Development and Application of the GenoBaits®WheatSNP16K Array to Accelerate Wheat Genetic Research and Breeding

Single nucleotide polymorphisms (SNPs) are widely used as molecular markers for constructing genetic linkage maps in wheat. Compared with available SNP-based genotyping platforms, a genotyping by target sequencing (GBTS) system with capture-in-solution (liquid chip) technology has become the favored genotyping technology because it is less demanding and more cost-effective, flexible and user-friendly. In this study, a new GenoBaits®WheatSNP16K (GBW16K) GBTS array was designed based on data sets generated by the wheat 660K SNP array and re-sequencing platforms in our previous studies. The GBW16K array contained 14,868 target SNP regions that were evenly distributed across the wheat genome and 37,669 SNPs in those regions were identified in a diversity panel consisting of 239 wheat accessions from around the world. Principal component and neighbor-joining analysis using the calling SNPs were consistent with the pedigree information and geographical distribution or ecological environments of the accessions. For the GBW16K marker panel, the average genetic diversity among the 239 accessions was 0.270 which is sufficient for linkage map construction and preliminary mapping of targeted genes/QTLs. A genetic linkage map of a RIL population derived from a cross of CIMMYT wheat line Yaco"S" and Chinese landrace Mingxian169 constructed using the GBW16K array enabled identification of Yr27, Yr30 and QYr.nwafu-2BL.4 for adult plant resistance (APR) to stripe rust from Yaco"S" and Yr18 from Mingxian169. QYr.nwafu-2BL.4 was different from any previously reported gene/QTL. Three haplotypes and six candidate genes have been identified for QYr.nwafu-2BL.4 based on haplotype analysis, micro-collinearity, gene annotation, RNA-seq and SNP data. This array provides a new resource tool for wheat genetic analysis and breeding studies and for achieving durable control of wheat stripe rust.