Increasing genome sampling and improving SNP genotyping for genotyping-by-sequencing (GBS) with new combinations of restriction enzymes

GBS commonly samples a genome unevenly and can generate large missing data. These technical features would limit the power of various GBS-based genetic and genomic analyses. We examined 51 pairs of restriction enzymes through in silico analysis of 22 model organisms. Three enzyme pairs were then empirically evaluated with different runs of Illumina MiSeq sequencing in 12 plant species.