A site-specific insertion sequence in flax genotrophs induced by environment

Heredity determined by the environment: Lamarckian ideas in modern molecular biology

Inheritance of acquired characteristics (IAC) is a well-documented phenomenon occurring both in eukaryotes and prokaryotes. However, it is not included in current biological theories, and the risks of IAC induction are not assessed by genetic toxicology. Furthermore, different kinds of IAC (transgenerational and intergenerational inheritance, genotrophic changes, dauermodifications, vernalization, and some others) are traditionally considered in isolation, thus impeding the development of a comprehensive view on IAC as a whole. Herein, we discuss all currently known kinds of IAC as well as their mechanisms, if unraveled. We demonstrate that IAC is a special case of genotype × environment interactions requiring certain genotypes and, as a rule, prolonged exposure to the inducing influence. Most mechanisms of IAC are epigenetic; these include but not limited to DNA methylation, histone modifications, competition of transcription factors, induction of non-coding RNAs, inhibition of plastid translation, and curing of amyloid and non-amyloid prions. In some cases, changes in DNA sequences or host-microbe interactions are involved as well. The only principal difference between IAC and other environmentally inducible hereditary changes such as the effects of radiation is the origin of the changes: in case of IAC they are definite (determined by the environment), while the others are indefinite (arise from environmentally provoked molecular stochasticity). At least some kinds of IAC are adaptive and could be regarded as the elements of natural selection, though non-canonical in their origin and molecular nature. This is a probable way towards synthesis of the Lamarckian and Darwinian evolutionary conceptions. Applied issues of IAC are also discussed.

Darwin's Pangenesis and the Lamarckian Inheritance of Acquired Characters

Since the earliest days of evolutionary thought, the problem of the inheritance of acquired characters has been a central debate. Darwin accepted the inheritance of acquired characters as an established fact and gave many instances. His Pangenesis was more than anything else an attempt to provide a theory for its explanation. Over the past several decades, there has been increasing evidence for the inheritance of acquired habit and immunity, and for heritable changes induced by food and fertilizer, stress, chemicals, temperature, light and other environmental factors. Many studies also suggest that parental age has certain influences on the characters of offspring. The current explanations include environmentally induced DNA changes (mainly DNA rearrangements and DNA methylation), RNA-mediated inheritance, and horizontal gene transfer. These mechanistic explanations are consistent with Darwin's Pangenesis.

Gene expression profiling of flax (Linum usitatissimum L.) under edaphic stress

BACKGROUND

Cultivated flax (Linum usitatissimum L.) is widely used for production of textile, food, chemical and pharmaceutical products. However, various stresses decrease flax production. Search for genes, which are involved in stress response, is necessary for breeding of adaptive cultivars. Imbalanced concentration of nutrient elements in soil decrease flax yields and also results in heritable changes in some flax lines. The appearance of Linum Insertion Sequence 1 (LIS-1) is the most studied modification. However, LIS-1 function is still unclear.

RESULTS

High-throughput sequencing of transcriptome of flax plants grown under normal (N), phosphate deficient (P), and nutrient excess (NPK) conditions was carried out using Illumina platform. The assembly of transcriptome was performed, and a total of 34924, 33797, and 33698 unique transcripts for N, P, and NPK sequencing libraries were identified, respectively. We have not revealed any LIS-1 derived mRNA in our sequencing data. The analysis of high-throughput sequencing data allowed us to identify genes with potentially differential expression under imbalanced nutrition. For further investigation with qPCR, 15 genes were chosen and their expression levels were evaluated in the extended sampling of 31 flax plants. Significant expression alterations were revealed for genes encoding WRKY and JAZ protein families under P and NPK conditions. Moreover, the alterations of WRKY family genes differed depending on LIS-1 presence in flax plant genome. Besides, we revealed slight and LIS-1 independent mRNA level changes of KRP2 and ING1 genes, which are adjacent to LIS-1, under nutrition stress.

