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ARS Home » Plains Area » Manhattan, Kansas » Center for Grain and Animal Health Research » Hard Winter Wheat Genetics Research » Research » Publications at this Location » Publication #307448
Title: Spiked GBS: A unified, open platform for single marker genotyping and whole-genome profiling

Author
item RIFE, TREVOR - Kansas State University
item WU, SHUANGYE - Kansas State University
item Bowden, Robert
item POLAND, JESSE - Kansas State University

Submitted to: BMC Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/25/2015
Publication Date: 3/28/2015
Publication URL: http://www.biomedcentral.com/content/pdf/s12864-015-1404-9.pdf
Citation: Rife, T.W., Wu, S., Bowden, R.L., Poland, J.A. 2015. Spiked GBS: A unified, open platform for single marker genotyping and whole-genome profiling. Biomed Central (BMC) Genomics. 16:248. DOI:10.1186/s12864-015-1404-9.

Interpretive Summary: In plant breeding, there are two primary applications for DNA markers in selection: 1) selection of known genes using a single marker assay (known as marker-assisted selection); and 2) whole-genome profiling and prediction (known as genomic selection). Typically, marker platforms have addressed only one of these objectives. We have developed a new method called spiked genotyping-by-sequencing (sGBS), which combines targeted gene sequencing with whole-genome scanning. In breeding applications, the sGBS approach will allow breeders to obtain a whole-genome profile of important individuals while simultaneously targeting specific genes that are important. This should lead to greater speed and efficiency of selection strategies.

Technical Abstract: 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. 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 available 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 enables simultaneous assessment of multiple, single-target loci and whole-genome profiling while allowing different sets of samples to be evaluated on the two-marker system. 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. 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.