TY - JOUR
T1 - Spiked GBS: A unified, open platform for single marker genotyping and whole-genome profiling
AU - Rife, Trevor W.
AU - Wu, Shuangye
AU - Bowden, Robert L.
AU - Poland, Jesse A.
N1 - Generated from Scopus record by KAUST IRTS on 2022-09-13
PY - 2015/3/28
Y1 - 2015/3/28
N2 - 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.
AB - 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.
UR - https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-015-1404-9
UR - http://www.scopus.com/inward/record.url?scp=84928140867&partnerID=8YFLogxK
U2 - 10.1186/s12864-015-1404-9
DO - 10.1186/s12864-015-1404-9
M3 - Article
SN - 1471-2164
VL - 16
JO - BMC genomics [electronic resource]
JF - BMC genomics [electronic resource]
IS - 1
ER -