To investigate the effect of structural variation of rye 6RL arms on their meiotic behavior and to locate powdery mildew resistance gene(s), we developed a wheat–rye T6BS.6RL^Ar translocation chromosome and its deleted translocations, T6BS.6RL^Ar-2 and T6BS.6RL^Ar-4. Some 6RL-specific markers were used to determine that the segments from 733.91 to 849.52 Mb and from 832.72 Mb to the telomere of 6RL^Ar arms were deleted from T6BS.6RL^Ar-2 and T6BS.6RL^Ar-4, respectively. Translocations T6BS.6RL^Ar and T6BS.6RL^Ar-4 were resistant to powdery mildew and T6BS.6RL^Ar-2 was susceptible. The segment of 6RL^Ar with powdery mildew resistance was about 100 Mb. Deletion of the 6RL^Ar telomeric region inhibited the pairing and recombination of T6BS.6RL^Ar-4. Compared with T6BS.6RL^Ar and T6BS.6RL^Ar-4, T6BS.6RL^Ar-2 showed a normal meiotic behavior. Immunolocalization using anti-ZYP1, anti-DMC1 and anti-MLH1 proteins indicated that more DSBs (DNA double-strand breaks) and crossovers formed on the 6RL^Ar arm in T6BS.6RL^Ar, and this might be related to the formation of anaphase I bridges of 6RL^Ar. Although the 6RL^Ar deletions were used to physically locate powdery mildew resistance gene(s), more accurate location through meiotic recombination was needed. The results in this study indicated that altering the structure of the 6RL^Ar arm promoted normal meiotic behavior, and this might facilitate the localization of resistance genes through meiotic homologous recombination.

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 4R^Ku and to the confirmation of 4RL^Ku breakpoints in wheat-rye 4RL^Ku 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.