Greenhouse Spatial Effects Detected in the Barley (Hordeum vulgare L.) Epigenome Underlie Stochasticity of DNA Methylation

Environmental cues are known to alter the methylation profile of genomic DNA, and thereby change the expression of some genes. A proportion of such modifications may become adaptive by adjusting expression of stress response genes but others have been shown to be highly stochastic, even under controlled conditions. The influence of environmental flux on plants adds an additional layer of complexity that has potential to confound attempts to interpret interactions between environment, methylome, and plant form. We therefore adopt a positional and longitudinal approach to study progressive changes to barley DNA methylation patterns in response to salt exposure during development under greenhouse conditions. Methylation-sensitive amplified polymorphism (MSAP) and phenotypic analyses of nine diverse barley varieties were grown in a randomized plot design, under two salt treatments (0 and 75 mM NaCl). Combining environmental, phenotypic and epigenetic data analyses, we show that at least part of the epigenetic variability, previously described as stochastic, is linked to environmental micro-variations during plant growth. Additionally, we show that differences in methylation increase with time of exposure to micro-variations in environment. We propose that subsequent epigenetic studies take into account microclimate-induced epigenetic variability

Greenhouse Spatial Effects Detected in the Barley (\u3cem\u3eHordeum vulgare\u3c/em\u3e L.) Epigenome Underlie Stochasticity of DNA Methylation

Environmental cues are known to alter the methylation profile of genomic DNA, and thereby change the expression of some genes. A proportion of such modifications may become adaptive by adjusting expression of stress response genes but others have been shown to be highly stochastic, even under controlled conditions. The influence of environmental flux on plants adds an additional layer of complexity that has potential to confound attempts to interpret interactions between environment, methylome, and plant form. We therefore adopt a positional and longitudinal approach to study progressive changes to barley DNA methylation patterns in response to salt exposure during development under greenhouse conditions. Methylation-sensitive amplified polymorphism (MSAP) and phenotypic analyses of nine diverse barley varieties were grown in a randomized plot design, under two salt treatments (0 and 75 mM NaCl). Combining environmental, phenotypic and epigenetic data analyses, we show that at least part of the epigenetic variability, previously described as stochastic, is linked to environmental micro-variations during plant growth. Additionally, we show that differences in methylation increase with time of exposure to micro-variations in environment. We propose that subsequent epigenetic studies take into account microclimate-induced epigenetic variability

Atlas of Age- and Tissue-Specific DNA Methylation during Early Development of Barley (<em>Hordeum vulgare</em>)

The barley (Hordeum vulgare) genome comprises over 32,000 genes, with differentiated cells expressing only a subset of genes; the remainder being silent. Mechanisms by which tissue-specific genes are regulated are not entirely understood, although DNA methylation is likely to be involved. To shed light on the dynamic of DNA methylation during development and its variation between organs, methylation-sensitive genotyping by sequencing (ms-GBS) was used to generate methylation profiles for roots, leaf-blades and leaf-sheaths from five barley varieties, using seedlings at the three-leaf stage. Robust differentially methylated markers (DMMs) were characterised by pairwise comparisons of roots, leaf-blades and leaf-sheaths of three different ages. While very many DMMs were found between roots and leaf parts, only a few existed between leaf-blades and leaf-sheaths, with differences decreasing with leaf rank. Organ-specific DMMs appeared to target mainly repeat regions, implying that organ differentiation partially relies on the spreading of DNA methylation from repeats to promoters of adjacent genes. Identified DMMs indicate that different organs do possess diagnostic methylation profiles and suggest that DNA methylation is important for both tissue differentiation and organ function and will provide the basis to the understanding of the role of DNA methylation in plant organ differentiation and development

Salt Stress Induces Non-CG Methylation in Coding Regions of Barley Seedlings (Hordeum vulgare)

Salinity can negatively impact crop growth and yield. Changes in DNA methylation are known to occur when plants are challenged by stress and have been associated with the regulation of stress-response genes. However, the role of DNA-methylation in moderating gene expression in response to salt stress has been relatively poorly studied among crops such as barley. Here, we assessed the extent of salt-induced alterations of DNA methylation in barley and their putative role in perturbed gene expression. Using Next Generation Sequencing, we screened the leaf and root methylomes of five divergent barley varieties grown under control and three salt concentrations, to seek genotype independent salt-induced changes in DNA methylation. Salt stress caused increased methylation in leaves but diminished methylation in roots with a higher number of changes in leaves than in roots, indicating that salt induced changes to global methylation are organ specific. Differentially Methylated Markers (DMMs) were mostly located in close proximity to repeat elements, but also in 1094 genes, of which many possessed gene ontology (GO) terms associated with plant responses to stress. Identified markers have potential value as sentinels of salt stress and provide a starting point to allow understanding of the functional role of DNA methylation in facilitating barley&rsquo;s response to this stressor

Salt Stress Induces Non-CG Methylation in Coding Regions of Barley Seedlings (\u3cem\u3eHordeum vulgare\u3c/em\u3e)

Salinity can negatively impact crop growth and yield. Changes in DNA methylation are known to occur when plants are challenged by stress and have been associated with the regulation of stress-response genes. However, the role of DNA-methylation in moderating gene expression in response to salt stress has been relatively poorly studied among crops such as barley. Here, we assessed the extent of salt-induced alterations of DNA methylation in barley and their putative role in perturbed gene expression. Using Next Generation Sequencing, we screened the leaf and root methylomes of five divergent barley varieties grown under control and three salt concentrations, to seek genotype independent salt-induced changes in DNA methylation. Salt stress caused increased methylation in leaves but diminished methylation in roots with a higher number of changes in leaves than in roots, indicating that salt induced changes to global methylation are organ specific. Differentially Methylated Markers (DMMs) were mostly located in close proximity to repeat elements, but also in 1094 genes, of which many possessed gene ontology (GO) terms associated with plant responses to stress. Identified markers have potential value as sentinels of salt stress and provide a starting point to allow understanding of the functional role of DNA methylation in facilitating barley’s response to this stressor

