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Genotyping-by-sequencing enables linkage mapping in three octoploid cultivated strawberry families

, , , , , ,
1 Horticulture, Oregon State University, Corvallis, Oregon, United States
2 University of Florida, Wimauma, Florida, United States
3 Department of Integrative Biology, Oregon State University, Corvallis, Oregon, United States
4 National Clonal Germplasm Repository, United States Department of Agriculture, Agricultural Research Service, Corvallis, Oregon, United States
5 Research and Innovation Centre, Fondazione Edmund Mach,, San Michele all’Adige, Italy
6 East Malling Enterprise Centre, Driscoll’s Genetics Limited, East Malling, United Kingdom
7 Horticulture, Michigan State University, East Lansing, Michigan, United States
DOI
10.7287/peerj.preprints.2975v1
Published
Accepted
Subject Areas
Agricultural Science, Genetics, Genomics, Plant Science
Keywords
Genotyping, Genotyping-by-sequencing, Fragaria, linkage mapping, SNP, phylogeny
Copyright
© 2017 Vining et al.
Licence
This is an open access article distributed under the terms of the Creative Commons Attribution License, 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 Preprints) and either DOI or URL of the article must be cited.
Cite this article
Vining KJ, Salinas N, Tennessen JA, Zurn JD, Sargent DJ, Hancock J, Bassil NV. 2017. Genotyping-by-sequencing enables linkage mapping in three octoploid cultivated strawberry families. PeerJ Preprints 5:e2975v1

Abstract

With the goal of evaluating genotyping-by-sequencing (GBS) in a species with a complex octoploid genome, GBS was used to survey genome-wide single-nucleotide polymorphisms (SNPs) in three biparental strawberry (Fragaria ×ananassa) populations. 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.

Author Comment

This is a submission to PeerJ for review.

Supplemental Information

Holiday 6D integrated linkage map

Mapping data for Axiom markers was obtained from Bassil et al. (2015).

DOI: 10.7287/peerj.preprints.2975v1/supp-1

Additional Information

Competing Interests

The authors declare that they have no competing interests.

Author Contributions

Kelly J Vining analyzed the data, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.

Natalia Salinas conceived and designed the experiments, performed the experiments, analyzed the data, wrote the paper, reviewed drafts of the paper.

Jacob A Tennessen analyzed the data, contributed reagents/materials/analysis tools, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.

Jason D Zurn analyzed the data, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.

Daniel James Sargent reviewed drafts of the paper.

James Hancock reviewed drafts of the paper.

Nahla V Bassil conceived and designed the experiments, performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, wrote the paper, reviewed drafts of the paper.

DNA Deposition

The following information was supplied regarding the deposition of DNA sequences:

The data is available via the NCBI Sequence Read Archive, BioProject PRJNA385347 https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA385347

Data Deposition

The following information was supplied regarding data availability:

The POLiMAPS pipeline was previously published, and is cited in the manuscript. The research in this article did not make use of any previously unpublished code.

Funding

This work was partially funded by USDA’s National Institute of Food and Agriculture—Specialty Crop Research Initiative projects, ‘RosBREED: Enabling Marker-Assisted Breeding in Rosaceae’ (2009-51181-05808). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

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Genotyping-by-sequencing enables linkage mapping in three octoploid cultivated strawberry families
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