ND-FISH-positive oligonucleotide probes for detecting specific segments of rye (Secale cereale L.) chromosomes and new tandem repeats in rye

Abstract Rye (Secale cereale L.) has been widely used to improve wheat (Triticum aestivum L.) cultivars. Oligo probes combined with non-denaturing fluorescence in situ hybridization (ND-FISH) technology provide a convenient and efficient way to identify individual rye chromosomes. However, suitable ND-FISH-positive oligo probes for recognizing specific segments of rye chromosomes are lacking. Five new ND-FISH-positive oligo probes: Oligo-5BL.46, Oligo-5A8080, Oligo-5A8080.1, Oligo-1AL.73, and Oligo-0R3, combined with two previously reported oligo probes, Oligo-44 and Oligo-45, were used in this study. Probes Oligo-5BL.46, Oligo-5A8080 and Oligo-44 produced signals only in intercalary regions of arms 1RS, 5RS, and 5RL, respectively. Probe Oligo-5A8080.1 combined with probe Oligo-45 distinguished the intercalary regions of arms 1RS, 5RS, and 6RS simultaneously. Oligo-5A8080 and Oligo-5A8080.1 revealed variation in the distribution of 5S rDNA sequences and polymorphism among 5R chromosomes. Probe Oligo-1AL.73 produced signals only on chromosomes 4R and 7R and contributed to the construction of an improved FISH map of chromosome 4RKu and to the confirmation of 4RLKu breakpoints in wheat-rye 4RLKu translocation chromosomes. Oligo-0R3 produced signals in the telomeric and subtelomeric regions of 14 rye chromosomes. These oligo probes also revealed five new tandem repeats in rye. Using the oligo probes reported in this study, the short arms of 1R, 5R, and 6R and the long arms of 4R and 7R can be easily discriminated when these chromosomes are broken.