Genetic variation associated with healthy traits and environmental conditions in Vaccinium vitis-idaea
Abstract 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, ag...
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ftdatacite:10.6084/m9.figshare.c.3965682.v1 2023-05-15T17:22:49+02:00 Genetic variation associated with healthy traits and environmental conditions in Vaccinium vitis-idaea Zobayer Alam Roncal, Julissa PeĂąa-Castillo, Lourdes 2018 https://dx.doi.org/10.6084/m9.figshare.c.3965682.v1 https://figshare.com/collections/Genetic_variation_associated_with_healthy_traits_and_environmental_conditions_in_Vaccinium_vitis-idaea/3965682/1 unknown Figshare https://dx.doi.org/10.1186/s12864-017-4396-9 https://dx.doi.org/10.6084/m9.figshare.c.3965682 CC BY 4.0 https://creativecommons.org/licenses/by/4.0 CC-BY Medicine Genetics FOS Biological sciences Evolutionary Biology Ecology 69999 Biological Sciences not elsewhere classified Plant Biology 60506 Virology Collection article 2018 ftdatacite https://doi.org/10.6084/m9.figshare.c.3965682.v1 https://doi.org/10.1186/s12864-017-4396-9 https://doi.org/10.6084/m9.figshare.c.3965682 2021-11-05T12:55:41Z Abstract 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. Article in Journal/Newspaper Newfoundland DataCite Metadata Store (German National Library of Science and Technology) Canada Newfoundland |
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DataCite Metadata Store (German National Library of Science and Technology) |
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ftdatacite |
language |
unknown |
topic |
Medicine Genetics FOS Biological sciences Evolutionary Biology Ecology 69999 Biological Sciences not elsewhere classified Plant Biology 60506 Virology |
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Medicine Genetics FOS Biological sciences Evolutionary Biology Ecology 69999 Biological Sciences not elsewhere classified Plant Biology 60506 Virology Zobayer Alam Roncal, Julissa PeĂąa-Castillo, Lourdes Genetic variation associated with healthy traits and environmental conditions in Vaccinium vitis-idaea |
topic_facet |
Medicine Genetics FOS Biological sciences Evolutionary Biology Ecology 69999 Biological Sciences not elsewhere classified Plant Biology 60506 Virology |
description |
Abstract 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. |
format |
Article in Journal/Newspaper |
author |
Zobayer Alam Roncal, Julissa PeĂąa-Castillo, Lourdes |
author_facet |
Zobayer Alam Roncal, Julissa PeĂąa-Castillo, Lourdes |
author_sort |
Zobayer Alam |
title |
Genetic variation associated with healthy traits and environmental conditions in Vaccinium vitis-idaea |
title_short |
Genetic variation associated with healthy traits and environmental conditions in Vaccinium vitis-idaea |
title_full |
Genetic variation associated with healthy traits and environmental conditions in Vaccinium vitis-idaea |
title_fullStr |
Genetic variation associated with healthy traits and environmental conditions in Vaccinium vitis-idaea |
title_full_unstemmed |
Genetic variation associated with healthy traits and environmental conditions in Vaccinium vitis-idaea |
title_sort |
genetic variation associated with healthy traits and environmental conditions in vaccinium vitis-idaea |
publisher |
Figshare |
publishDate |
2018 |
url |
https://dx.doi.org/10.6084/m9.figshare.c.3965682.v1 https://figshare.com/collections/Genetic_variation_associated_with_healthy_traits_and_environmental_conditions_in_Vaccinium_vitis-idaea/3965682/1 |
geographic |
Canada Newfoundland |
geographic_facet |
Canada Newfoundland |
genre |
Newfoundland |
genre_facet |
Newfoundland |
op_relation |
https://dx.doi.org/10.1186/s12864-017-4396-9 https://dx.doi.org/10.6084/m9.figshare.c.3965682 |
op_rights |
CC BY 4.0 https://creativecommons.org/licenses/by/4.0 |
op_rightsnorm |
CC-BY |
op_doi |
https://doi.org/10.6084/m9.figshare.c.3965682.v1 https://doi.org/10.1186/s12864-017-4396-9 https://doi.org/10.6084/m9.figshare.c.3965682 |
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1766109689136807936 |