Simple sequence repeat marker development from bacterial artificial chromosome end sequences and expressed sequence tags of flax (Linum usitatissimum L.).

Sylvie Cloutier,Andrzej Walichnowski,Raja Ragupathy,Gordon Rowland,Natasa Radovanovic,Evelyn Miranda,Elsa Reimer,Scott Duguid,Raju Datla,Kerry Ward

doi:10.1007/s00122-012-1860-4

Abstract

Flax is an important oilseed crop in North America and is mostly grown as a fibre crop in Europe. As a self-pollinated diploid with a small estimated genome size of ~370 Mb, flax is well suited for fast progress in genomics. In the last few years, important genetic resources have been developed for this crop. Here, we describe the assessment and comparative analyses of 1,506 putative simple sequence repeats (SSRs) of which, 1,164 were derived from BAC-end sequences (BESs) and 342 from expressed sequence tags (ESTs). The SSRs were assessed on a panel of 16 flax accessions with 673 (58 %) and 145 (42 %) primer pairs being polymorphic in the BESs and ESTs, respectively. With 818 novel polymorphic SSR primer pairs reported in this study, the repertoire of available SSRs in flax has more than doubled from the combined total of 508 of all previous reports. Among nucleotide motifs, trinucleotides were the most abundant irrespective of the class, but dinucleotides were the most polymorphic. SSR length was also positively correlated with polymorphism. Two dinucleotide (AT/TA and AG/GA) and two trinucleotide (AAT/ATA/TAA and GAA/AGA/AAG) motifs and their iterations, different from those reported in many other crops, accounted for more than half of all the SSRs and were also more polymorphic (63.4 %) than the rest of the markers (42.7 %). This improved resource promises to be useful in genetic, quantitative trait loci (QTL) and association mapping as well as for anchoring the physical/genetic map with the whole genome shotgun reference sequence of flax.Electronic supplementary materialThe online version of this article (doi:10.1007/s00122-012-1860-4) contains supplementary material, which is available to authorized users.

Highlights

Flax (Linum usitatissimum L.) has been cultivated for several thousand years mainly for its seed oil and its highquality stem fibres
A total of 382 putative novel expressed sequence tags (ESTs)-simple sequence repeats (SSRs) were identified from the EST assembly and 342 primer pairs were designed
We described the development and analysis of 818 novel polymorphic SSR primer pairs in flax detecting 869 loci, of which 145 primer pairs were derived from ESTs and 673 from bacterial artificial chromosome (BAC)-end sequences (BESs), more than doubling the combined previously available flax SSR collections of 508 (Table 3)

Summary

Introduction

Flax (Linum usitatissimum L.) has been cultivated for several thousand years mainly for its seed oil and its highquality stem fibres. In North America, flax is grown primarily as an oilseed crop used for food and feed as well as in bio-product applications such as linoleum flooring, paint and varnishes. Most oilseed flax varieties are rich in omega-3 (alpha linolenic acid, 55–57 %) fatty acid which has been functionally associated with numerous health claims. ‘Solin’ varieties with loss of function mutations in the fatty acid desaturase 3 (fad3) genes are low in omega-3 (2–3 %) and high in omega-6 (*70 %) fatty acids, characteristics required for margarine processing. Flax oil extraction generates a meal which is rich in protein and is sought after as animal feed.

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