The nonrandom distribution of long clusters of all possible classes of trinucleotide repeats in barley chromosomes

This paper is the first to report the long-range organization of all possible classes of trinucleotide motifs in a higher plant genome. Fluorescent in situ hybridization (FISH), employing the synthetic oligonucleotides (AAC)5, (AAG)5, (AAT)5, (AGG)5, (CAC)5, (CAT)5, (CAG)5, (ACT)5, (ACG)5 and (GCC)5, was used to characterize the nonrandom and motif-dependent distribution of tandem arrays of trinucleotide repeats in the metaphase chromosomes and interphase nuclei of barley (Hordeum vulgare L.). This provided detailed information on the sequence content of barley chromatin and allowed the saturation of the physical map of all barley chromosomes. The following conclusions were also drawn: (1) Except for (AAT)5 and (GCC)5, the studied repetitive motifs have a characteristic pattern of distribution in terms of their in situ FISH signals. Some permit the accurate identification of individual chromosomes. (2) (CAG)5, (CAT)5 and (ACT)5 are not found in all barley chromosomes. (3) With the exception of (ACT)5, the remaining trinucleotide repeats occur predominantly in the heterochromatin and are largely absent from the euchromatic regions. Moreover, (CAC)5, (ACG)5 and (CAG)5 are exclusively concentrated in the centromeres. The employment of simple synthetic probes for the identification of chromosomes and genomic characterization, and their importance in studies on genome organization, function and evolution, are discussed.