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

BMC Genomics. 2015 Mar 28;16(1):248. doi: 10.1186/s12864-015-1404-9.

Abstract

Background: In 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.

Results: We 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.

Conclusions: The 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.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Algorithms
  • Alleles
  • Breeding
  • Cluster Analysis
  • DNA Primers / metabolism
  • Genetic Markers / genetics*
  • Genome, Plant
  • Genotype
  • Genotyping Techniques / methods*
  • High-Throughput Nucleotide Sequencing / methods*
  • Sequence Analysis, DNA
  • Triticum / genetics

Substances

  • DNA Primers
  • Genetic Markers