Genotyping-by-sequencing: a promising tool for plant genetics research and breeding

Abstract

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 of genetic analyses that includes molecular marker discovery and genotyping using NGS technologies, has opened new possibilities in plant breeding and plant genetics studies. It offers cost-effective genome-wide scanning and multiplexed sequencing platforms. The GBS method uses restriction enzymes coupled with DNA barcoded adapters to reduce complexity. GBS can simultaneously perform SNP discovery and genotyping with or without reference genome sequences. Therefore, GBS can be applied to various approaches for plant breeding and plant genetics studies, including linkage maps, genome-wide association studies, genomic selection, and genomic diversity studies. These features make GBS an ideal tool for studies ranging from single-gene markers to whole-genome profiling.