Genetic variation associated with healthy traits and environmental conditions in Vaccinium vitis-idaea

Abstract

BackgroundLingonberry (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.ResultsWe 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.ConclusionsThe 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.Electronic supplementary materialThe online version of this article (10.1186/s12864-017-4396-9) contains supplementary material, which is available to authorized users.

Traditional uses and beneficial effects of various species of berry-producing plants in eastern Canada

“…Lingonberry (Vaccinium vitis-idaea) (see Figure 1) is a small, evergreen shrub with edible red fruits that grows in boreal, northern temperate, and subarctic climates (Isaak et al, 2015). This species has historically been a popular wild fruit and is also widely cultivated and consumed in Scandinavian countries, although the popularity of the fruit has been growing in North America within recent years (Alam et al, 2018;Isaak et al, 2015). There are over 25 common names for lingonberry used worldwide.…”

Recent Large-Scale Genotyping and Phenotyping of Plant Genetic Resources of Vegetatively Propagated Crops

“…The diploid lingonberry ( V. vitis-idaea L.) is still harvested mostly from wild shrubs in Northern Hemisphere forests, and there has been little genetic research. Still, 1586 GBS-derived SNPs were developed to genotype 56 Canadian samples and find correlations with six environmental variables and two phenotypic traits: total phenolic content and antioxidant capacity of fruit [ 105 ].…”

Lingonberry (Vaccinium vitis-idaea L.) Fruit as a Source of Bioactive Compounds with Health-Promoting Effects—A Review

“…Therefore, lingonberries are not as popular and available in the marketplace as cranberries or blueberries. Lingonberry ( Vaccinium vitis-idaea L.) is also one of the least studied fruit in the Ericaceae family [ 15 ]. Nonetheless, the health benefits and diversity of phenolics in lingonberries could provide efforts to develop and expand their commercial production successfully [ 16 ].…”