Comparison of the phenolic contents and epigenetic and genetic variability of wild and cultivated watercress ( Rorippa nasturtium var. aquaticum L.)

Chemical Composition of Wild Collected and Cultivated Edible Plants (Sonchus oleraceus L. and Sonchus tenerrimus L.)

The present work investigates the nutritional and bioactive composition, as well as the organoleptic and sensory properties, of S. oleraceus and S. tenerrimus, two wild plant species traditionally used in the gastronomy of the Mediterranean area. Additionally, the effect of cultivation on leaf composition was assessed to explore their potential for large-scale production and commercialization from the point of view of possible losses or gains in quality. Both species were characterized as a good source of bioactive compounds, such as vitamins, pro-vitamins and carotenoids, with health-promoting and antioxidant properties that are highly appreciated. The sensory profile revealed a good general acceptance of S. oleraceus and S. tenerrimus, indicating that they could be included in the diet. Although the cultivation of S. oleraceus resulted in a decrease in the concentration of phenolic compounds when compared to wild-harvested plants, the opposite occurred for vitamin C. In S. tenerrimus, cultivation also increased the concentration of other compounds with important nutritional and healthy properties, such as sugars, organic acids and β-carotene. The results of the composition, organoleptic and sensory properties of S. oleraceus and S. tenerrimus support the idea of their potential to be used as edible leafy vegetables and as promising assets for functional foods.

Genome Wide MeDIP-Seq Profiling of Wild and Cultivated Olives Trees Suggests DNA Methylation Fingerprint on the Sensory Quality of Olive Oil

Secondary metabolites are particularly important to humans due to their pharmaceutical properties. Moreover, secondary metabolites are key compounds in climate change adaptation in long-living trees. Recently, it has been described that the domestication of Olea subspecies had no major selection signature on coding variants and was mainly related to changes in gene expression. In addition, the phenotypic plasticity in Olea subspecies was linked to the activation of transposable elements in the genes neighboring. Here, we investigated the imprint of DNA methylation in the unassigned fraction of the phenotypic plasticity of the Olea subspecies, using methylated DNA immuno-precipitation sequencing (MeDIP-seq) for a high-resolution genome-wide DNA methylation profiling of leaves and fruits during fruit development in wild and cultivated olives from Turkey. Notably, the methylation profiling showed a differential DNA methylation in secondary metabolism responsible for the sensory quality of olive oil. Here, we highlight for the first time the imprint of DNA methylation in modulating the activity of the Linoleate 9S lipoxygenase in the biosynthesis of volatile aromatic compounds. Unprecedently, the current study reveals the methylation status of the olive genome during fruit ripening.

Patterns of Epigenetic Diversity in Two Sympatric Fish Species: Genetic vs. Environmental Determinants

Epigenetic components are hypothesized to be sensitive to the environment, which should permit species to adapt to environmental changes. In wild populations, epigenetic variation should therefore be mainly driven by environmental variation. Here, we tested whether epigenetic variation (DNA methylation) observed in wild populations is related to their genetic background, and/or to the local environment. Focusing on two sympatric freshwater fish species (Gobio occitaniae and Phoxinus phoxinus), we tested the relationships between epigenetic differentiation, genetic differentiation (using microsatellite and single nucleotide polymorphism (SNP) markers), and environmental distances between sites. We identify positive relationships between pairwise genetic and epigenetic distances in both species. Moreover, epigenetic marks better discriminated populations than genetic markers, especially in G. occitaniae. In G. occitaniae, both pairwise epigenetic and genetic distances were significantly associated to environmental distances between sites. Nonetheless, when controlling for genetic differentiation, the link between epigenetic differentiation and environmental distances was not significant anymore, indicating a noncausal relationship. Our results suggest that fish epigenetic variation is mainly genetically determined and that the environment weakly contributed to epigenetic variation. We advocate the need to control for the genetic background of populations when inferring causal links between epigenetic variation and environmental heterogeneity in wild populations.

Comparison of Three Domestications and Wild-Harvested Plants for Nutraceutical Properties and Sensory Profiles in Five Wild Edible Herbs: Is Domestication Possible?

