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Genotyping-by-sequencing enables linkage mapping in three octoploid cultivated strawberry families
Genotyping-by-sequencing (GBS) was used to survey genome-wide single-nucleotide polymorphisms (SNPs) in three biparental strawberry (Fragaria × ananassa) populations with the goal of evaluating this technique in a species with a complex octoploid genome. GBS sequence data were aligned to the F. vesc...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
PeerJ Inc.
2017
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5581533/ https://www.ncbi.nlm.nih.gov/pubmed/28875078 http://dx.doi.org/10.7717/peerj.3731 |
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author | Vining, Kelly J. Salinas, Natalia Tennessen, Jacob A. Zurn, Jason D. Sargent, Daniel James Hancock, James Bassil, Nahla V. |
author_facet | Vining, Kelly J. Salinas, Natalia Tennessen, Jacob A. Zurn, Jason D. Sargent, Daniel James Hancock, James Bassil, Nahla V. |
author_sort | Vining, Kelly J. |
collection | PubMed |
description | Genotyping-by-sequencing (GBS) was used to survey genome-wide single-nucleotide polymorphisms (SNPs) in three biparental strawberry (Fragaria × ananassa) populations with the goal of evaluating this technique in a species with a complex octoploid genome. GBS sequence data were aligned to the F. vesca ‘Fvb’ reference genome in order to call SNPs. Numbers of polymorphic SNPs per population ranged from 1,163 to 3,190. Linkage maps consisting of 30–65 linkage groups were produced from the SNP sets derived from each parent. The linkage groups covered 99% of the Fvb reference genome, with three to seven linkage groups from a given parent aligned to any particular chromosome. A phylogenetic analysis performed using the POLiMAPS pipeline revealed linkage groups that were most similar to ancestral species F. vesca for each chromosome. Linkage groups that were most similar to a second ancestral species, F. iinumae, were only resolved for Fvb 4. The quantity of missing data and heterogeneity in genome coverage inherent in GBS complicated the analysis, but POLiMAPS resolved F. × ananassa chromosomal regions derived from diploid ancestor F. vesca. |
format | Online Article Text |
id | pubmed-5581533 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2017 |
publisher | PeerJ Inc. |
record_format | MEDLINE/PubMed |
spelling | pubmed-55815332017-09-05 Genotyping-by-sequencing enables linkage mapping in three octoploid cultivated strawberry families Vining, Kelly J. Salinas, Natalia Tennessen, Jacob A. Zurn, Jason D. Sargent, Daniel James Hancock, James Bassil, Nahla V. PeerJ Agricultural Science Genotyping-by-sequencing (GBS) was used to survey genome-wide single-nucleotide polymorphisms (SNPs) in three biparental strawberry (Fragaria × ananassa) populations with the goal of evaluating this technique in a species with a complex octoploid genome. GBS sequence data were aligned to the F. vesca ‘Fvb’ reference genome in order to call SNPs. Numbers of polymorphic SNPs per population ranged from 1,163 to 3,190. Linkage maps consisting of 30–65 linkage groups were produced from the SNP sets derived from each parent. The linkage groups covered 99% of the Fvb reference genome, with three to seven linkage groups from a given parent aligned to any particular chromosome. A phylogenetic analysis performed using the POLiMAPS pipeline revealed linkage groups that were most similar to ancestral species F. vesca for each chromosome. Linkage groups that were most similar to a second ancestral species, F. iinumae, were only resolved for Fvb 4. The quantity of missing data and heterogeneity in genome coverage inherent in GBS complicated the analysis, but POLiMAPS resolved F. × ananassa chromosomal regions derived from diploid ancestor F. vesca. PeerJ Inc. 2017-08-30 /pmc/articles/PMC5581533/ /pubmed/28875078 http://dx.doi.org/10.7717/peerj.3731 Text en ©2017 Vining et al. http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ) and either DOI or URL of the article must be cited. |
spellingShingle | Agricultural Science Vining, Kelly J. Salinas, Natalia Tennessen, Jacob A. Zurn, Jason D. Sargent, Daniel James Hancock, James Bassil, Nahla V. Genotyping-by-sequencing enables linkage mapping in three octoploid cultivated strawberry families |
title | Genotyping-by-sequencing enables linkage mapping in three octoploid cultivated strawberry families |
title_full | Genotyping-by-sequencing enables linkage mapping in three octoploid cultivated strawberry families |
title_fullStr | Genotyping-by-sequencing enables linkage mapping in three octoploid cultivated strawberry families |
title_full_unstemmed | Genotyping-by-sequencing enables linkage mapping in three octoploid cultivated strawberry families |
title_short | Genotyping-by-sequencing enables linkage mapping in three octoploid cultivated strawberry families |
title_sort | genotyping-by-sequencing enables linkage mapping in three octoploid cultivated strawberry families |
topic | Agricultural Science |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5581533/ https://www.ncbi.nlm.nih.gov/pubmed/28875078 http://dx.doi.org/10.7717/peerj.3731 |
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