Cytological and molecular characterization of Thinopyrum bessarabicum chromosomes and structural rearrangements introgressed in wheat

Thinopyrum bessarabicum is an important genetic resource for wheat improvement by chromosome engineering. However, the present low-resolution karyotype limits identification of its chromosomes. Oligonucleotide probes to identify tandem repeats provide an efficient way to produce high-resolution karyotypes in many species. In this study, putative tandem repeats were identified using unassembled sequence reads of Th. bessarabicum, and 306 repeat clusters were identified. Among them, 17 had conserved motifs that varied in size from 71 to 856 bp and occupied 0.01% to 1.30% of the genome. Thirty-nine oligonucleotides from 17 clusters were developed, and 21 from 8 clusters produced clear and stable signals in Th. bessarabicum chromosomes. Five tandem repeat clusters were distributed only at the telomeric or subtelomeric regions, and the BSCL242 probe produced signals only on chromosome 7JL. The other three were mainly in intercalary and centromeric regions with a few weak signals in telomeric regions. A new multiplex oligonucleotide probe (ONPM#7) containing 13 oligonucloetides distinguished all wheat and Th. bessarabicum chromosomes after one round of FISH. The high-resolution karyotype of Th. bessarabicum in corresponding with the seven homoeologous group chromosomes of wheat has been developed. Three spontaneous translocations and one isochromosome among Th. bessarabicum chromosomes introgressed into wheat thus have been characterized in combined with molecular marker analysis. The ONPM#7 probe and molecular markers provide powerful tools for engineering transfer of chromosomal segments from Th. bessarabicum to wheat.