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.
Highlights
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
Vaccinium vitis-idaea L. commonly known as lingonberry, is a perennial, evergreen dwarf shrub, which belongs to the Ericaceae family, that has high breeding potential for leaf and fruit quality traits such as high concentration of healthy bioactive compounds
To elucidate the genetic variation across environmental conditions, we considered the following six variables: mean annual temperature (MAT), mean summer temperature (MST), mean annual precipitation (MAP), mean annual runoff (MAR), surface water pH (SWp), and surface water sensitivity to acid rain (SWS)
Summary
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. Vaccinium vitis-idaea L. commonly known as lingonberry, is a perennial, evergreen dwarf shrub, which belongs to the Ericaceae family, that has high breeding potential for leaf and fruit quality traits such as high concentration of healthy bioactive compounds. Neither the complete nuclear genome nor the plastome have been sequenced for this species, and no single nucleotide polymorphisms (SNP) or expressed sequence tags (EST) are available as genetic resources. Genetic markers are needed to facilitate the selection of wild populations with desirable climatic adaptations, agronomic and nutritious characteristics. Polymorphism of genes encoding isoflavone synthase, an enzyme involved in the phenylpropanoid pathway, was associated with isoflavone concentrations in soybean seeds [17]
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