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Background   Thinopyrum intermedium  (2n = 6x = 42) is an important wild perennial  Triticeae  species exhibiting many potentially favorable traits for wheat improvement. Wheat- Th .  intermedium  partial amphiploids serve as a bridge to transfer desirable genes from  Th .  intermedium  into common wheat.    Results  Three octoploid  Trititrigia  accessions (TE261–1, TE266–1, and TE346–1) with good resistances to stripe rust, powdery mildew and aphids were selected from hybrid progenies between  Th .  intermedium  and the common wheat variety ‘Yannong 15’ (YN15). Genomic in situ hybridization (GISH), fluorescence in situ hybridization (FISH) and multicolor GISH (McGISH) analyses demonstrated that the three octoploid  Trititrigia  possess 42 wheat chromosomes and 14  Th. intermedium  chromosomes. The 14 alien ( Th. intermedium ) chromosomes belong to a mixed genome consisting of J-, J S - and St-genome chromosomes rather than a single J, J S  or St genome. Different types of chromosomal structural variation were also detected in the 1A, 6A, 6B, 2D and 7D chromosomes via FISH, McGISH and molecular marker analysis. The identity of the alien chromosomes and the variationes in the wheat chromosomes in the three  Trititrigia  octoploids were also different.    Conclusions  The wheat- Th. intermedium  partial amphiploids possess 14 alien chromosomes which belong to a mixed genome consisting of J-, J S - and St- chromosomes, and 42 wheat chromosomes with different structural variations. These accessions could be used as genetic resources in wheat breeding for the transfer of disease and pest resistance genes from  Th. intermedium  to common wheat.    Supplementary Information  The online version contains supplementary material available at 10.1186/s12870-021-02896-9.

bmc plant biology

Characterization of chromosome constitution in three wheat - Thinopyrum intermedium amphiploids revealed frequent rearrangement of alien and wheat chromosomes