Optimization of SNP Identification By the Genotyping-By-Sequencing (GBS) in Polyploid Zoysiagrass.

Single nucleotide polymorphisms (SNPs) have become a popular genetic marker in marker-assisted selection breeding. Genotyping-by-sequencing (GBS) provides a rapid and low-cost tool for SNP discovery and genotyping of breeding populations. However, SNP identification in polyploid crops is more challenging due to increased genome complexity. In this study, the GBS SNP-Calling Reference Optional Pipeline (GBS-SNP-CROP) was used to call SNPs from a GBS library of tetraploid zoysiagrass. The library was constructed for 174 F₁ progeny and two parental lines (cultivars ‘Meyer’ and ‘Victoria’). The published genome sequence of zoysiagrass (Z. japonica Steud) was used as reference genome. After optimization of depth-based genotyping criteria and population-level filters, GBS-SNP-CROP called 1,292 potential SNPs (average read depth = 9.0). All SNPs were mapped to 20 chromosomes and at least 50% individuals were genotyped. This investigation provides guidance for determining the most suitable SNP calling approach for polyploid Zoysiagrass.