Biology subjects

Rodriguez Lopez, C. M.

Publications and source records attributed to Rodriguez Lopez, C. M..

11 recordsLinked to original sources

bioRxiv2024

Transcriptome Analysis Reveals Long-Term Somatic Memory of Stress in The Woody Perennial Crop, Grapevine Vitis Vinifera cv. Cabernet Sauvignon

Plants can generate a molecular memory of stress resulting in primed plants that are more resilient to subsequent stresses occurring days to weeks after the priming event. Whether such a priming effect is maintained over longer periods, and after winter dormancy in perennial plants, is less studied. Here, we used whole transcriptome and methylome sequencing of grapevine plants over two growing seasons to characterize grapevines response to combined drought and heat stress in naive and primed plants. Our results showed changes in expression of genes associated with epigenetic modifications during stress and after stress removal, suggesting the establishment of epigenetic memory of stress. Primed plants had a small number of differentially expressed genes associated with stress response one year after the priming event even in the absence of second stress and presented a stronger transcriptional response than naive plants when re-exposed to stress. Methylome analysis revealed an increase in DNA methylation in primed vines under combined stress, and that methylation patterns were less variable among plants under stress than control plants. We did not observe any correlation between DNA methylation and gene transcription, suggesting that stress-induced expression changes were, at least partially, independent of DNA methylation, with posttranscriptional regulation and histone modifications more likely candidates in the establishment of epigenetic memory. Additionally, we characterized stress responsive genes based on their transcriptional profile and function and propose a new comprehensive and intuitive classification model for stress memory genes in perennials.

plant biology↗

bioRxiv2023

Multi-Omics Insights into Grapevine Dormancy-Budburst Transition: Gene Expression, miRNA Regulation, and DNA Methylation

In grapevine, the transition from a dormant bud to budburst is a critical developmental process related to vegetative and reproductive growth. We generated a time series analysis (five sampling time points) and used transcriptome, small RNA, and whole-genome bisulfite sequencing to characterize this transition. Ecodormant buds took an average of 17 days to budburst. Transcriptome analysis identified a total of 7002 differentially expressed genes across all sampling times and revealed that the brassinosteroid metabolism and the linoleic acid metabolism pathways are upregulated and downregulated respectively across all time points. Gene expression cluster analysis identified the activation of the photosynthesis pathway and photosynthesis related genes during this transition. miRNA expression analysis identified a steady increase in expression of two miRNAs, miR159a and miR159b during the transition from dormancy to budburst. Our analysis suggests that these two miRNAs promote budburst by repressing the expression of auxin responsive genes. Finally, a continued increase in CG methylation levels was observed during the dormancy to budburst transition. Differential methylation analysis, considering dormant buds as the control stage, yielded 6354 differentially methylated regions across the genome. Two glucosidase genes exhibited increases in promoter methylation and a corresponding decrease in gene expression in our analysis. This study provides a multi-omics view of grapevine bud transition from dormancy to bud burst and unveils the interacting genetic and epigenetic networks regulating this process.

plant biology↗

bioRxiv2023

Epigenetic differences between wild and cultivated grapevines highlight the contribution of DNA methylation during crop domestication

The domestication process in grapevine facilitated the fixation of desired traits. The vegetative propagation of grapevines through cuttings has allowed for easier preservation of these genotypes compared to sexual reproduction. Nonetheless, even with vegetative propagation, different phenotypes often emerge within the same vineyard due to potential genetic somatic mutations in the genome. These mutations, however, are not the sole factors influencing phenotype. Alongside somatic variations, epigenetic variation has been proposed as pivotal player in regulating phenotypic variability acquired during domestication. The emergence of these epialleles might have significantly influenced grapevine domestication over time. This study aims to investigate the impact of the domestication process on the methylation patterns in cultivated grapevines. Reduced-representation bisulphite sequencing was conducted on 18 cultivated and wild accessions. Results revealed that cultivated grapevines exhibited higher methylation levels than their wild counterparts. Differential Methylation Analysis between wild and cultivated grapevines identified a total of 9955 differentially methylated cytosines, of which 78% where hypermethylated in cultivated grapevines. Functional analysis shows that core methylated genes (those consistently methylated in wild and cultivated accessions) are associated to stress response and terpenoid/isoprenoid metabolic processes. While genes presenting differential methylation are associated with proteins targeting to the peroxisome, ethylene regulation, histone modifications, and defense response. Additionally, our findings reveal that environmentally induced DNA methylation patterns are, at least partially, guided by the region of origin of wild grapevine accessions. Collectively, our results shed light on the pivotal roles that epialleles might have played throughout the domestication history of grapevines.

