Spiked GBS: a unified, open platform for single marker genotyping and whole-genome profiling.

Trevor W Rife,Robert L Bowden,Shuangye Wu,Jesse A Poland

doi:10.1186/s12864-015-1404-9

Trevor W Rife, Robert L Bowden + Show 2 more

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https://doi.org/10.1186/s12864-015-1404-9

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Abstract

BackgroundIn plant breeding, there are two primary applications for DNA markers in selection: 1) selection of known genes using a single marker assay (marker-assisted selection; MAS); and 2) whole-genome profiling and prediction (genomic selection; GS). Typically, marker platforms have addressed only one of these objectives.ResultsWe have developed spiked genotyping-by-sequencing (sGBS), which combines targeted amplicon sequencing with reduced representation genotyping-by-sequencing. To minimize the cost of targeted assays, we utilize a small percent of sequencing capacity available in runs of GBS libraries to “spike” amplified targets of a priori alleles tagged with a different set of unique barcodes. This open platform allows multiple, single-target loci to be assayed while simultaneously generating a whole-genome profile. This dual-genotyping approach allows different sets of samples to be evaluated for single markers or whole genome-profiling. Here, we report the application of sGBS on a winter wheat panel that was screened for converted KASP markers and newly-designed markers targeting known polymorphisms in the leaf rust resistance gene Lr34.ConclusionsThe flexibility and low-cost of sGBS will enable a range of applications across genetics research. Specifically in breeding applications, the sGBS approach will allow breeders to obtain a whole-genome profile of important individuals while simultaneously targeting specific genes for a range of selection strategies across the breeding program.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1404-9) contains supplementary material, which is available to authorized users.

Highlights

In plant breeding, there are two primary applications for DNA markers in selection: 1) selection of known genes using a single marker assay; and 2) whole-genome profiling and prediction
Contemporary marker technologies for assaying single targets that are often used with Marker-assisted selection (MAS) include Kompetitive Allele specific PCR (KASP), targeted amplicon sequencing, and SNP arrays
To test the approach of spiked GBS, we assayed a panel of diverse wheat lines using GBS to create a whole-genome profile and spiked genotyping-by-sequencing (sGBS) to target 11 known polymorphic sites

Summary

Introduction

There are two primary applications for DNA markers in selection: 1) selection of known genes using a single marker assay (marker-assisted selection; MAS); and 2) whole-genome profiling and prediction (genomic selection; GS). Marker-assisted selection (MAS) is used in plant breeding to identify the allele present at a specific locus, allowing the breeder to select based on genotype [1]. MAS has been used for plant breeding in many crops to identify specific individuals with known genes of interest [2,3,4], primarily to target large-effect, single targets [5,6]. Since each locus is generally genotyped independently, breeders tend to consider per data point costs when utilizing MAS within breeding programs. Contemporary marker technologies for assaying single targets that are often used with MAS include KASP, targeted amplicon sequencing, and SNP arrays. Targeted amplicon sequencing (TAS) amplifies known gene targets and attaches a barcode in a second PCR reaction for multiplexing [8]. TAS was further extended to a single PCR reaction that utilized linker sequences

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