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.
Partridgeberry (Vaccinium vitis-idaea L.) is a good source of food and pharmaceutical ingredients, for which cultivation interest is increasing in North America. Nutrition-oriented breeding programs will benefit from an understanding of how the environment affects the biochemical traits of interest in wild populations. Total phenolic content (TPC) and antioxidant capacity (AC) as measured by the ability to capture free radicals were evaluated simultaneously in leaves and fruit of 56 wild populations across Newfoundland and Labrador, Canada. We tested variation in TPC and AC as a function of eight environmental factors, which showed different effects in leaves and fruit. Contrary to our expectations, TPC was not correlated with AC in either leaves or fruit, and mean TPC and AC were higher in fruit than in leaves. We propose a series of environment-based models for the selection of wild populations. Models for fruit involved ecoregion, temperature, and coastal proximity, and explained up to 51% of variation. While leaf models included surface water pH and sensitivity to acid rain, explaining up to 31%. We conclude that wild population selection in the province should target the North Shore Forest ecoregion and warm temperatures for fruit; and regions with low water alkalinity and pH > 6.6 for leaves.
Growth and yield of pea crops are severely affected by various fungal diseases, including root rot, Ascochyta blight, powdery mildew, and rust, in different parts of the world. Conventional breeding methods have led to enhancement of host plant resistance against these diseases in adapted cultivars, which is the primary option to minimize the yield losses. To support the breeding programs for marker-assisted selection, several successful attempts have been made to detect the genetic loci associated with disease resistance, based on SSR and SNP markers. In recent years, advances in next-generation sequencing platforms, and resulting improvements in high-throughput and economical genotyping methods, have been used to make rapid progress in identification of these loci. The first reference genome sequence of pea was published in 2019 and provides insights on the distribution and architecture of gene families associated with disease resistance. Furthermore, the genome sequence is a resource for anchoring genetic linkage maps, markers identified in multiple studies, identification of candidate genes, and functional genomics studies. The available pea genomic resources and the potential application of genomic technologies for development of disease-resistant cultivars with improved agronomic profile will be discussed, along with the current status of the arising improved pea germplasm.
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