Aegilops crassa Boiss. repeatome characterized using low-coverage NGS as a source of new FISH markers: Application in phylogenetic studies of the Triticeae

Pavel Yu Kroupin; Ekaterina D Badaeva; Victoria M Sokolova; Nadezhda N Chikida; Maria Kh Belousova; Sergei A Surzhikov; Ekaterina A Nikitina; Alina A Kocheshkova; Daniil S Ulyanov; Aleksey S Ermolaev; Thi Mai Luong Khuat; Olga V Razumova; Anna I Yurkina; Gennady I Karlov; Mikhail G Divashuk

doi:10.3389/fpls.2022.980764

Aegilops crassa Boiss. repeatome characterized using low-coverage NGS as a source of new FISH markers: Application in phylogenetic studies of the Triticeae

Front Plant Sci. 2022 Oct 5:13:980764. doi: 10.3389/fpls.2022.980764. eCollection 2022.

Authors

Pavel Yu Kroupin¹, Ekaterina D Badaeva^{2

3}, Victoria M Sokolova¹, Nadezhda N Chikida⁴, Maria Kh Belousova⁴, Sergei A Surzhikov³, Ekaterina A Nikitina¹, Alina A Kocheshkova¹, Daniil S Ulyanov¹, Aleksey S Ermolaev¹, Thi Mai Luong Khuat⁵, Olga V Razumova¹, Anna I Yurkina¹, Gennady I Karlov¹, Mikhail G Divashuk¹

Affiliations

¹ All-Russia Research Institute of Agricultural Biotechnology, Kurchatov Genomics Centre - ARRIAB, Moscow, Russia.
² N.I.Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia.
³ Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.
⁴ All-Russian Institute of Plant Genetic Resources (VIR), Department of Wheat Genetic Resources, St. Petersburg, Russia.
⁵ Agricultural Genetics Institute, Department of Molecular Biology, Hanoi, Vietnam.

Abstract

Aegilops crassa Boiss. is polyploid grass species that grows in the eastern part of the Fertile Crescent, Afghanistan, and Middle Asia. It consists of tetraploid (4x) and hexaploid (6x) cytotypes (2n = 4x = 28, D¹D (Abdolmalaki et al., 2019) X^crX^cr and 2n = 6x = 42, D¹D (Abdolmalaki et al., 2019) X^crX^crD²D (Adams and Wendel, 2005), respectively) that are similar morphologically. Although many Aegilops species were used in wheat breeding, the genetic potential of Ae. crassa has not yet been exploited due to its uncertain origin and significant genome modifications. Tetraploid Ae. crassa is thought to be the oldest polyploid Aegilops species, the subgenomes of which still retain some features of its ancient diploid progenitors. The D¹ and D² subgenomes of Ae. crassa were contributed by Aegilops tauschii (2n = 2x = 14, DD), while the X^cr subgenome donor is still unknown. Owing to its ancient origin, Ae. crassa can serve as model for studying genome evolution. Despite this, Ae. crassa is poorly studied genetically and no genome sequences were available for this species. We performed low-coverage genome sequencing of 4x and 6x cytotypes of Ae. crassa, and four Ae. tauschii accessions belonging to different subspecies; diploid wheatgrass Thinopyrum bessarabicum (J^b genome), which is phylogenetically close to D (sub)genome species, was taken as an outgroup. Subsequent data analysis using the pipeline RepeatExplorer2 allowed us to characterize the repeatomes of these species and identify several satellite sequences. Some of these sequences are novel, while others are found to be homologous to already known satellite sequences of Triticeae species. The copy number of satellite repeats in genomes of different species and their subgenome (D¹ or X^cr) affinity in Ae. crassa were assessed by means of comparative bioinformatic analysis combined with quantitative PCR (qPCR). Fluorescence in situ hybridization (FISH) was performed to map newly identified satellite repeats on chromosomes of common wheat, Triticum aestivum, 4x and 6x Ae. crassa, Ae. tauschii, and Th. bessarabicum. The new FISH markers can be used in phylogenetic analyses of the Triticeae for chromosome identification and the assessment of their subgenome affinities and for evaluation of genome/chromosome constitution of wide hybrids or polyploid species.

Keywords: Aegilops; chromosomes; fluorescence in situ hybridization; repeatome; satellite repeats; shallow whole-genome sequencing.