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

Abstract

Genotyping-by-sequencing (GBS) was used to survey genome-wide single-nucleotide polymorphisms (SNPs) in three biparental strawberry (<i>Fragaria</i> × <i>ananassa</i>) populations with the goal of evaluating this technique in a species with a complex octoploid genome. GBS sequence data were aligned to the <i>F. vesca</i> '<i>Fvb</i>' 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 <i>Fvb</i> 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 <i>F. vesca</i> for each chromosome. Linkage groups that were most similar to a second ancestral species, <i>F. iinumae</i>, were only resolved for <i>Fvb</i> 4. The quantity of missing data and heterogeneity in genome coverage inherent in GBS complicated the analysis, but POLiMAPS resolved <i>F.</i> × <i>ananassa</i> chromosomal regions derived from diploid ancestor <i>F. vesca.</i>