Development and application of new chromosome-specific oligonucleotide probes for Thinopyrum elongatum

The E genome of Thinopyrum elongatum is an important alien genetic resource for the breeding of Triticum aestivum. The purpose of this study was to develop chromosome-specific oligonucleotide probes for Th. elongatum. Based on the Th. elongatum reference genome, 1,522,611 tandem repeats were identified using bioinformatics methods. By further merging tandem repeats using bedtools in sliding windows of 10 kb, we obtained 15,500 high-copy sequences with a copy number exceeding 100. We identified 1,609 unique high-copy tandem repeats of Th. elongatum as candidate sequences by comparing them with the wheat reference genome. Based on their chromosome specificity and distribution sites, 19 Th. elongatum oligonucleotide probes were developed and applied to material identification. The results showed that the Oligo-7ES-2 probe produced a clear and stable in situ hybridization signal on the chromosome of the CS-7E addition line material, located on the long arm of 7E chromosome. The Oligo-7ES-2 probe developed in this study can help the traditional E genome GISH probe for mapping chromosomes or chromosome fragments of 7E and 7EL derived lines of wheat and Th. elongatum. This lays a foundation for the efficient identification of exogenous chromosomes of Th. elongatum in wheat genetic improvement.