleotide motifs were the most abundant (76.9%), followed by dinucleotides (13.9%). Tetra-, penta- and hexanucleotide motifs represented <10% of the SSRs identified. A total of 83 SSR motifs were identified. Motif (TTC/GAA)n was the most abundant (10.2%) followed by (CTT/AAG)n (8.7%), (TCT/AGA)n (8.6%), (CT/AG)n (6.7%) and (TC/GA)n (5.3%). A total of 662 primer pairs were designed, of which 610 primer pairs yielded amplicons in a set of 23 flax accessions. Polymorphism between the accessions was found for 248 primer pairs which detected a total of 275 EST-SSR loci. Two to seven alleles were detected per marker. The polymorphism information content value for these markers ranged from 0.08 to 0.82 and averaged 0.35. The 635 alleles detected by the 275 polymorphic EST-SSRs were used to study the genetic relationship of 23 flax accessions. Four major clusters and two singletons were observed. Sub-clusters within the main clusters correlated with the pedigree relationships amongst accessions. The EST-SSRs developed herein represent the first large-scale development of SSR markers in flax. They have potential to be used for the development of genetic and physical maps, quantitative trait loci mapping, genetic diversity studies, association mapping and fingerprinting cultivars for example.

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Acknowledgments

The authors are grateful to Andrzej Walichnowski for manuscript review, Joanne Schiavoni for manuscript preparation and Mike Shillinglaw for the preparation of figures. Technical assistance of Laura Marginet, Natalie Middlestead, Mira Popovic, Elsa Reimer and Andrzej Walichnowski is also acknowledged. Travis Banks provided most helpful bioinformatics expertise throughout the project. This work was financially supported by AAFC A-base project for high-value flax development. This is AAFC contribution number 1972.

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Authors and Affiliations

  1. Cereal Research Centre, Agriculture and Agri-Food Canada, 195 Dafoe Road, Winnipeg, MB, R3T 2M9, Canada

    Sylvie Cloutier & Zhixia Niu

  2. National Research Council, Plant Biotechnology Institute, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada

    Raju Datla

  3. Morden Research Station, Agriculture and Agri-Food Canada, Route 100, Morden, MB, R6M 1Y5, Canada

    Scott Duguid

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  1. Sylvie Cloutier
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  2. Zhixia Niu
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  3. Raju Datla
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  4. Scott Duguid
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Correspondence to Sylvie Cloutier.

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Communicated by Y. Xue.

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Cloutier, S., Niu, Z., Datla, R. et al. Development and analysis of EST-SSRs for flax (Linum usitatissimum L.). Theor Appl Genet 119, 53–63 (2009). https://doi.org/10.1007/s00122-009-1016-3

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