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ARS Home » Plains Area » Lincoln, Nebraska » Wheat, Sorghum and Forage Research » Research » Publications at this Location » Publication #416162
Research Project: Identification, Characterization, and Utilization of Priority Traits for the Genetic Improvement of Winter Wheat and Barley Germplasm Adapted to the Great Plains

Location: Wheat, Sorghum and Forage Research

Title: Comparative analysis of Aegilops speltoides and wheat repetitive elements and development of S genome-specific FISH painting

Author
item Danilova, Tatiana
item AKHUNOVA, ALINA - Kansas State University
item Cai, Xiwen

Submitted to: Genome
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/18/2024
Publication Date: 2/27/2025
Citation: Danilova, T.V., Akhunova, A., Cai, X. 2025. Comparative analysis of Aegilops speltoides and wheat repetitive elements and development of S genome-specific FISH painting. Genome. 68:1-12(2025). https://doi.org/10.1139/gen-2024-0090.
DOI: https://doi.org/10.1139/gen-2024-0090

Interpretive Summary: U.S. produces about 6-7 percent of the world’s wheat but ranks among the top five global wheat exporters. Wheat production continually challenged by climate variability, the rise of new diseases and pests, and a continue growing demand for food. Wild species are rich resources of genes for resistances drought, diseases and pests not available in the cultivated wheat. Goatgrass, Aegilops speltoides is a wild wheat relative and one of the ancestors of modern wheat. This study extracted and characterized the repetitive DNA portion of the goatgrass genome. The repetitive DNA sequences unique to goatgrass and not found in wheat were identified. These DNA sequences are used as tools to identify chromosome segments containing goatgrass genes incorporate into wheat in genetic and breeding experiments. The methods used to identify the unique repetitive DNA sequences form the basis to identify, characterize and utilize these sequences from other wild relatives of wheat to develop new climate resilient and disease resistant wheat varieties.

Technical Abstract: Aegilops speltoides is a wild relative of common wheat (Triticum aestivum), and a donor of useful traits for wheat improvement. According to several whole-genome studies which compared genic regions of Aegilops from the Sitopsis section and wheat, Ae. speltoides is most closely related to the wheat B subgenome but is not its direct progenitor. The results showed that a B subgenome ancestor diverged from Ae. speltoides more than 4 mya and either has not yet been discovered, or extinct. To further explore the evolutionary relationship between wheat and Ae. speltoides, we performed comparative analysis of repetitive fractions of their genomes. The low coverage sequence data was analyzed with RepeatExplorer pipeline to annotate dispersed and tandem repeats and estimate their content. The LTR-retrotransposons comprise about 80% of repeats in the four genomes and about two-third of them are LTR/Ty3-Gypsy, though Ae. speltoides has 1.5 times more LTR/Ty-Copia repeats and 1.5 times less DNA transposons than wheat subgenomes. We found and annotated several S genome-specific dispersed repeats which belong to the LTR/Ty-Copia group. Their sequences were used to develop S genome-specific paints for detection of Ae. speltoides chromosomes at wheat background using fluorescent in situ hybridization (FISH). We also mapped some S-genome tandem repeats by FISH. The FISH paints were used to trace S-chromatin in wheat gene introgression projects.