Evaluation of Genotyping by Sequencing in Octoploid Strawberry

An objective of the multi-institutional RosBREED project is to develop genome scans in strawberry and other rosaceous crops and use them for identifying and validating QTL for fruit quality. Single nucleotide polymorphisms (SNPs) are useful genetic polymorphisms as they are very abundant in the genome and are amenable to high-throughput genotyping. The objective of this study was to evaluate genotyping-by-sequencing (GBS) as a genome scan in the allo-octoploid strawberry. One hundred and eighty nine individuals were chosen for GBS including: three mapping populations, cultivars and selections that are pedigree-linked to these mapping populations, and a set of diverse reference individuals with available genome-wide sequence data. The methylation-sensitive restriction enzyme ApeKI was used to construct the GBS libraries. The first GBS library was prepared from 96 individuals and sequenced in one lane of an Illumina flow-cell using the HiSeq2000 sequencing platform. Sequences with high quality were trimmed and aligned to the strawberry F. vesca v. 1.0 genome reference using the Discovery Tassel Pipeline. The proportion of missing data in the hapmap files ranged from 14% to 100%. The missing data was > 58% in 12 samples and ranged from 25% to 58% in the next 12 samples. Two new GBS libraries being constructed include samples with > 25% missing data in the first experiment and the additional chosen strawberry individuals. We will evaluate the proportion of missing data, number of observed markers, cost efficiency, and genome coverage of markers on the physical F. vesca map and marker performance by constructing genetic linkage maps for the three mapping populations.