Genome-Wide Distribution of Novel Ta-3A1 Mini-Satellite Repeats and Its Use for Chromosome Identification in Wheat and Related Species

Abstract

A large proportion of the genomes of grasses is comprised of tandem repeats (TRs), which include satellite DNA. A mini-satellite DNA sequence with a length of 44 bp, named Ta-3A1, was found to be highly accumulated in wheat genome, as revealed by a comprehensive sequence analysis. The physical distribution of Ta-3A1 in chromosomes 3A, 5A, 5B, 5D, and 7A of wheat was confirmed by nondenaturing fluorescence in situ hybridization (ND-FISH) after labeling the oligonucleotide probe. The analysis of monomer variants indicated that rapid sequence amplification of Ta-3A1 occurred first on chromosomes of linkage group 5, then groups 3 and 7. Comparative ND-FISH analysis suggested that rapid changes occurred in copy number and chromosomal locations of Ta-3A1 among the different species in the tribe Triticeae, which may have been associated with chromosomal rearrangements during speciation and polyploidization. The labeling and subsequent use of Ta-3A1 by ND-FISH may assist in the precise identification and documentation of novel wheat germplasm engineered by chromosome manipulation.

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

“…intermedium, respectively. We did not find this repeat in the X cr subgenome, Lang et al (2019b) did not detect it in barley and Dasypyrum breviaristatum. Thus, we can assume that the X cr subgenome donor diverged from a common ancestor after barley and D. breviaristatum, but prior to active amplification of this repeat in Triticum/Aegilops/Thinopyrum/D.…”

“…In Th . bessarabicum , we detected signals on two chromosome pairs (with one and two hybridization sites), while Lang et al (2019b) identified two and four chromosomes carrying a single Oligo-3A1 site each in Th . ponticum and Th .…”

“…We also identified a few chromosome-or group-specific repeats. Thus, CL241, which is homologous to Oligo-3A1 ( Lang et al, 2018 ; Lang et al, 2019b ) and Oligo-44 ( Tang et al, 2018 ; Supplementary Table S9 ), was mapped to the same wheat or Ae . tauschii chromosomal regions as was described in literature.…”

Chromosome Manipulation for Plant Breeding Purposes

“…Fluorescence in situ hybridisation has also been used to visualize the chromosomal localization of repetitive sequences that might contribute to chromosome identification. For example, the identification of a novel mini-satellite repeat (Ta-3A1) in wheat has allowed a phylogenetic analysis between wheat and some related species [6]. Non-denaturing in situ hybridisation (ND-FISH) was conducted using the Ta-3A1 sequence as a probe on chromosome preparations of wheat and in a long number of related wild and cultivated species, included in the tribe Triticeae dumort, as well as in other wheat-alien species amphiploids.…”

Development of new cytogenetic markers for Thinopyrum ponticum (Podp.) Z.-W. Liu & R.-C. Wang

“…Simultaneous localization of multiple tandem repeats gives a pattern unique for each chromosome of Th. ponticum , different from wheat. This makes it possible to use repeats both newly identified wheatgrass-specific and common for wheatgrass and wheat in the cytogenetic characteristics of interspecific hybrids, as well as for fundamental evolutionary-phylogenetic studies (Mo et al 2017, Komuro et al 2013, Zhu et al 2017; Lang et al 2019). The development of genome-wide sequencing technologies made it possible to develop cytogenetic markers based on bioinformatic analysis of DNA sequences.…”