Comparison of Three Genotyping by Sequencing Pipelines for Variant Identification and Linkage Mapping in the Cultivated Octoploid Strawberry

Genotyping By Sequencing (GBS) is believed to provide a rapid and economical method of single nucleotide polymorphism (SNP) discovery. The objective of this study was to evaluate the usefulness of GBS in the allo-octoploid cultivated strawberry, Fragaria ×ananassa. Five GBS libraries were constructed, each containing DNA from 66 to 96 individuals. Each library was sequenced in one lane (single end) with the Illumina HiSeq 2000 platform. Sequences were trimmed  to 64 bp and analyzed after alignment to the strawberry F. vesca Fvb genome reference [Genome Biol. Evol. 6(12):3295–3313]. Three analyses pipelines, POLiMAPS, Stacks and TASSEL, were used to identify SNPs in five bi-parental populations ranging in size from 10 to 63 progeny. We compared the number of markers generated by each pipeline, and placed markers on linkage groups representing the 56 (= 2N = 8×) chromosomes for each of the five populations. Our results compare the performance of the three bioinformatic pipelines in resolving GBS data from polyploid species.