CONCLUSIONS

Differentially expressed genes were identified in flax plants, which were grown under phosphate deficiency and excess nutrition, on the basis of high-throughput sequencing and qPCR data. We showed that WRKY and JAS gene families participate in flax response to imbalanced nutrient content in soil. Besides, we have not identified any mRNA, which could be derived from LIS-1, in our transcriptome sequencing data. Expression of LIS-1 flanking genes, ING1 and KRP2, was suggested not to be nutrient stress-induced. Obtained results provide new insights into edaphic stress response in flax and the role of LIS-1 in these process.

Identification, Expression Analysis, and Target Prediction of Flax Genotroph MicroRNAs Under Normal and Nutrient Stress Conditions

Cultivated flax (Linum usitatissimum L.) is an important plant valuable for industry. Some flax lines can undergo heritable phenotypic and genotypic changes (LIS-1 insertion being the most common) in response to nutrient stress and are called plastic lines. Offspring of plastic lines, which stably inherit the changes, are called genotrophs. MicroRNAs (miRNAs) are involved in a crucial regulatory mechanism of gene expression. They have previously been assumed to take part in nutrient stress response and can, therefore, participate in genotroph formation. In the present study, we performed high-throughput sequencing of small RNAs (sRNAs) extracted from flax plants grown under normal, phosphate deficient and nutrient excess conditions to identify miRNAs and evaluate their expression. Our analysis revealed expression of 96 conserved miRNAs from 21 families in flax. Moreover, 475 novel potential miRNAs were identified for the first time, and their targets were predicted. However, none of the identified miRNAs were transcribed from LIS-1. Expression of seven miRNAs (miR168, miR169, miR395, miR398, miR399, miR408, and lus-miR-N1) with up- or down-regulation under nutrient stress (on the basis of high-throughput sequencing data) was evaluated on extended sampling using qPCR. Reference gene search identified ETIF3H and ETIF3E genes as most suitable for this purpose. Down-regulation of novel potential lus-miR-N1 and up-regulation of conserved miR399 were revealed under the phosphate deficient conditions. In addition, the negative correlation of expression of lus-miR-N1 and its predicted target, ubiquitin-activating enzyme E1 gene, as well as, miR399 and its predicted target, ubiquitin-conjugating enzyme E2 gene, was observed. Thus, in our study, miRNAs expressed in flax plastic lines and genotrophs were identified and their expression and expression of their targets was evaluated using high-throughput sequencing and qPCR for the first time. These data provide new insights into nutrient stress response regulation in plastic flax cultivars.

Floral-dip transformation of flax (Linum usitatissimum) to generate transgenic progenies with a high transformation rate

Agrobacterium-mediated plant transformation via floral-dip is a widely used technique in the field of plant transformation and has been reported to be successful for many plant species. However, flax (Linum usitatissimum) transformation by floral-dip has not been reported. The goal of this protocol is to establish that Agrobacterium and the floral-dip method can be used to generate transgenic flax. We show that this technique is simple, inexpensive, efficient, and more importantly, gives a higher transformation rate than the current available methods of flax transformation. In summary, inflorescences of flax were dipped in a solution of Agrobacterium carrying a binary vector plasmid (T-DNA fragment plus the Linum Insertion Sequence, LIS-1) for 1 - 2 min. The plants were laid flat on their side for 24 hr. Then, plants were maintained under normal growth conditions until the next treatment. The process of dipping was repeated 2 - 3 times, with approximately 10 - 14 day intervals between dipping. The T1 seeds were collected and germinated on soil. After approximately two weeks, treated progenies were tested by direct PCR; 2 - 3 leaves were used per plant plus the appropriate T-DNA primers. Positive transformants were selected and grown to maturity. The transformation rate was unexpectedly high, with 50 - 60% of the seeds from treated plants being positive transformants. This is a higher transformation rate than those reported for Arabidopsis thaliana and other plant species, using floral-dip transformation. It is also the highest, which has been reported so far, for flax transformation using other methods for transformation.

