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.