4.6 Article

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

期刊

PEERJ
卷 5, 期 -, 页码 -

出版社

PEERJ INC
DOI: 10.7717/peerj.3731

关键词

Genotyping; Genotyping-by-sequencing; Fragaria; Linkage mapping; SNP; Phylogeny

资金

  1. USDA's National Institute of Food and Agriculture Specialty Crop Research Initiative project, 'RosBREED: Enabling Marker-Assisted Breeding in Rosaceae' [2009-51181-05808]

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Genotyping-by-sequencing (GBS) was used to survey genome-wide single -nucleotide polymorphisms (SNPs) in three biparental strawberry (Fragaria x 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 lspecies 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. x ananassa chromosomal regions derived from diploid ancestor F. vesca.

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