Vaccinium vitis-idaea var. minus
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA377297 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR5826970.fastq.gz | Fastqsanger.gz | |||
| SRR5826980.fastq.gz | Fastqsanger.gz | |||
| SRR5826990.fastq.gz | Fastqsanger.gz | |||
| SRR5827000.fastq.gz | Fastqsanger.gz | |||
| SRR5827010.fastq.gz | Fastqsanger.gz |
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Project description:Vaccinium vitis-idaea two-subspecies Genome sequencing and assembly
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Project description:Genome sequencing of Vaccinium vitis-idaea L. after fire Genome sequencing and assembly
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Project description:BACKGROUND:Lingonberry (Vaccinium vitis-idaea L.), one of the least studied fruit crops in the Ericaceae family, has a dramatically increased worldwide demand due to its numerous health benefits. Genetic markers can facilitate the selection of berries with desirable climatic adaptations, agronomic and nutritious characteristics to improve cultivation programs. However, no genomic resources are available for this species. RESULTS:We used Genotyping-by-Sequencing (GBS) to analyze the genetic variation of 56 lingonberry samples from across Newfoundland and Labrador, Canada. To elucidate a potential adaptation to environmental conditions we searched for genotype-environment associations by applying three distinct approaches to screen the identified single nucleotide polymorphisms (SNPs) for correlation with six environmental variables. We also searched for an association between the identified SNPs and two phenotypic traits: the total phenolic content (TPC) and antioxidant capacity (AC) of fruit. We identified 1586 high-quality putative SNPs using the UNEAK pipeline available in TASSEL. We found 132 SNPs likely associated with at least one of the environmental or phenotypic variables. To obtain insights on the function of the genomic sequences containing the SNPs likely to be associated with the environmental or phenotypic variables, we performed a sequence-based functional annotation and identified homologous protein-coding sequences with functional roles related to abiotic stress response, pathogen defense, RNA metabolism, and, most interestingly, phenolic compound biosynthesis. CONCLUSIONS:The putative SNPs discovered are the first genomic resource for lingonberry. This resource might prove useful in high-density quantitative trait locus analysis, and association mapping. The identified candidate genes containing the SNPs need further studies on their potential role in local adaptation of lingonberry. Altogether, the present study provides new resources that can be used to breed for desirable traits in lingonberry.
| S-EPMC5748963 | biostudies-literature
Project description:In the mountain terrain, ice holes are little depressions between rock boulders that are characterized by the exit of cold air able to cool down the rock surface even in summer. This cold air creates cold microrefugia in warmer surroundings that preserve plant species probably over thousands of years under extra-zonal climatic conditions. We hypothesized that ice hole populations of the model species Vaccinium vitis-idaea (Ericaceae) show genetic differentiation from nearby zonal subalpine populations, and high functional trait distinctiveness, in agreement with genetic patterns. We genotyped almost 30,000 single nucleotide polymorphisms using restriction site-associated DNA sequencing and measured eight functional traits indicative of individual performance and ecological strategies. Genetic results showed high differentiation among the six populations suggesting isolation. On siliceous bedrock, ice hole individuals exhibited higher levels of admixture than those from subalpine populations which could have experienced more bottlenecks during demographic fluctuations related to glacial cycles. Ice hole and subalpine calcareous populations clearly separated from siliceous populations, indicating a possible effect of bedrock in shaping genetic patterns. Trait analysis reflected the bedrock effect on populations' differentiation. The significant correlation between trait and genetic distances suggests the genetic contribution in shaping intraspecific functional differentiation. In conclusion, extra-zonal populations reveal a prominent genetic and phenotypic differentiation determined by history and ecological contingency. Therefore, microrefugia populations can contribute to the overall variability of the species and lead to intraspecific-driven responses to upcoming environmental changes.
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Project description:Lingonberry leaves and fruits are associated with a range of potential bioactivities related to their phenolic content and composition, but the identification of major biological activity markers remains limited. The present study aimed at the isolation of lingonberry phenolic fractions and biological activity evaluation of them. Crude dry extracts of lingonberry leaves and fruits were fractionated by chromatography using Sephadex LH-20 and analyzed by validated HPLC-PDA method. For each fraction, the anticancer activity against human clear cell renal cell carcinoma (CaKi-1), human colon adenocarcinoma (HT-29), and human malignant melanoma (IGR39) cell lines was determined using MTT assay, and the radical scavenging, reducing, and chelating activities were investigated using ABTS, FRAP, and FIC assays, respectively. Further, 28 phenolics were identified and quantified in the crude extract of lingonberry leaves and 37 in the extract of fruits. These compounds, during fractionation steps, were selectively eluted into active fractions, enriched with different groups of phenolics-monophenols, anthocyanins, phenolic acids, catechins, flavonols, or proanthocyanidins. Fractions of lingonberry leaves and fruits, obtained by the last fractionation step, proved to be the most active against tested cancer cell lines and possessed the greatest antioxidant activity. In this perspective, the predominant compounds of these fractions-polymeric and mainly A-type dimeric proanthocyanidins-also quercetin can be considered to be anticancer and antioxidant activity markers of lingonberries.
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Project description:Vaccinium vitis-idaea L. (lingonberry) fruits are promising sources of bioactive components with high potential in biomedical applications. Selection in plant breeding, determination of perspective wild clones with optimal growing conditions, and appropriate harvesting time leading to standardized extracts are key factors for achieving phytochemical quality to meet consumer's needs. In the present study, lingonberry fruits collected along different phenological stages and from different geographical locations were analyzed for the composition of 56 constituents using validated chromatographic techniques. Early stages of lingonberries vegetation were determined as the best stages for obtaining high levels of most phenolics and triterpenoids, while the end of berry vegetation could be chosen as the optimal harvesting time in terms of anthocyanins. Furthermore, intensified continuous biosynthesis of triterpenoids and phenolic acids precursors after vegetation season in the winter sample was observed. Chemodiversity of lingonberries was affected by geographical factors as well as climatic and edaphic conditions, indicating different favorable growing conditions for the accumulation of particular compounds. Present findings could serve for breeders to obtain the highest yields of desirable lingonberry constituents, relevant in food and pharmaceutical industries.
| S-EPMC8535033 | biostudies-literature
Project description:Lingonberry leaves have been proposed as a potential raw material for nutraceutical products and functional food due to the richness of phenolic and triterpenic compounds. However, contents of these bioactive compounds tend to vary greatly with physiological, climatic, and edaphic conditions, resulting in lingonberry leaves' nutritional-pharmaceutical quality changes. In this context, we examined the effects of seasonal and geographical factors on phenolic and triterpenoid contents in lingonberry leaves. Quantitative and qualitative differences between samples were determined using validated HPLC-PDA methods. A total of 43 bioactive compounds were found at a detectable level throughout the year in young and old lingonberry leaves, with the highest contents of most compounds observed in samples collected in autumn-first half of spring. This suggests the potential to exploit the continuous biosynthesis for a longer harvesting season. Considerable variations in phytochemical profiles of lingonberry leaves, obtained from 28 locations in Lithuania, were found. Correlation analyses revealed significant negative correlations between contents of particular constituents and sunshine duration, temperature, and precipitation, and positive correlation with air humidity, longitudes, and altitudes of collecting locations and macronutrients in soil. These results suggest that harsh weather is favorable for most identified compounds and it may be possible to achieve appropriate accumulation of secondary metabolites by adjusting edaphic conditions. Taken together, the accumulation of phenolics and triterpenoids in lingonberry leaves highly depends on phenological and geographical factors and the influence of both variables differ for the particular compounds due to different metabolic processes in response to stresses.
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