Epigenetic regulation in plant responses to the environment

In this article, we review environmentally mediated epigenetic regulation in plants using two case histories. One of these, vernalization, mediates adaptation of plants to different environments and it exemplifies processes that are reset in each generation. The other, virus-induced silencing, involves transgenerationally inherited epigenetic modifications. Heritable epigenetic marks may result in heritable phenotypic variation, influencing fitness, and so be subject to natural selection. However, unlike genetic inheritance, the epigenetic modifications show instability and are influenced by the environment. These two case histories are then compared with other phenomena in plant biology that are likely to represent epigenetic regulation in response to the environment.

De novo genetic variation revealed in somatic sectors of single Arabidopsis plants

Concern over the tremendous loss of genetic diversity among many of our most important crops has prompted major efforts to preserve seed stocks derived from cultivated species and their wild relatives.  Arabidopsis thaliana propagates mainly by self-fertilizing, and therefore, like many crop plants, theoretically has a limited potential for producing genetically diverse offspring. Despite this, inbreeding has persisted in Arabidopsis for over a million years suggesting that some underlying adaptive mechanism buffers the deleterious consequences of this reproductive strategy. Using presence-absence molecular markers we demonstrate that single Arabidopsis plants can have multiple genotypes. Sequence analyses reveal single nucleotide changes, loss of sequences and, surprisingly, acquisition of unique genomic insertions. Estimates based on quantitative analyses suggest that these genetically discordant sectors are very small but can have a complex genetic makeup. In ruling out more trivial explanations for these data, our findings raise the possibility that intrinsic drivers of genetic variation are responsible for the targeted sequence changes we detect. Given the evolutionary advantage afforded to populations with greater genetic diversity, we hypothesize that organisms that primarily self-fertilize or propagate clonally counteract the genetic cost of such reproductive strategies by leveraging a cryptic reserve of extra-genomic information.

Identification, characterization and distribution of transposable elements in the flax (Linum usitatissimum L.) genome

BACKGROUND

Flax (Linum usitatissimum L.) is an important crop for the production of bioproducts derived from its seed and stem fiber. Transposable elements (TEs) are widespread in plant genomes and are a key component of their evolution. The availability of a genome assembly of flax (Linum usitatissimum) affords new opportunities to explore the diversity of TEs and their relationship to genes and gene expression.

RESULTS

Four de novo repeat identification algorithms (PILER, RepeatScout, LTR_finder and LTR_STRUC) were applied to the flax genome assembly. The resulting library of flax repeats was combined with the RepBase Viridiplantae division and used with RepeatMasker to identify TEs coverage in the genome. LTR retrotransposons were the most abundant TEs (17.2% genome coverage), followed by Long Interspersed Nuclear Element (LINE) retrotransposons (2.10%) and Mutator DNA transposons (1.99%). Comparison of putative flax TEs to flax transcript databases indicated that TEs are not highly expressed in flax. However, the presence of recent insertions, defined by 100% intra-element LTR similarity, provided evidence for recent TE activity. Spatial analysis showed TE-rich regions, gene-rich regions as well as regions with similar genes and TE density. Monte Carlo simulations for the 71 largest scaffolds (≥ 1 Mb each) did not show any regional differences in the frequency of TE overlap with gene coding sequences. However, differences between TE superfamilies were found in their proximity to genes. Genes within TE-rich regions also appeared to have lower transcript expression, based on EST abundance. When LTR elements were compared, Copia showed more diversity, recent insertions and conserved domains than the Gypsy, demonstrating their importance in genome evolution.

CONCLUSIONS

The calculated 23.06% TE coverage of the flax WGS assembly is at the low end of the range of TE coverages reported in other eudicots, although this estimate does not include TEs likely found in unassembled repetitive regions of the genome. Since enrichment for TEs in genomic regions was associated with reduced expression of neighbouring genes, and many members of the Copia LTR superfamily are inserted close to coding regions, we suggest Copia elements have a greater influence on recent flax genome evolution while Gypsy elements have become residual and highly mutated.

