Chromosome painting reveals inter‐chromosomal rearrangements and evolution of subgenome D of wheat

Abstract

Aegilops species represent the most important gene pool for breeding bread wheat (Triticum aestivum). Thus, understanding the genome evolution, including chromosomal structural rearrangements and syntenic relationships among Aegilops species or between Aegilops and wheat, is important for both basic genome research and practical breeding applications. In the present study, we attempted to develop subgenome Dspecific fluorescence in situ hybridization (FISH) probes by selecting D-specific oligonucleotides based on the reference genome of Chinese Spring. The oligo-based chromosome painting probes consisted of approximately 26 000 oligos per chromosome and their specificity was confirmed in both diploid and polyploid species containing the D subgenome. Two previously reported translocations involving two D chromosomes have been confirmed in wheat varieties and their derived lines. We demonstrate that the oligo painting probes can be used not only to identify the translocations involving D subgenome chromosomes, but also to determine the precise positions of chromosomal breakpoints. Chromosome painting of 56 accessions of Ae. tauschii from different origins led us to identify two novel translocations: a reciprocal 3D-7D translocation in two accessions and a complex 4D-5D-7D translocation in one accession. Painting probes were also used to analyze chromosomes from more diverse Aegilops species. These probes produced FISH signals in four different genomes. Chromosome rearrangements were identified in Aegilops umbellulata, Aegilops markgrafii, and Aegilops uniaristata, thus providing syntenic information that will be valuable for the application of these wild species in wheat breeding.

Chromosome Rearrangement in Elymus dahuricus Revealed by ND-FISH and Oligo-FISH Painting

“…For example, high-resolution multiple oligonucleotide FISH revealed 14 structural rearrangements from 373 Chinese wheat cultivars [ 30 ]. FISH using D-specific oligo probes characterized specific CRs involved 3D-7D and complex 4D-5D-7D in Aegilops tauschii from different origins [ 31 ]. Meanwhile, Li et al [ 20 ] developed seven oligonucleotide pools for Oligo-FISH painting techniques, and demonstrated the multiple CRs for 3R, 4R, 6R and 7R occurred in rye.…”

“…Our study distinguished all 42-chromosomes in E. dahuricus by different combination of probes, and compare the relative CENH3 fluorescence intensity of each chromosome in H subgenome ( Figure 6 g). A high variable of CENH3 in 6H chromosome was detected, which implied the existence of the dynamic CENH3 expression among each H chromosome in E. dahuricus during evolution of polyploid [ 31 ].…”