Physical Location of New PCR-Based Markers and Powdery Mildew Resistance Gene(s) on Rye (Secale cereale L.) Chromosome 4 Using 4R Dissection Lines

Rye (Secale cereale L.) 4R chromosome contains elite genes that are applicable for wheat (Triticum aestivum L.) cultivar improvement. PCR-based 4R-specific markers can benefit the detection of elite genes on 4R in wheat backgrounds. In this study, a new fluorescence in situ hybridization (FISH) map of the 4R(Ku) chromosome of rye Kustro has been constructed. A set of 4R(Ku) dissection lines was obtained and 301 new 4R(Ku)-specific markers were developed using specific length amplified fragment sequencing (SLAF-seq) technology. These markers were combined with the 99 4R(Ku)-specific markers previously developed, and were physically mapped to 4R(Ku) chromosome using the new FISH map and the 4R(Ku) dissection lines. A total of 338 of the 400 markers have been successfully mapped to six regions of 4R(Ku) chromosome. Additionally, the powdery mildew resistance gene(s) on the 4RL(Ku) arm was located to the segment between L.4 and L.8, the same region where 115 4RL(Ku)-specific markers were mapped. The markers developed in this study can be used to identify a specific segment of 4R chromatin in wheat backgrounds, help construct a high-density physical map of 4R chromosome, and facilitate the utilization of elite genes on 4R chromosome in wheat breeding programs.