The genome of flax (Linum usitatissimum) assembled de novo from short shotgun sequence reads

Flax (Linum usitatissimum) is an ancient crop that is widely cultivated as a source of fiber, oil and medicinally relevant compounds. To accelerate crop improvement, we performed whole-genome shotgun sequencing of the nuclear genome of flax. Seven paired-end libraries ranging in size from 300 bp to 10 kb were sequenced using an Illumina genome analyzer. A de novo assembly, comprised exclusively of deep-coverage (approximately 94× raw, approximately 69× filtered) short-sequence reads (44-100 bp), produced a set of scaffolds with N(50) =694 kb, including contigs with N(50)=20.1 kb. The contig assembly contained 302 Mb of non-redundant sequence representing an estimated 81% genome coverage. Up to 96% of published flax ESTs aligned to the whole-genome shotgun scaffolds. However, comparisons with independently sequenced BACs and fosmids showed some mis-assembly of regions at the genome scale. A total of 43384 protein-coding genes were predicted in the whole-genome shotgun assembly, and up to 93% of published flax ESTs, and 86% of A. thaliana genes aligned to these predicted genes, indicating excellent coverage and accuracy at the gene level. Analysis of the synonymous substitution rates (K(s) ) observed within duplicate gene pairs was consistent with a recent (5-9 MYA) whole-genome duplication in flax. Within the predicted proteome, we observed enrichment of many conserved domains (Pfam-A) that may contribute to the unique properties of this crop, including agglutinin proteins. Together these results show that de novo assembly, based solely on whole-genome shotgun short-sequence reads, is an efficient means of obtaining nearly complete genome sequence information for some plant species.

Genetic and epigenetic effects of plant-pathogen interactions: an evolutionary perspective

Recent reports suggest that exposure to stress is capable of influencing the frequency and pattern of inherited changes in various parts of the genome. In this review, we will discuss the influence of viral pathogens on somatic and meiotic genome stability of Nicotiana tabacum and Arabidopsis thaliana. Plants infected with a compatible pathogen generate a systemic recombination signal that precedes the spread of pathogens and results in changes in the somatic and meiotic recombination frequency. The progeny of infected plants exhibit changes in global and locus-specific DNA methylation patterns, genomic rearrangements at transgenic reporter loci and resistance gene-like-loci, and even tolerance to pathogen infection and abiotic stress. Here, we will discuss the contribution of environmental stresses to genome evolution and will focus on the role of heritable epigenetic changes in response to pathogen infection.

Genome instability and epigenetic modification--heritable responses to environmental stress?

As sessile organisms, plants need to continuously adjust their responses to external stimuli to cope with changing growth conditions. Since the seed dispersal range is often rather limited, exposure of progeny to the growth conditions of parents is very probable. The plasticity of plant phenotypes cannot be simply explained by genetic changes such as point mutations, deletions, insertions and gross chromosomal rearrangements. Since many environmental stresses persist for only one or several plant generations, other mechanisms of adaptation must exist. The heritability of reversible epigenetic modifications that regulate gene expression without changing DNA sequence makes them an attractive alternative mechanism. In this review, we discuss recent advances in understanding how changes in genome stability and epigenetically mediated changes in gene expression could contribute to plant adaptation. We provide examples of environmentally induced transgenerational epigenetic effects that include the appearance of new phenotypes in successive generations of stressed plants. We also describe several cases in which exposure to stress leads to nonrandom heritable but reversible changes in stress tolerance in the progeny of stressed plants.

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

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.

Environmentally induced heritable changes in flax

Some flax varieties respond to nutrient stress by modifying their genome and these modifications can be inherited through many generations. Also associated with these genomic changes are heritable phenotypic variations ^1,2. The flax variety Stormont Cirrus (Pl) when grown under three different nutrient conditions can either remain inducible (under the control conditions), or become stably modified to either the large or small genotroph by growth under high or low nutrient conditions respectively. The lines resulting from the initial growth under each of these conditions appear to grow better when grown under the same conditions in subsequent generations, notably the Pl line grows best under the control treatment indicating that the plants growing under both the high and low nutrients are under stress. One of the genomic changes that are associated with the induction of heritable changes is the appearance of an insertion element (LIS-1) ^{3, 4} while the plants are growing under the nutrient stress. With respect to this insertion event, the flax variety Stormont Cirrus (Pl) when grown under three different nutrient conditions can either remain unchanged (under the control conditions), have the insertion appear in all the plants (under low nutrients) and have this transmitted to the next generation, or have the insertion (or parts of it) appear but not be transmitted through generations (under high nutrients) ⁴. The frequency of the appearance of this insertion indicates that it is under positive selection, which is also consistent with the growth response in subsequent generations. Leaves or meristems harvested at various stages of growth are used for DNA and RNA isolation. The RNA is used to identify variation in expression associated with the various growth environments and/or t he presence/absence of LIS-1. The isolated DNA is used to identify those plants in which the insertion has occurred.