In this study, five wild edible herbs traditionally consumed in the Tuscany region (Italy) were evaluated for their potential in human nutrition. The nutraceutical characterization of Rumex acetosa, Cichorium intybus, Picris hieracioides, Sanguisorba minor, and Plantago coronopus, as well as their sensory profile were reported. Additionally, a preliminary assessment of completely different domestication of the wild species (named "soilless", pot, and open field) was conducted to verify the possibility of their marketability, which is impossible if the plants are only gathered as wild. The open field domestication allowed to obtain plants with nutraceutical and sensory profiles similar to those of the wild species, especially in C. intybus, P. hieracioides, and S. minor. The pot domestication allow to obtain plants with chlorophyll and carotenoid contents close to those of the wild species, as well as a lower total phenolic and flavonoid content and ascorbic acid content than wild species. In the "soilless" method, R. acetosa and P. coronopus exhibited a high quality in terms of phytochemicals and antioxidant activity. Afterward, the sensory profile was strongly affected by the domestication in terms of the palatability, except for R. acetosa and P. coronopus, which displayed Hedonic Index (HI) values close to the consumer acceptability limit (HI = 6). A sensory profile similar to that of wild species was reported in open field domestication, whereas a worse sensory profile was reported in P. hieracioides and C. intybus domesticated using the soilless method. Finally, according to the preliminary assessment carried out in this study through an analysis of the general nutraceutical properties, S. minor was shown to be the most promising species thanks to its intrinsically highest nutraceutical properties considering the marketability of wild edible herbs as "new" functional food. However, further research on the bioavailability and bioactivity tests of nutraceutical compounds present in this species are required to confirm the findings of this study.

Wild and Cultivated Centaurea raphanina subsp. mixta: A Valuable Source of Bioactive Compounds

Centaurea raphanina subsp. mixta (DC.) Runemark is a wild edible species endemic to Greece. This study evaluated the chemical composition and bioactive properties of wild and cultivated C. raphanina subsp. mixta plants. Wild plants had higher nutritional value than cultivated ones, whereas cultivated plants contained more tocopherols. Glucose and sucrose were higher in cultivated plants and trehalose in wild ones. Oxalic and total organic acids were detected in higher amounts in cultivated samples. The main fatty acids were α-linolenic, linoleic and palmitic acid, while wild plants were richer in polyunsaturated fatty acids. Two pinocembrin derivatives were the main phenolic compounds being detected in higher amounts in wild plants. Regarding the antioxidant activity, wild and cultivated plants were more effective in the oxidative haemolysis (OxHLIA) and thiobarbituric acid reactive substances (TBARS) assays, respectively. Moreover, both extracts showed moderate cytotoxicity in non-tumor cell lines (PLP2), while cultivated plants were more effective against cervical carcinoma (HeLa), breast carcinoma (MCF-7) and non-small lung cancer (NCI-H460) cell lines. Finally, wild plants showed higher antimicrobial activity than cultivated plants against specific pathogens. In conclusion, the cultivation of C.raphanina subsp. mixta showed promising results in terms of tocopherols content and antiproliferative effects, however further research is needed to decrease oxalic acid content.

A high-density genetic map and QTL mapping of leaf traits and glucosinolates in Barbarea vulgaris

Background

Barbarea vulgaris is a wild cruciferous plant and include two distinct types: the G- and P-types named after their glabrous and pubescent leaves, respectively. The types differ significantly in resistance to a range of insects and diseases as well as glucosinolates and other chemical defenses. A high-density linkage map was needed for further progress to be made in the molecular research of this plant.

Results

We performed restriction site-associated DNA sequencing (RAD-Seq) on an F₂ population generated from G- and P-type B. vulgaris. A total of 1545 SNP markers were mapped and ordered in eight linkage groups, which represents the highest density linkage map to date for the crucifer tribe Cardamineae. A total of 722 previously published genome contigs (50.2 Mb, 30% of the total length) can be anchored to this high density genetic map, an improvement compared to a previously published map (431 anchored contigs, 38.7 Mb, 23% of the assembly genome). Most of these (572 contigs, 31.2 Mb) were newly anchored to the map, representing a significant improvement. On the basis of the present high-density genetic map, 37 QTL were detected for eleven traits, each QTL explaining 2.9–71.3% of the phenotype variation. QTL of glucosinolates, leaf size and color traits were in most cases overlapping, possibly implying a functional connection.

Conclusions

This high-density linkage map and the QTL obtained in this study will be useful for further understanding of the genetic of the B. vulgaris and molecular basis of these traits, many of which are shared in the related crop watercress.

Electronic supplementary material

The online version of this article (10.1186/s12864-019-5769-z) contains supplementary material, which is available to authorized users.