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Complex chromosome rearrangements (CCRs) are defined as structural abnormalities involving more than two chromosome breaks, coupled with exchanges of chromosomal segments. Information on CCRs in plants is limited. In the present study, a plant (26-4) harboring translocation chromosomes 1RS.1BL and 4RS.4DL was selected from a double monosomic (1R and 4R) addition line, which was derived from the hybrid between wheat cultivar MY11 and a Chinese local rye variety. The genome of the plant with double alien translocation chromosomes in the monosomic form showed more instability than that harboring a single translocation. The CCRs involving chromosomes 1RS.1BL and 3B, which were generated de novo in this plant, showed double monosomic translocation chromosomes. A new CCR line with balanced reciprocal translocations 1RS.3BL and 3BS.1BL was developed, which presented normal morphological traits of wheat and underwent rapid growth in the field. A new 1RS.1BL translocation line was also selected from the progeny of plant 26-4. The CCRs and simple 1RS.1BL translocation lines showed significant improvement in grain yield, number of spikes per square meter, kernel number per spike, and resistance to stripe rust and powdery mildew. The CCR line exhibited better agronomic traits and adult plant resistance in the field than its sister line, which harbored a simple 1RS.1BL translocation. The CCRs are remarkable genetic resources for crop improvement.

We present the first characterization of 360 sequences in six species of the genus Secale of both cultivated and wild accessions. These include four distinct kinds of dispersed repetitive DNA sequences named pSc20H, pSc119.1, pSaO5411, and pSaD15940 belonging to the Revolver family. During the evolution of the genus Secale from wild to cultivated accessions, the pSaO5411-like sequences became shorter mainly because of the deletion of a trinucleotide tandem repeating unit, the pSc20H-like sequences displayed apparent homogenization in cultivated rye, and the second intron of Revolver became longer. In addition, the pSc20H-, pSc119.1-, and pSaO5411-like sequences cloned from wild rye and cultivated rye could be divided into two large clades. No single case of the four kinds of repetitive elements has been inherited by each Secale accession from a lone ancestor. It is reasonable to consider the vertical transmission of the four repetitive elements during the evolution of the genus Secale. The pSc20H- and pSaO5411-like sequences showed evolutionary elimination at specific chromosomal locations from wild species to cultivated species. These cases imply that different repetitive DNA sequences have played different roles in the chromosome development and genomic evolution of rye. The present study adds important information to the investigations dealing with characterization of dispersed repetitive elements in wild and cultivated rye.