Ty1-copia elements reveal diverse insertion sites linked to polymorphisms among flax (Linum usitatissimum L.) accessions

Galindo-González et al. BMC Genomics (2016) 17:1002 DOI 10.1186/s12864-016-3337-3 RESEARCH ARTICLE Open Access Ty1-copia elements reveal diverse insertion sites linked to polymorphisms among flax (Linum usitatissimum L.) accessions Leonardo Galindo-González1* , Corinne Mhiri2, Marie-Angèle Grandbastien2 and Michael K. Deyholos3 Abstract Background: Initial characterization of the flax genome showed that Ty1-copia retrotransposons are abundant, with several members being recently inserted, and in close association with genes. Recent insertions indicate a potential for ongoing transpositional activity that can create genomic diversity among accessions, cultivars or varieties. The polymorphisms generated constitute a good source of molecular markers that may be associated with phenotype if the insertions alter gene activity. Flax, where accessions are bred mainly for seed nutritional properties or for fibers, constitutes a good model for studying the relationship of transpositional activity with diversification and breeding. In this study, we estimated copy number and used a type of transposon display known as Sequence-Specific Amplification Polymorphisms (SSAPs), to characterize six families of Ty1-copia elements across 14 flax accessions. Polymorphic insertion sites were sequenced to find insertions that could potentially alter gene expression, and a preliminary test was performed with selected genes bearing transposable element (TE) insertions. Results: Quantification of six families of Ty1-copia elements indicated different abundances among TE families and between flax accessions, which suggested diverse transpositional histories. SSAPs showed a high level of polymorphism in most of the evaluated retrotransposon families, with a trend towards higher levels of polymorphism in low-copy number families. Ty1-copia insertion polymorphisms among cultivars allowed a general distinction between oil and fiber types, and between spring and winter types, demonstrating their utility in diversity studies. Characterization of polymorphic insertions revealed an overwhelming association with genes, with insertions disrupting exons, introns or within 1 kb of coding regions. A preliminary test on the potential transcriptional disruption by TEs of four selected genes evaluated in three different tissues, showed one case of significant impact of the insertion on gene expression. Conclusions: We demonstrated that specific Ty1-copia families have been active since breeding commenced in flax. The retrotransposon-derived polymorphism can be used to separate flax types, and the close association of many insertions with genes defines a good source of potential mutations that could be associated with phenotypic changes, resulting in diversification processes. Keywords: Ty1-copia, Transposable elements, Flax, Cultivars, Sequence-Specific Amplification Polymorphism (SSAP) * Correspondence: 1 Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada Full list of author information is available at the end of the article © The Author(s). 2016 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. Galindo-González et al. BMC Genomics (2016) 17:1002 Background Transposable elements (TEs) are DNA fragments that can move between genomic locations using a cut and paste mechanism (DNA transposons), or a copy and paste mechanism via an RNA intermediate (retrotransposons). Transposition can result in alterations of gene expression and diversification between individuals, populations and species. TEs are commonly activated upon stresses that include tissue culture, wounding, microbial elicitors and pathogen attack [1–8]. Polyploidization (whether spontaneous or induced) also mobilizes transposable elements, resulting in genome restructuring, and genetic and epigenetic effects on gene activity (reviewed in [9]). Selective breeding can also affect TE activity. For example, in vegetatively propagated grape clones, TE insertional polymorphisms constitute the largest class of mutations [10]. Genetic diversity associated with TE polymorphisms has been commonly explored in plant varieties and species such as pepper and tomato [2, 11], barley [12], strawberry [13], coffee [14], blue agave [15] and cashew [16]. We previously showed that more than 20% of the flax (Linum usitatissimum) genome is made of TEs [17, 18]. The main group represented in the genome are LTR (Long Terminal Repeat) retrotransposons, from which the Ty1-copia elements are the most abundant. Ty1-copia have five main domains encoding proteins required for the retrotransposition cycle: group-specific antigen (GAG), protease (PR), integrase (INT), reverse transcriptase (RT) and ribonuclease H (RH). Because of their retrotransposition mechanism, LTRs are identical at the time of TE insertion [19], and thus sequence variations in them can be used as a molecular clock of insertion. LTRs act as promoter sequences since they contain cis-acting elements that respond to different stress elicitors [20–25]. Ty1-copia elements can spread randomly throughout the genome and are more often associated with genes than Ty3-gypsy elements [17, 26, 27]. Therefore, Ty1-copia elements can alter gene regulation [28–30], promote transduction events of one or more genes to other genomic locations [31–33], or result in epigenetic gene silencing [34, 35]. Additionally, they can also fall inside genes disrupting gene function or altering splice patterns [36–39]. Numerous Ty1-copia members have been recently inserted in flax, as inferred from their LTR similarity and gene domain conservation (at least 83 Ty1-copia elements have 100% LTR similarity) [17]. Furthermore, Ty1-copia elements have had increasing activity in the flax genome starting five million years ago [17]. These observations indicate that Ty1-copia elements could generate polymorphisms among closely related flax cultivars. Flax is a valuable source of bioproducts derived from the seed (i.e. linseed) and stem fiber [40]. Its breeding for either seed or fiber traits in diverse climates has resulted Page 2 of 18 in diverse cultivars and an array of agrobotanic characteristics that have been artificially selected [40]. While flax grown for human consumption (seeds are used for nutrition but also for oil derived industrial products), is the same species as the flax grown mainly to manufacture linen, they represent two different flax types (oil and fiber) and (...truncated)