Stability of transgenes in trees: expression of two reporter genes in poplar over three field seasons

High stability of transgene expression is essential for functional genomics studies using transformation approaches and for application of genetic engineering to commercial forestry. We quantified expression of two reporter genes, green fluorescent protein (GFP) and the herbicide bialaphos resistance gene (BAR), in 2256 transgenic poplar trees derived from 404 primary events, and in 106 in vitro-redifferentiated subevents, over 3 years in the greenhouse and in the field. No gene silencing (complete breakdown of expression) was observed for GFP or BAR expression in any of the primary transgenic events during the course of the study. Transgenic cassettes were physically eliminated in four subevents (2.5%) derived from three different primary events during re-organogenesis. Transgene copy number was positively correlated with transgene expression level; however, a majority of transformants (85%) carried single-copy transgenes. About one-third of the events containing two-copy inserts had repeats formed at the same chromosomal position, with direct repeats being the main type observed (87%). All events containing more than two transgene copies showed repeat formation at least at one locus, with direct repeats again dominant (77%). Loci with two direct repeats had substantially greater transgene expression level than other types of two-copy T-DNA configurations, but insert organization was not associated with stability of transgene expression. Use of the poplar rbcS promoter, which drove BAR in the transgenic constructs, had no adverse effect on transgene expression levels or stability compared with the heterologous CaMV 35S promoter, which directed GFP expression.

Epigenetic control of plant stress response

Living organisms have the clearly defined strategies of stress response. These strategies are predefined by a genetic make-up of the organism and depend on a complex regulatory network of molecular interactions. Although in most cases, the plant response to stress based on the mechanisms of tolerance, resistance, and avoidance has clearly defined metabolic pathways, the ability to acclimate/adapt after a single generation exposure previously observed in several studies (Boyko A et al. [2007]: Nucleic Acids Res 35:1714-1725; Boyko and Kovalchuk, unpublished data), represents an interesting phenomenon that cannot be explained by Mendelian genetics. The latest findings in the field of epigenetics and the process of a reversible control over gene expression and inheritance lead to believe that organisms, especially plants, may have a flexible short-term strategy of the response to stress. Indeed, the organisms that can modify gene expression reversibly have an advantage in evolutionary terms, since they can avoid unnecessary excessive rearrangements and population diversification. This review covers various epigenetic processes involved in plant stress response. We focus on the mechanisms of DNA methylation and histone modifications responsible for the protection of somatic cells and inheritance of stress memories.

Molecular mechanisms of canalization: Hsp90 and beyond

The Hsp90 chaperone machine facilitates the maturation of a diverse set of 'client' proteins. Many of these Hsp90 clients are essential nodes in signal transduction pathways and regulatory circuits,accounting for the important role Hsp90 plays in organismal development and responses to the environment. Recent findings suggest a broader impact of the chaperone on phenotype: fully functional Hsp90 canalizes wild-type phenotypes by suppressing underlying genetic and epigenetic variation. This variation can be expressed upon challenging the Hsp90 machinery by environmental stress, genetic or pharmaceutical targeting of Hsp90. The existence of Hsp90-buffered genetic and epigenetic variation together with plausible release mechanisms has wide-ranging implication for phenotype and possibly evolutionary processes. Here,we discuss the role of Hsp90 in canalization and organismal plasticity,and highlight important questions for future experimental inquiry.