Genotyping-by-Sequencing in Plants

Abstract

The advent of next-generation DNA sequencing (NGS) technologies has led to the development of rapid genome-wide Single Nucleotide Polymorphism (SNP) detection applications in various plant species. Recent improvements in sequencing throughput combined with an overall decrease in costs per gigabase of sequence is allowing NGS to be applied to not only the evaluation of small subsets of parental inbred lines, but also the mapping and characterization of traits of interest in much larger populations. Such an approach, where sequences are used simultaneously to detect and score SNPs, therefore bypassing the entire marker assay development stage, is known as genotyping-by-sequencing (GBS). This review will summarize the current state of GBS in plants and the promises it holds as a genome-wide genotyping application.

Figure 1

Schematic diagram of a representative GBS procedure. Two parents (AA and BB) are selected to create a mapping population. The parents are deeply sequenced using NGS technologies. SNPs and other variations between them are identified. The RILs are prepared using the same library construction strategy as the two parents (see text for details) and sequenced at lower coverage using NGS technologies. The resulting sequences are used to determine allelic diversity for each individual. Genotypes are assigned based on parental information. Haplotypes and recombination maps are created for each RIL. Blocks of haplotypes can be used directly as markers for mapping applications.