Chromosome-specific painting in Thinopyrum species using bulked oligonucleotides

Chen Chen, Yangshuo Han, He Xiao, Bingcan Zou, Dandan Wu, Lina Sha, Cairong Yang, Songqing Liu, Yiran Cheng, Yi Wang, Houyang Kang, Xing Fan, Yonghong Zhou, Tao Zhang & Haiqin Zhang

Theoretical and Applied Genetics August 2023; vol. 136, Article number: 177

Key message

Chromosome-specific painting probes were developed to identify the individual chromosomes from 1 to 7E in Thinopyrum species and detect alien genetic material of the E genome in a wheat background.

Abstract

The E genome of Thinopyrum is closely related to the ABD genome of wheat (Triticum aestivum L.) and harbors genes conferring beneficial traits to wheat, including high yield, disease resistance, and unique end-use quality. Species of Thinopyrum vary from diploid (2n = 2x = 14) to decaploid (2n = 10x = 70), and chromosome structural variation and differentiation have arisen during polyploidization. To investigate the variation and evolution of the E genome, we developed a complete set of E genome-specific painting probes for identification of the individual chromosomes 1E to 7E based on the genome sequences of Th. elongatum (Host) D. R. Dewey and wheat. By using these new probes in oligonucleotide-based chromosome painting, we showed that Th. bessarabicum (PI 531711, E^bE^b) has a close genetic relationship with diploid Th. elongatum (E^eE^e), with five chromosomes (1E, 2E, 3E, 6E, and 7E) maintaining complete synteny in the two species except for a reciprocal translocation between 4 and 5E^b. All 14 pairs of chromosomes of tetraploid Th. elongatum have maintained complete synteny with those of diploid Th. elongatum (Thy14), but the two sets of E genomes have diverged. This study also demonstrated that the E genome-specific painting probes are useful for rapid and effective detection of the alien genetic material of E genome in wheat–Thinopyrum derived lines.

See https://link.springer.com/article/10.1007/s00122-023-04423-w