Transient Stability of Epigenetic Population Differentiation in a Clonal Invader

Epigenetic variation may play an important role in how plants cope with novel environments. While significant epigenetic differences among plants from contrasting habitats have often been observed in the field, the stability of these differences remains little understood. Here, we combined field monitoring with a multi-generation common garden approach to study the dynamics of DNA methylation variation in invasive Chinese populations of the clonal alligator weed (Alternanthera philoxeroides). Using AFLP and MSAP markers, we found little variation in DNA sequence but substantial epigenetic population differentiation. In the field, these differences remained stable across multiple years, whereas in a common environment they were maintained at first but then progressively eroded. However, some epigenetic differentiation remained even after 10 asexual generations. Our data indicate that epigenetic variation in alligator weed most likely results from a combination of environmental induction and spontaneous epimutation, and that much of it is neither rapidly reversible (phenotypic plasticity) nor long-term stable, but instead displays an intermediate level of stability. Such transient epigenetic stability could be a beneficial mechanism in novel and heterogeneous environments, particularly in a genetically impoverished invader

Genome-Wide Expression and Alternative Splicing in Domesticated Sunflowers (Helianthus annuus L.) under Flooding Stress

Approximately 10% of agricultural land is subject to periodic flooding, which reduces the growth, survivorship, and yield of most crops, reinforcing the need to understand and enhance flooding resistance in our crops. Here, we generated RNA-Seq data from leaf and root tissue of domesticated sunflower to explore differences in gene expression and alternative splicing (AS) between a resistant and susceptible cultivar under both flooding and control conditions and at three time points. Using a combination of mixed model and gene co-expression analyses, we were able to separate general responses of sunflower to flooding stress from those that contribute to the greater tolerance of the resistant line. Both cultivars responded to flooding stress by upregulating expression levels of known submergence responsive genes, such as alcohol dehydrogenases, and slowing metabolism-related activities. Differential AS reinforced expression differences, with reduced AS frequencies typically observed for genes with upregulated expression. Significant differences were found between the genotypes, including earlier and stronger upregulation of the alcohol fermentation pathway and a more rapid return to pre-flooding gene expression levels in the resistant genotype. Our results show how changes in the timing of gene expression following both the induction of flooding and release from flooding stress contribute to increased flooding tolerance.Science, Faculty ofNon UBCBotany, Department ofReviewedFacult

Data from: Local habitat condition rather than geographic distance determines the genetic structure of Tamarix chinensis populations in Yellow River Delta, China

Understanding the extent of genetic diversity in natural populations and the correlations between population structure and environmental heterogeneity is of great importance to estimation of the potential for species to undergo rapid adaptive changes in response to environmental variation. In this study, we systematically sampled 800 individuals from 26 Tamarix chinensis populations distributed throughout the Yellow River Delta (YRD) region in China, where a mosaic of habitat patches varying in soil salinity was detected. By exploring the micro-geographic genetic structure using the co-dominant microsatellite (SSR) markers, we aimed to answer questions as to what extent the populations diverged and how habitat heterogeneity affected the local population structure and dynamics of T. chinensis in YRD. The results demonstrated a moderate high level of genetic diversity and a low level of genetic differentiation in T. chinensis populations. The genetic variation was mainly maintained within populations, with a weak but significant genetic differentiation being detected among populations (Fst = 0.053, P < 0.001). While the overall genetic diversity within populations decreased progressively along with the increasing soil salinity, the locus T1D12 exhibited an elevated variation among populations, with the allele 558 (T1D12) showing a significantly higher frequency in highly saline habitats than in other sites, suggesting that the ecological differences among patchy habitats led to weak but significant adaptive divergence among populations. Local habitat conditions rather than geographic distances determine the genetic structure of T. chinensis populations in YRD

Genetic structure of Tamarix chinensis populations in Yellow River Delta, China

Genetic structure of Tamarix chinensis populations in Yellow River Delta, Chin

Spatial Genetic Structure in Natural Populations of <em>Phragmites australis</em> in a Mosaic of Saline Habitats in the Yellow River Delta, China

<div><p>Determination of spatial genetic structure (SGS) in natural populations is important for both theoretical aspects of evolutionary genetics and their application in species conservation and ecological restoration. In this study, we examined genetic diversity within and among the natural populations of a cosmopolitan grass <em>Phragmites australis</em> (common reed) in the Yellow River Delta (YRD), China, where a mosaic of habitat patches varying in soil salinity was detected. We demonstrated that, despite their close geographic proximity, the common reed populations in the YRD significantly diverged at six microsatellite loci, exhibiting a strong association of genetic variation with habitat heterogeneity. Genetic distances among populations were best explained as a function of environmental difference, rather than geographical distance. Although the level of genetic divergence among populations was relatively low (<em>F</em>’_ST = 0.073), weak but significant genetic differentiation, as well as the concordance between ecological and genetic landscapes, suggests spatial structuring of genotypes in relation to patchy habitats. These findings not only provided insights into the population dynamics of common reed in changing environments, but also demonstrated the feasibility of using habitat patches in a mosaic landscape as test systems to identify appropriate genetic sources for ecological restoration.</p> </div

Differentially Expressed microRNAs and Target Genes Associated with Plastic Internode Elongation in Alternanthera philoxeroides in Contrasting Hydrological Habitats

Phenotypic plasticity is crucial for plants to survive in changing environments. Discovering microRNAs, identifying their targets and further inferring microRNA functions in mediating plastic developmental responses to environmental changes have been a critical strategy for understanding the underlying molecular mechanisms of phenotypic plasticity. In this study, the dynamic expression patterns of microRNAs under contrasting hydrological habitats in the amphibious species Alternanthera philoxeroides were identified by time course expression profiling using high-throughput sequencing technology. A total of 128 known and 18 novel microRNAs were found to be differentially expressed under contrasting hydrological habitats. The microRNA:mRNA pairs potentially associated with plastic internode elongation were identified by integrative analysis of microRNA and mRNA expression profiles, and were validated by qRT-PCR and 5′ RLM-RACE. The results showed that both the universal microRNAs conserved across different plants and the unique microRNAs novelly identified in A. philoxeroides were involved in the responses to varied water regimes. The results also showed that most of the differentially expressed microRNAs were transiently up-/down-regulated at certain time points during the treatments. The fine-scale temporal changes in microRNA expression highlighted the importance of time-series sampling in identifying stress-responsive microRNAs and analyzing their role in stress response/tolerance

Correlation between the frequency of the 203(<i>PaGT9</i>) homozygote and soil salinity, showing the increasing tendency of the 203(<i>PaGT9</i>) homozygote in populations inhabiting saline habitats in YRD.

<p>Correlation between the frequency of the 203(<i>PaGT9</i>) homozygote and soil salinity, showing the increasing tendency of the 203(<i>PaGT9</i>) homozygote in populations inhabiting saline habitats in YRD.</p

Sampling sites of the common reed in Yellow River Delta.

<p> <b>Soil salinity class:</b></p>*<p>slightly saline;</p>**<p>mediately saline;</p>***<p>highly saline.</p

Estimated population structure for common reed from STRUCTURE analysis.

<p>(A) Plot of the log probability of the data [LnP(D)] given values for K from 1 to 7. Circles represent the likelihood values of 5 replicate runs at each K value. (B) Population clustering for K = 2. Each individual is represented by a thin vertical line, which is partitioned into K coloured segments that represent the individual’s estimated membership fractions. Black lines separate individuals from different sampling sites, which are labelled below the figure.</p