A chromosome-specific painting technique has been developed which combines the most recent approaches of the companion disciplines of molecular cytogenetics and genome research. We developed seven oligonucleotide (oligo) pools derivd from single-copy sequences on chromosomes 1 to 7 of barley (Hordeum vulgare L.) and corresponding collinear regions of wheat (Triticum aestivum L.). The seven groups of pooled oligos comprised between 10 986 and 12 496 45-bp monomers, and these then produced stable fluorescence in situ hybridization (FISH) signals on chromosomes of each linkage group of wheat and barley. The pooled oligo probes were applied to high-throughput karyotyping of the chromosomes of other Triticeae species in the genera Secale, Aegilops, Thinopyrum, and Dasypyrum, and the study also extended to some wheat-alien amphiploids and derived lines. We demonstrated that a complete set of whole-chromosome oligo painting probes facilitated the study of inter-species chromosome homologous relationships and visualized non-homologous chromosomal rearrangements in Triticeae species and some wheat-alien species derivatives. When combined with other non-denaturing FISH procedures using tandem-repeat oligos, the newly developed oligo painting techniques provide an efficient tool for the study of chromosome structure, organization, and evolution among any wild Triticeae species with non-sequenced genomes.

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The perennial species <i>Dasypyrum breviaristatum</i> (genome V^b) contains many potentially valuable genes for the improvement of common wheat. Construction of a detailed karyotype of <i>D. breviaristatum</i> chromosomes will be useful for the detection of <i>Dasypyrum</i> chromatin in wheat background. We established the standard karyotype of 1V^b-7V^b chromosomes through non-denaturing fluorescence <i>in situ</i> hybridization (ND-FISH) technique using 28 oligonucleotide probes from the wheat-<i>D. breviaristatum</i> partial amphiploid TDH-2 (AABBV^bV^b) and newly identified wheat-<i>D. breviaristatum</i> disomic translocation and addition lines D2138 (6V^bS.2V^bL), D2547 (4V^b) and D2532 (3V^bS.6V^bL) by comparative molecular marker analysis. The ND-FISH with multiple oligo probes were conducted on the durum wheat-<i>D. villosum</i> amphiploid TDV-1 and large karyotype differences between <i>D. breviaristatum</i> and <i>D. villosum</i> was revealed. These ND-FISH probes will be valuable for screening the wheat-<i>Dasypyrum</i> derivative lines for chromosome identification, and newly developed wheat-<i>D. breviaristatum</i> addition lines may broaden the gene pool of wheat breeding. The differences between <i>D. villosum</i> and <i>D. breviaristatum</i> chromosomes revealed by ND-FISH will help us understand evolutionary divergence of repetitive sequences within the genus <i>Dasypyrum</i>.

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, pSaO5(411), and pSaD15(940) belonging to the Revolver family. During the evolution of the genus Secale from wild to cultivated accessions, the pSaO5(411)-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 pSaO5(411)-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 pSaO5(411)-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.