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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ftdoajarticles:oai:doaj.org/article:f17475248f664e5283c18d82756a04b0 2023-05-15T17:22:49+02:00 Genetic variation associated with healthy traits and environmental conditions in Vaccinium vitis-idaea Zobayer Alam Julissa Roncal Lourdes Peña-Castillo 2018-01-01T00:00:00Z https://doi.org/10.1186/s12864-017-4396-9 https://doaj.org/article/f17475248f664e5283c18d82756a04b0 EN eng BMC http://link.springer.com/article/10.1186/s12864-017-4396-9 https://doaj.org/toc/1471-2164 doi:10.1186/s12864-017-4396-9 1471-2164 https://doaj.org/article/f17475248f664e5283c18d82756a04b0 BMC Genomics, Vol 19, Iss 1, Pp 1-13 (2018) Antioxidant capacity Environmental adaptation Functional annotation Genetic diversity Genotyping-by-sequencing Lingonberry Biotechnology TP248.13-248.65 Genetics QH426-470 article 2018 ftdoajarticles https://doi.org/10.1186/s12864-017-4396-9 2022-12-31T10:32:27Z 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 ... Article in Journal/Newspaper Newfoundland Directory of Open Access Journals: DOAJ Articles Canada Newfoundland BMC Genomics 19 1 |
institution |
Open Polar |
collection |
Directory of Open Access Journals: DOAJ Articles |
op_collection_id |
ftdoajarticles |
language |
English |
topic |
Antioxidant capacity Environmental adaptation Functional annotation Genetic diversity Genotyping-by-sequencing Lingonberry Biotechnology TP248.13-248.65 Genetics QH426-470 |
spellingShingle |
Antioxidant capacity Environmental adaptation Functional annotation Genetic diversity Genotyping-by-sequencing Lingonberry Biotechnology TP248.13-248.65 Genetics QH426-470 Zobayer Alam Julissa Roncal Lourdes Peña-Castillo Genetic variation associated with healthy traits and environmental conditions in Vaccinium vitis-idaea |
topic_facet |
Antioxidant capacity Environmental adaptation Functional annotation Genetic diversity Genotyping-by-sequencing Lingonberry Biotechnology TP248.13-248.65 Genetics QH426-470 |
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 ... |
format |
Article in Journal/Newspaper |
author |
Zobayer Alam Julissa Roncal Lourdes Peña-Castillo |
author_facet |
Zobayer Alam Julissa Roncal Lourdes Peña-Castillo |
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 |
BMC |
publishDate |
2018 |
url |
https://doi.org/10.1186/s12864-017-4396-9 https://doaj.org/article/f17475248f664e5283c18d82756a04b0 |
geographic |
Canada Newfoundland |
geographic_facet |
Canada Newfoundland |
genre |
Newfoundland |
genre_facet |
Newfoundland |
op_source |
BMC Genomics, Vol 19, Iss 1, Pp 1-13 (2018) |
op_relation |
http://link.springer.com/article/10.1186/s12864-017-4396-9 https://doaj.org/toc/1471-2164 doi:10.1186/s12864-017-4396-9 1471-2164 https://doaj.org/article/f17475248f664e5283c18d82756a04b0 |
op_doi |
https://doi.org/10.1186/s12864-017-4396-9 |
container_title |
BMC Genomics |
container_volume |
19 |
container_issue |
1 |
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1766109689748127744 |