Past, Present and Future Perspectives on Groundnut Breeding in Burkina Faso

Groundnut (Arachis hypogaea L.) is a major food and cash crop in Burkina Faso. Due to the growing demand for raw oilseeds, there is an increasing interest in groundnut production from traditional rain-fed areas to irrigated environments. However, despite implementation of many initiatives in the past to increase groundnut productivity and production, the groundnut industry still struggles to prosper due to the fact of several constraints including minimal development research and fluctuating markets. Yield penalty due to the presence of drought and biotic stresses continue to be a major drawback for groundnut production. This review traces progress in the groundnut breeding that started in Burkina Faso before the country&rsquo;s political independence in 1960 through to present times. Up to the 1980s, groundnut improvement was led by international research institutions such as IRHO (Institute of Oils and Oleaginous Research) and ICRISAT (International Crops Research Institute for the Semi-Arid Tropics). However, international breeding initiatives were not sufficient to establish a robust domestic groundnut breeding programme. This review also provides essential information about opportunities and challenges for groundnut research in Burkina Faso, emphasising the need for institutional attention to genetic improvement of the crop

Assessment of stress-induced and developmentally-induced DNA methylation changes in barley (Hordeum vulgare L.)

DNA methylation is involved in both plant development and adaptation to environmental stress. Changes in DNA methylation can affect the expression of genes that are important for both plant tissue differentiation and stress response. Characterisation of tissue and stress specific methylation markers generates an invaluable tool for epiallele discovery that can be used for future functional and crop improvement studies. We used barley as a plant model, and salinity as a stress model, to study methylation markers that discriminate the plant tissues and that are specific to salinity stress. This choice presented the advantage of using a crop plant with a reference genome sequence, which allows for genomic analyses; and an abiotic stress factor that is relatively easy to control. Nine barley varieties subjected to mild salt stress (75 mM NaCl) were studied for their response to the stress by measuring phenotypic traits, such as biomass, yield and ion accumulation in the leaves. Then, Methylation Sensitive Amplified Polymorphisms (MSAP) were used to analyse changes induced by salt stress in their DNA methylation profiles, which were tested for correlation with the phenotypic data from the same plants. This study revealed that, although the MSAP approach can detect differentially methylated markers induced by a mild salt stress in barley, it presented a limitation in the number of differentially methylated markers (DMMs) detected. This study also revealed that the detection of DMMs by MSAPs was significantly influenced by genotypic differences among varieties. Finally, analysis of the epigenetic variability detected by MSAP indicated that microclimatic differences experienced by different plants in the study contributed to what was previously considered to be stochastic variability. The results from the MSAP suggested an alternative approach was required to identify DMMs that are conserved across barley varieties. Using the high throughput DNA sequencing approach methylation-sensitive genotyping by sequencing (ms-GBS), we detected thousands of saltinduced DMMs and similar numbers of tissue-specific DMMs. Ms-GBS-generated DMMs were potentially universal, since they were conserved in five barley varieties used in the study. Sequence analysis of the ms-GBS generated DMMs indicate that both tissue-specific and salt induced changes in DNA methylation happen preferentially in repeat regions, but also target other gene types, such as protein-coding and Transfer RNA genes. Ontology analysis of differentially methylated protein-coding genes revealed that many are likely to play a role in stress response and organ-specific functions. However, further studies, including expression analyses, are needed to link gene methylation to gene expression.Thesis (Ph.D.) (Research by Publication) -- University of Adelaide, School of Agriculture, Food and Wine, 2017

Global DNA Methylation Patterns Can Play a Role in Defining Terroir in Grapevine (Vitis vinifera cv. Shiraz)

Understanding how grapevines perceive and adapt to different environments will provide us with an insight into how to better manage crop quality. Mounting evidence suggests that epigenetic mechanisms are a key interface between the environment and the genotype that ultimately affect the plant’s phenotype. Moreover, it is now widely accepted that epigenetic mechanisms are a source of useful variability during crop varietal selection that could affect crop performance. While the contribution of DNA methylation to plant performance has been extensively studied in other major crops, very little work has been done in grapevine. To study the genetic and epigenetic diversity across 22 vineyards planted with the cultivar Shiraz in six wine sub-regions of the Barossa, South Australia. Methylation sensitive amplified polymorphisms (MSAPs) were used to obtain global patterns of DNA methylation. The observed epigenetic profiles showed a high level of differentiation that grouped vineyards by their area of provenance despite the low genetic differentiation between vineyards and sub-regions. Pairwise epigenetic distances between vineyards indicate that the main contributor (23–24%) to the detected variability is associated to the distribution of the vineyards on the N–S axis. Analysis of the methylation profiles of vineyards pruned with the same system increased the positive correlation observed between geographic distance and epigenetic distance suggesting that pruning system affects inter-vineyard epigenetic differentiation. Finally, methylation sensitive genotyping by sequencing identified 3,598 differentially methylated genes in grapevine leaves that were assigned to 1,144 unique gene ontology terms of which 8.6% were associated with response to environmental stimulus. Our results suggest that DNA methylation differences between vineyards and sub-regions within The Barossa are influenced both by the geographic location and, to a lesser extent, by pruning system. Finally, we discuss how epigenetic variability can be used as a tool to understand and potentially modulate terroir in grapevine