plant biology↗

bioRxiv2021

Identification of marker-trait associated SNPs for fruit weight and plant height in a wild and domesticated jujube fruit tree (Ziziphus spp.) collection using genotyping-by-sequencing

Ziziphus are economically and nutritionally important fruiting plants that were domesticated in China around 7000 years ago. We identified genetic diversity in 141 accessions of four, different species collected in Pakistan and in China, including wild species of Ziziphus mauritiana, Z. nummularia and Z. oxyphllya, and both wild and domesticated Z. jujuba Mill. Population structure, phylogenetic analysis and principal coordinates analysis based on 10,889 high-quality SNPs derived from genotyping-by-sequencing indicated that the accessions clustered into two major groups. The wild Pakistani Z. jujuba and Z. nummularia exhibited higher genetic diversity and polymorphic information content (0.37 and 0.23 respectively) than other species. We further conducted a genome-wide association study and discovered six highly significant marker-trait associations for fruit weight and plant height in this population. Our study provides important information for future breeding of Ziziphus species.

plant biology↗

bioRxiv2021

Genetic similarity enhances the strength of the relationship between gut bacteria and host DNA methylation

Factors such as host age, sex, diet, health status and genotype constitute the environmental envelope shaping microbial communities in the hosts gut. It has also been proposed that gut microbiota may be influenced by host epigenetics. Although the relationship between the hosts genotype/epigenotype and its associated microbiota has been the focus of a number of recent studies, the relative importance of these interactions and their biological relevance are still poorly understood. We used methylation-sensitive genotyping by sequencing to genotype and epigenotype invasive cane toads (Rhinella marina) from the species Australian range-core (three sites) and the invasion-front (three sites), and 16S rRNA gene sequencing to characterize their gut bacterial communities. We tested the effect of host genotype and epigenotype (i.e., methylome) on gut bacterial communities. Our results indicate that the genotypes, epigenotypes and gut communities of the range-core and invasion-front are significantly different from one another. We found a positive association between host pairwise genetic and epigenetic distances. More importantly, a positive relationship was found between the hosts epigenetic and gut bacterial pairwise distances. Interestingly, this association was stronger in individuals with low genetic differentiation. Our findings suggest that in range-expanding populations, where individuals are often genetically similar, the interaction between gut bacterial communities and host methylome may provide a mechanism through which invaders increase the plasticity of their response to novel environments, potentially increasing their invasion success.

molecular biology↗

bioRxiv2020

Wine terroir and the soil microbiome: an amplicon sequencing-based assessment of the Barossa Valley and its sub-regions

Soil is an important factor that contributes to the uniqueness of a wine produced by vines grown in specific conditions. Recent data shows that the composition, diversity and function of soil microbial communities may play important roles in determining wine quality and indirectly affect its economic value. Here, we evaluated the impact of environmental variables on the soil microbiomes of 22 Barossa Valley vineyard sites based on the 16S rRNA gene hypervariable region 4. In this study, we report that environmental heterogeneity (soil plant-available P content, elevation, rainfall, temperature, spacing between row and spacing between vine) caused more microbial dissimilarity than geographic distance. Vineyards located in cooler and wetter regions showed lower beta diversity and a higher ratio of dominant taxa. Differences in microbial community composition were significantly associated with differences in fruit traits and in wine chemical and metabolomic profiles, highlighting the potential influence of microbial communities on the phenotype of grapevines. Our results suggest that environmental factors affect wine terroir, and this may be mediated by changes in microbial structure, thus providing a basic understanding of how growing conditions affect interactions between plants and their soil microbiomes.

microbiology↗

bioRxiv2020

Additive and non-additive epigenetic signatures of hybridisation between fish species with different mating systems

Hybridisation is a major source of evolutionary innovation. However, several prezygotic and postzygotic factors influence its likelihood and evolutionary outcomes. Differences in mating systems can have a major effect on the extent and direction of hybridisation and introgression. In plants, epigenetic mechanisms help to stabilize hybrid genomes and contribute to reproductive isolation, but the relationship between genetic and epigenetic changes in animal hybrids is unclear. We analysed the extent of a unique case of natural hybridisation between two genetically distant mangrove killifish species with different mating systems, Kryptolebias hermaphroditus (self-fertilising) and K. ocellatus (outcrossing), and the methylation patterns of their hybrids. Hybridisation rate between the species ranged between 14% and 26%. Although co-existing parental species displayed highly distinct genetic (microsatellites and SNPs) and methylation patterns (37,000 differentially methylated cytosines), our results indicate that F1 hybrids are viable and able to backcross with parental species. Hybrids had predominantly intermediate methylation patterns (88.5% of the sites) suggesting additive effects, as expected from hybridisation between genetically distant species. Differentially methylated cytosines between hybrids and both parental species (5,800) suggest that introgressive hybridisation may play a role in generating novel genetic and epigenetic variation which could lead to species diversification. We also found a small percentage of non-additive epigenetic effects which might act as an evolutionary bet-hedging strategy and increase fitness under environmental change.

