title: Spiked GBS: a unified, open platform for single marker genotyping and whole-genome profiling.
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.
authors.affiliation: Interdepartmental Genetics, Kansas State University, 4024 Throckmorton Hall, Manhattan, KS, 66506, USA. trife@ksu.edu.|Wheat Genetics Resource Center, Department of Plant Pathology, Kansas State University, 4024 Throckmorton Hall, Manhattan, KS, 66506, USA. trife@ksu.edu.
authors.forename: Trevor W
authors.initials: TW
authors.lastname: Rife
authors.affiliation: Wheat Genetics Resource Center, Department of Plant Pathology, Kansas State University, 4024 Throckmorton Hall, Manhattan, KS, 66506, USA. swu4455@ksu.edu.
authors.forename: Shuangye
authors.initials: S
authors.lastname: Wu
authors.affiliation: USDA-ARS, Hard Winter Wheat Genetics Research Unit, 4008 Throckmorton Hall, Manhattan, KS, 66506, USA. Robert.Bowden@ARS.USDA.GOV.
authors.forename: Robert L
authors.initials: RL
authors.lastname: Bowden
authors.affiliation: Wheat Genetics Resource Center, Department of Plant Pathology, Kansas State University, 4024 Throckmorton Hall, Manhattan, KS, 66506, USA. jpoland@ksu.edu.|Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA. jpoland@ksu.edu.
authors.forename: Jesse A
authors.initials: JA
authors.lastname: Poland
mesh_terms: D000465:Algorithms; D000483:Alleles; D001947:Breeding; D016000:Cluster Analysis; D017931:DNA Primers / Q000378:metabolism; D005819:Genetic Markers / Q000235:genetics*; D018745:Genome, Plant; D005838:Genotype; D060005:Genotyping Techniques / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D017422:Sequence Analysis, DNA; D014908:Triticum / Q000235:genetics
chemical_list: D017931:DNA Primers; D005819:Genetic Markers