Origin of wheat B-genome chromosomes inferred from RNA sequencing analysis of leaf transcripts from section Sitopsis species of Aegilops

Background: Following allopolyploidization, nascent polyploid wheat species react with massive genomic rearrangements, including deletion of transposable element-containing sequences. While such massive rearrangements are considered to be a prominent process in wheat genome evolution and speciation, their structure, extent, and underlying mechanisms remain poorly understood. Results: In this study, we retrieved ~3500 insertions of a specific variant of Fatima, one of the most dynamic gypsy long-terminal repeat retrotransposons in wheat from the recently available high-quality genome drafts of Triticum aestivum (bread wheat) and Triticum turgidum ssp. dicoccoides or wild emmer, the allotetraploid mother of all modern wheats. The dynamic nature of Fatima facilitated the identification of large (i.e., up to ~ 1 million bases) Fatima-containing insertions/deletions (indels) upon comparison of bread wheat and wild emmer genomes. We characterized 11 such indels using computer-assisted analysis followed by PCR validation, and found that they occurred via unequal intra-strand recombination or double-strand break (DSB) events. In most cases, indels breakpoints were located within transposable element sequences. Additionally, we observed one case of introgression of novel DNA fragments from an unknown source into the wheat genome. Conclusions: Our data thus indicate that massive large-scale DNA rearrangements might play a prominent role in wheat speciation.

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“…dicoccoides (genome AABB) [1][2][3][4]. The initial domestication of the wild emmer gave rise to the domesticated emmer wheat T. turgidum ssp.…”

Section: Introductionmentioning

confidence: 99%

Identification of large-scale genomic rearrangements during wheat evolution and the underlying mechanisms

Bariah

Keidar-Friedman

Kashkush

2019

Preprint

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“…speltoides and the B genome of durum and bread wheats is still being debated, even though Ae. speltoides is considered the most likely B donor [15,36]. SSRs, which are abundant components present in wheat, is an e cient tool to study genomic alterations in eukaryotes [6,17,18,20,22,30].…”

Section: Discussionmentioning

confidence: 99%

Genome Evolution During Bread Wheat Formation Unveiled by the Distribution Dynamics of SSR Sequences on Chromosomes using FISH

Zhang

Fan

Chen

et al. 2020

Preprint

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Background: During the bread wheat speciation by polyploidization, a series of genome rearrangement and sequence recombination occurred. Simple sequence repeat (SSR) sequences, predominately located in heterochromatic regions of chromosomes, are the effective marker for tracing the genomic DNA sequence variations. However, to date the distribution dynamics of SSRs on chromosomes of bread wheat and its donors, including diploid and tetraploid Triticum urartu, Aegilops speltoides, Ae. tauschii, T. turgidum ssp. dicocoides, reflecting the genome evolution events during bread wheat formation had not been comprehensively investigated.Results: The genome evolution was studied by comprehensively comparing the distribution patterns of (AAC)n, (AAG)n, (AGC)n and (AG)n in bread wheat Triticum aestivum var. Chinese Spring and its progenitors T. urartu, A. speltoides, Ae. tauschii, wild tetroploid emmer wheat T. dicocoides, and cultivated emmer wheat T. dicoccum. Results indicated that there are specific distribution patterns in different chromosomes from different species for each SSRs. They provided efficient visible markers for identification of some individual chromosomes and SSR sequence evolution tracing from the diploid progenitors to hexaploid wheat. During wheat speciation, the SSR sequence expansion occurred predominately in the centromeric and pericentromeric regions of B genome chromosomes accompanied by little expansion and elimination on other chromosomes. This feature might be an adaptation mechanism of the wheat genome to the “genome shock”.Conclusions: During the bread wheat evolution, SSRs including (AAC)n, (AAG)n, (AGC)n and (AG)n in B genome displayed the greatest changes (sequence expansion) especially in centromeric and pericentromeric regions during the polyploidization from Ae. speltoides S genome, the most likely donor of B genome. This work would enable a better understanding of the wheat genome formation and evolution and reinforce the viewpoint that B genome was originated from S genome.

