Rife Trevor W, Wu Shuangye, Bowden Robert L, Poland Jesse A
Interdepartmental Genetics, Kansas State University, 4024 Throckmorton Hall, Manhattan, KS, 66506, USA.
Wheat Genetics Resource Center, Department of Plant Pathology, Kansas State University, 4024 Throckmorton Hall, Manhattan, KS, 66506, USA.
BMC Genomics. 2015 Mar 28;16(1):248. doi: 10.1186/s12864-015-1404-9.
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 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.
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.
在植物育种中，DNA标记在选择方面有两个主要应用：1）使用单标记分析（标记辅助选择；MAS）选择已知基因；2）全基因组分析和预测（基因组选择；GS）。通常，标记平台仅针对其中一个目标。
我们开发了加标测序基因分型（sGBS），它将靶向扩增子测序与简化代表性测序基因分型相结合。为了尽量降低靶向分析的成本，我们在GBS文库的测序运行中利用一小部分可用测序能力来“加标”带有不同独特条形码集的先验等位基因的扩增靶标。这个开放平台允许同时检测多个单靶点位点，同时生成全基因组图谱。这种双重基因分型方法允许对不同样本集进行单标记评估或全基因组分析。在此，我们报告了sGBS在一个冬小麦群体上的应用，该群体针对转化的KASP标记以及针对叶锈病抗性基因Lr34中已知多态性的新设计标记进行了筛选。
sGBS的灵活性和低成本将使其在遗传学研究中有一系列应用。特别是在育种应用中，sGBS方法将使育种者能够获得重要个体的全基因组图谱，同时针对育种计划中的一系列选择策略靶向特定基因。