evolutionary biology↗

bioRxiv2020

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 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 mM 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.

plant biology↗

bioRxiv2018

Common garden experiment reveals altered nutritional values and DNA methylation profiles in micropropagated three elite Ghanaian sweet potato genotypes

Micronutrient deficiency is the cause of multiple diseases in developing countries. Staple crop biofortification is an efficient means to combat such deficiencies in the diets of local consumers. Biofortified lines of sweet potato (Ipomoea batata L. Lam) with enhanced beta-carotene content have been developed in Ghana to alleviate Vitamin A Deficiency. These genotypes are propagated using meristem micropropagation to ensure the generation of virus-free propagules. In vitro culture exposes micropropagated plants to conditions that can lead to the accumulation of somaclonal variation with the potential to generate unwanted aberrant phenotypes. However, the effect of micropropagation induced somaclonal variation on the production of key nutrients by field-grown plants has not been previously studied. Here we assessed the extent of in vitro culture induced somaclonal variation, at a phenotypic, compositional and genetic/epigenetic level, by comparing field-maintained and micropropagated lines of three elite Ghanaian sweet potato genotypes grown in a common garden. Although micropropagated plants presented no observable morphological abnormalities compared to field maintained lines, they presented significantly lower levels of iron, total protein, zinc, and glucose. Methylation Sensitive Amplification Polymorphism analysis showed a high level of in vitro culture induced molecular variation in micropropagated plants. Epigenetic, rather than genetic variation, accounts for most of the observed molecular variability. Taken collectively, our results highlight the importance of ensuring the clonal fidelity of the micropropagated biofortified lines in order to reduce potential losses in the nutritional value prior to their commercial release.

plant biology↗

bioRxiv2017

Environmental Conditions And Agronomic Practices Induce Consistent Global Changes In DNA Methylation Patterns In Grapevine (Vitis vinifera cv Shiraz)

Fruit attributes that affect wine quality are thought to be largely driven by the interaction of grapevines genetic characteristics with environmental factors (i.e. climate, soil and topography) and vineyard management. All these variables, in conjunction with the wine making process, give a wine its distinctive character. Understanding how grapevines perceive and adapt to a changing environment 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 plants 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. Here we used Methylation Sensitive Amplified Polymorphisms to obtain global patterns of DNA methylation, and to identify the main drivers of epigenetic diversity across 22 vineyards planted with the cultivar Shiraz in six distinctive wine areas of a major wine zone, The Barossa, South Australia. 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. Furthermore, pairwise epigenetic distances between vineyards with similar management systems showed a significant correlation with geographic distance. Finally, methylation sensitive Genotyping By Sequencing identified 3,598 differentially methylated genes that were assigned to 1,144 unique GO terms of which 8.6% were associated with response to environmental stimulus. Taken together, our results indicate that the intensity and directionality of DNA methylation differentiation between vineyards and wine sub-regions within The Barossa are driven by management and local growing conditions. Finally, we discuss how epigenetic variability can be used as a tool to understand and potentially modulate terroir in grapevine.

plant biology↗

bioRxiv2017

MSAP In Tiger Snakes: Island Populations Are Epigenetically More Divergent

Research on changes in phenotypic plasticity within wild animal populations is centuries old, however far fewer studies have investigated the role that epigenetics play in the development or persistence of natural variation in response to environmental change. Tiger snakes (Notechis scutatus) are an ideal study organism to investigate the link between epigenetics and phenotypic responses to environmental change, as they live on a range of offshore islands with different environments and prey types while exhibiting gigantism and dwarfism in body and head size. In this study, we have generated methylation sensitive amplified polymorphism (MSAP) data and found that, in general, Tiger Snakes are more epigenetically differentiated than genetically differentiated. Each island group has a distinctive epigenetic signal, suggesting the Tiger Snakes on each island group have adapted to their specific environment. This is also supported by the strong positive relationship between epigenetic differentiation and isolation age, as well as between epigenetic/genetic signal and both temperature and precipitation. The Tiger Snakes from Kangaroo Island, which has a complex landscape/environment like the mainland rather than the simple landscape/environment of each of the smaller islands, are both genetically and epigenetically more like the mainland. As the MSAP loci are randomly distributed across the genome, we believe a closer examination of the epigenetic modifications near genes involved in growth, development, and lipid metabolism will allow us to investigate the epigenetic basis for the natural variation in head size and body size on the islands.

evolutionary biology↗