Genome, volume 68, pages 1-12

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

Tatiana Danilova 1, 2
Tatiana V. Danilova 3, 4, 5, 6, 7
Alina R Akhunova 8, 9, 10
Xiwen Cai 3, 4, 5, 11, 12, 13, 14
1
 
USDA-ARS, Wheat, Sorghum and Forage Research Unit, Lincoln, Nebraska, United States,
3
 
Wheat
4
 
Sorghum & Forage Research Unit
5
 
USDA-ARS
6
 
Department of Plant Sciences
9
 
Department of Plant Pathology
11
 
USDA-ARS, Wheat, Sorghum & Forage Research Unit, Lincoln, Nebraska, United States,
13
 
Department of Agronomy and Horticulture
Publication typeJournal Article
Publication date2025-01-01
Journal: Genome
scimago Q2
SJR0.591
CiteScore5.3
Impact factor2.3
ISSN08312796, 14803321
Abstract

<i>Aegilops speltoides</i> (2n=2x=14, genome SS) is a wild relative of wheat and a donor of useful traits for wheat improvement. Several whole-genome studies compared genic regions of <i>Aegilops</i> from the <i>Sitopsis</i> section and wheat and found that <i>Ae. speltoides</i> 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 <i>Ae. speltoides</i> more than 4 MYA and either has not yet been discovered, or is extinct. To further explore the evolutionary relationship between wheat and <i>Ae. speltoides</i> and develop <i>Ae. speltoides</i> chromosome paints, we performed comparative analysis of repetitive fractions of the S genome and three subgenomes of hexaploid wheat. The low coverage sequence data was analyzed with RepeatExplorer pipeline to annotate repeats and estimate their content. The LTR-retrotransposons comprised about 80% of repeats in <i>Ae. speltoides</i> and wheat datasets and about two-third of them were LTR/Ty3-Gypsy. <i>Ae. speltoides</i> had 1.5 times more LTR/Ty-Copia repeats and 1.5 times less DNA transposons than wheat subgenomes. Several S genome-specific dispersed repeats were found and annotated. Their sequences were used to develop S genome-specific paints for detecting <i>Ae. speltoides</i> chromatin in the wheat background using fluorescent <i>in situ</i> hybridization.

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