Genotyping-by-Sequencing and Its Application to Oat Genomic Research

Abstract

Genotyping-by-sequencing (GBS) has emerged as a useful genomic approach for sampling genome-wide genetic variation, performing genome-wide association mapping, and conducting genomic selection. It is a combined one-step process of SNP marker discovery and genotyping through genome reduction with restriction enzymes and SNP calling with or without a sequenced genome. This approach has the advantage of being rapid, high throughput, cost effective, and applicable to organisms without sequenced genomes. It has been increasingly applied to generate SNP genotype data for plant genetic and genomic studies. To facilitate a wider GBS application, particularly in oat genetic and genomic research, we describe the GBS approach, review the current applications of GBS in plant species, and highlight some applications of GBS to oat research. We also discuss issues in various applications of GBS and provide some perspectives in GBS research. Recent developments of bioinformatics pipelines in high-quality SNP discovery for polyploid crops will enhance the application of GBS to oat genetic and genomic research.

Genetic Diversity of Northern Wheatgrass (Elymus lanceolatus ssp. lanceolatus) as Revealed by Genotyping-by-Sequencing

“…More importantly, the total laboratory and sequencing cost for generating these genomic data on this set of studied samples was roughly $12,000, indicating the feasibility of a wider application of GBS to characterize native grass species. However, bias in SNP calling exists due to incomplete allele sampling [10]. It is difficult to separate true null tag-level haplotypes from missing sequence data, particularly at the sequence depth typically employed in GBS studies [12].…”

“…A GBS application can produce high-density, low-cost genotype information without the need for a reference genome sequence [6]. However, recent GBS applications have also revealed some weaknesses, including a large number of missing data points, uneven genome coverage, complex bioinformatics, and issues related to polyploidy [7][8][9][10]. To address some of these challenges, Tinker et al [11] developed a GBS-based pipeline called Haplotag that can generate tag-level haplotype and single nucleotide polymorphism (SNP) data for polyploid organisms.…”

Adapting Genotyping-by-Sequencing and Variant Calling for Heterogeneous Stock Rats

“…Of the existing reduced-representation protocols, the genotyping-by-sequencing (GBS) approach developed by Elshire et al ( Elshire et al 2011 ) has been frequently modified to accommodate other species: soybean ( Sonah et al 2013 ), rice ( Furuta et al 2017 ), oat ( Fu and Yang 2017 ), chicken ( Pértille et al 2016 ; Wang et al 2017 ), mouse ( Parker et al 2016 ), fox ( Johnson et al 2015 ), and cattle ( De Donato et al 2013 ), among others. The greatly varying genomic composition among organisms necessitates a diverse and customized set of approaches for obtaining high-quality genotypes.…”

Advancing crested wheatgrass [Agropyron cristatum (L.) Gaertn.] breeding through genotyping-by-sequencing and genomic selection

“…The sample-by-variant matrix obtained was used for genomic selection application. Irrespective of the robustness of the GBS application, there are many missing data points, uneven genome coverage, complex bioinformatics, and issues related to polyploidy, limiting its application [ 25 – 27 ]. These drawbacks can be overcome with a GBS-based pipeline, called Haplotag [ 28 ], which can generate tag-level haplotype and SNP data for polyploid organisms [ 15 ].…”