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

• Published in: The Plant journal : for cell and molecular biology Vol. 112; no. 1; pp. 55 - 67
• Main Authors: Shi, Peiyao, Sun, Haojie, Liu, Guanqing, Zhang, Xu, Zhou, Jiawen, Song, Rongrong, Xiao, Jin, Yuan, Chunxia, Sun, Li, Wang, Zongkuan, Lou, Qunfeng, Jiang, Jiming, Wang, Xiue, Wang, Haiyan
• Format: Journal Article
• Language: English
• Published: Oxford Blackwell Publishing Ltd 01.10.2022
• Subjects: Aegilops; Breakpoints; Breeding; chromosome rearrangement; Chromosome rearrangements; Chromosome translocations; Chromosomes; common wheat; Diploids; DNA probes; Evolution; Fluorescence; Fluorescence in situ hybridization; Gene pool; genetic relationship; Genomes; Goat grass; oligo painting; Oligonucleotides; oligo‐FISH; Plant breeding; Polyploidy; Probes; Species; Synteny; Translocation; Triticum aestivum; Wheat
• ISSN: 0960-7412; 1365-313X
• DOI: 10.1111/tpj.15926

SUMMARY 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 D‐specific 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. Significance Statement Oligo‐based chromosome painting probes were developed for all seven chromosomes, specific to subgenome D of wheat (Triticum aestivum), which can be used to precisely characterize translocations involving D chromosomes, not only in wheat but also in several Aegilops species. Comparative chromosome paints preliminarily revealed syntenic relationships and diversification among homoeologous chromosomes from different Aegilops species and identified chromosomal rearrangements in diploid Aegilops species.