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Plant genetics studies and breeding programs utilize the genetic variation caused by DNA polymorphisms. Molecular makers are used to detect these variations in the DNA. The advent of next-generation sequencing (NGS) technologies has conferred new opportunities for high-throughput genotyping in various plant species. Recent improvements in high-throughput sequencing have enabled sequences to be used to detect and score single nucleotide polymorphisms (SNPs) by bypassing the time-consuming process of marker development. With NGS, whole-genome sequencing data and millions of genome-wide SNPs for high-throughput genotyping have become available for a variety of genetic studies and breeding programs. SNP markers are powerful for analyses of integrated SNP sets in a species, although high costs hinder the wider use of SNPs. However, genotype-by-sequencing (GBS), a series …