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Title: Genotyping-by-sequencing in three octoploid cultivated strawberry families

item VINING, KELLY - Oregon State University
item SALINAS, NATALIA - University Of Florida
item TENNESSEN, JACOB - Oregon State University
item Zurn, Jason
item VAN DE WEG, ERIC - Wageningen University
item SARGENT, DANIEL - Driscoll'S
item HANDCOCK, JAMES - Michigan State University
item Bassil, Nahla

Submitted to: PeerJ
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/3/2017
Publication Date: 8/30/2017
Citation: Vining, K.J., Salinas, N., Tennessen, J.A., Zurn, J.D., Van De Weg, E., Sargent, D.J., Handcock, J., Bassil, N.V. 2017. Genotyping-by-sequencing in three octoploid cultivated strawberry families. PeerJ. 5:e3731

Interpretive Summary: Cultivated strawberry has a complex polyploid genome which has arisen through evolutionary duplications and hybridizations. New molecular techniques, such as genotyping-by-sequencing (GBS), are available for high throughput genotyping including linkage mapping. To assess the efficacy of GBS for mapping, three populations were investigated using a bioinformatics pipeline, POLiMAPS, that allows assignment of subgenomes to ancestral diploid progenitors. Despite the high proportion of missing genotypic data, high-quality data was obtained which integrated well with data from other marker systems. Numerous linkage groups were identified which were highly similar to the Fragaria vesca ancestral strawberry species. Bias to the F. vesca subgenome may have been caused by use of DNA sequence of 'Hawaii 4' to identify polymorphisms and needs further evaluation once a reference for the octoploid genome is available. The POLiMAPS pipeline was found to be an effective way to generate data and can be used in future experiments with other strawberry populations.

Technical 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.