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“…The RNA-seq reads of Ae. tauschii PI476874 and Ldn were respectively obtained from the DDBJ Sequence Read Archive accession numbers DRA000536 and DRA007097 [36,37]. The RNA-seq reads of Ldn were obtained using the MiSeq sequencer, whereas the RNA-seq data of PI476874 [36] was derived from the seedling leaf library using a Roche 454 sequencing platform (Roche Diagnostics, Mannheim, Germany).…”

Section: Rna-seq-based Genotypingmentioning

confidence: 99%

Introgression of chromosomal segments conferring early heading date from wheat diploid progenitor, Aegilops tauschii Coss., into Japanese elite wheat cultivars

et al. 2020

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The breeding of agriculturally useful genes from wild crop relatives must take into account recent and future climate change. In Japan, the development of early heading wheat cultivars without the use of any major gene controlling the heading date is desired to avoid overlap of the harvesting time before the rainy season. Here, we backcrossed two early heading lines of a synthetic hexaploid wheat, derived from a crossing between durum wheat and the wild wheat progenitor Aegilops tauschii, with four Japanese elite cultivars to develop early heading lines of bread wheat. In total, nine early heading lines that showed a heading date two to eight days earlier than their parental cultivars in field conditions were selected and established from the selfed progenies of the two-or three-times backcrossed populations. The whole appearance and spike shape of the selected early heading lines looked like their parental wheat cultivars. The mature grains of the selected lines had the parental cultivars' characteristics, although the grains exhibited longer and narrower shapes. RNA sequencingbased genotyping was performed to detect single nucleotide polymorphisms between the selected lines and their parental wheat cultivars, which revealed the chromosomal regions transmitted from the parental synthetic wheat to the selected lines. The introgression regions could shorten wheat heading date, and their chromosomal positions were dependent on the backcrossed wheat cultivars. Therefore, early heading synthetic hexaploid wheat is useful for fine-tuning of the heading date through introgression of Ae. tauschii chromosomal regions. OPEN ACCESS Citation: Takumi S, Mitta S, Komura S, Ikeda TM, Matsunaka H, Sato K, et al. (2020) Introgression of chromosomal segments conferring early heading date from wheat diploid progenitor, Aegilops tauschii Coss., into Japanese elite wheat cultivars. PLoS ONE 15(1): e0228397. https://doi.org/ 10.one of the most critical traits for environmental adaptation of higher plants to regional growth habitats. In Japan, harvesting common wheat before the rainy season is necessary to avoid severe damage of wheat grains such as pre-harvest sprouting and Fusarium head blight disease. Because Japanese wheat breeders must consider the climate characteristics peculiar to Japan, early heading and flowering time before the rainy season are among the most important traits in Japanese wheat breeding.Heading/flowering time is largely controlled by major loci, namely Vrn-1 and Ppd-1, in common wheat. The Vrn-1 loci determine vernalization requirement and are located on the long arms of homoeologous group 5 chromosomes [3], and encode an APETALA1/FRUIT-FUL-type MADS-box gene [4]. Structural mutations at the Vrn-1 loci, including insertions/ deletions in the promoter region and large deletions in the first intron, result in the generation of dominant spring-habit alleles [5,6]. Photoperiodic sensitivity is mainly determined by the Ppd-1 loci on the short arms of homoeologous group 2 chromosomes [7,8]. A dominant photoperiod-...

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Origin of wheat B-genome chromosomes inferred from RNA sequencing analysis of leaf transcripts from section Sitopsis species of Aegilops

Cited by 47 publications

References 66 publications

Identification of large-scale genomic rearrangements during wheat evolution and the underlying mechanisms

Identification of large-scale genomic rearrangements during wheat evolution and the underlying mechanisms

Genome Evolution During Bread Wheat Formation Unveiled by the Distribution Dynamics of SSR Sequences on Chromosomes using FISH

Introgression of chromosomal segments conferring early heading date from wheat diploid progenitor, Aegilops tauschii Coss., into Japanese elite wheat cultivars

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