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Research article
Zanmin Hu
Chinese Academy of Sciences
Corresponding Author
License:
This work is licensed under a CC BY 4.0 License. Read Full License
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 result indicated that the B genome might be more sensitive to the “genome shock” and more changeable during wheat polyplodization.
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.
Keywords
Bread wheat, Polyploidization, Simple sequence repeat, FISH
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This is a list of supplementary files associated with this preprint. Click to download.
- Additionalfile1.xlsx
Additional file 1. SSR sequence dynamics observed between wheat and its diploid progenitors.
- Additionalfile1.xlsx
Additional file 1. SSR sequence dynamics observed between wheat and its diploid progenitors.
- Additionalfile2.xlsx
Additional file 2. SSR sequence dynamics observed between wheat and its tetroploid progenitors.
- Additionalfile2.xlsx
Additional file 2. SSR sequence dynamics observed between wheat and its tetroploid progenitors.
- Additionalfile3.tif
Additional file 3. Physical mapping of (AAC)n on chromosomes of wheat and its diploid progenitors by using the web server B2DSC (http://mcgb.uestc.edu.cn/b2dsc) with default parameters for the blast and filter steps [27]. Yellow bars, the distribution of Oligo-CCS1 corresponding to the positions of centromeres of wheat. Blue-to-red bars, the number of HSPs per Mbp of SSR sequences (20 repeat units).
- Additionalfile3.tif
Additional file 3. Physical mapping of (AAC)n on chromosomes of wheat and its diploid progenitors by using the web server B2DSC (http://mcgb.uestc.edu.cn/b2dsc) with default parameters for the blast and filter steps [27]. Yellow bars, the distribution of Oligo-CCS1 corresponding to the positions of centromeres of wheat. Blue-to-red bars, the number of HSPs per Mbp of SSR sequences (20 repeat units).
- Additionalfile4.tif
Additional file 4. Physical mapping of (AAG)n on chromosomes of wheat and its diploid progenitors by B2DSC, using default parameters for the blast and filter steps. Yellow bars, the distribution of Oligo-CCS1 corresponding to the positions of centromeres of wheat. Blue-to-red bars, the number of HSPs per Mbp of SSR sequences (20 repeat units).
- Additionalfile4.tif
Additional file 4. Physical mapping of (AAG)n on chromosomes of wheat and its diploid progenitors by B2DSC, using default parameters for the blast and filter steps. Yellow bars, the distribution of Oligo-CCS1 corresponding to the positions of centromeres of wheat. Blue-to-red bars, the number of HSPs per Mbp of SSR sequences (20 repeat units).
- Additionalfile5.tif
Additional file 5. Physical mapping of (AGC)n on chromosomes of wheat and its diploid progenitors by B2DSC, using default parameters for the blast and filter steps. Yellow bars, the distribution of Oligo-CCS1 corresponding to the positions of centromeres of wheat. Blue-to-red bars, the number of HSPs per Mbp of SSR sequences (20 repeat units).
- Additionalfile5.tif
Additional file 5. Physical mapping of (AGC)n on chromosomes of wheat and its diploid progenitors by B2DSC, using default parameters for the blast and filter steps. Yellow bars, the distribution of Oligo-CCS1 corresponding to the positions of centromeres of wheat. Blue-to-red bars, the number of HSPs per Mbp of SSR sequences (20 repeat units).
- Additionalfile6.tif
Additional file 6. Physical mapping of (AG)n on chromosomes of wheat and its diploid progenitors by B2DSC, using default parameters for the blast and filter steps. Yellow bars, the distribution of Oligo-CCS1 corresponding to the positions of centromeres of wheat. Blue-to-red bars, the number of HSPs per Mbp of SSR sequences (20 repeat units).
- Additionalfile6.tif
Additional file 6. Physical mapping of (AG)n on chromosomes of wheat and its diploid progenitors by B2DSC, using default parameters for the blast and filter steps. Yellow bars, the distribution of Oligo-CCS1 corresponding to the positions of centromeres of wheat. Blue-to-red bars, the number of HSPs per Mbp of SSR sequences (20 repeat units).
- Additionalfile7.xlsx
Additional file 7. The accession list of wheat and its progenitor materials in this study.
- Additionalfile7.xlsx
Additional file 7. The accession list of wheat and its progenitor materials in this study.
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Received 16 Dec, 2020
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On 25 Nov, 2020
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Received 25 Nov, 2020
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On 17 Nov, 2020
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On 17 Nov, 2020
Editor invited
On 17 Nov, 2020
No comments provided
Editorial decision: Minor revision
On 29 Oct, 2020
Reviewer #4 agreed
On 21 Oct, 2020
Reviewer #3 agreed
On 20 Oct, 2020
Review #2 received
Received 06 Oct, 2020
Review #1 received
Received 06 Oct, 2020
Reviewer #2 agreed
On 15 Sep, 2020
Reviewer #1 agreed
On 08 Sep, 2020
Reviewers invited
Invitations sent on 07 Sep, 2020
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On 22 Aug, 2020
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Epigenetics & Genomics
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See the published version of this preprint at BMC Genomics.
This is a preprint, a preliminary version of a manuscript that has not completed peer review at a journal. Research Square does not conduct peer review prior to posting preprints. The posting of a preprint on this server should not be interpreted as an endorsement of its validity or suitability for dissemination as established information or for guiding clinical practice.
Learn more about In Review
Research article
Zanmin Hu
Chinese Academy of Sciences
Corresponding Author
Badges
Prescreen
This manuscript passed our Prescreen assessment
Complete author information
Appropriate declaration statements
Potential risks to human health
Prescreen
Peer Review Timeline
CURRENT STATUS: Published
View the published article at BMC Genomics.
No community comments so far
Submission checks complete
On 29 Dec, 2020
Editorial decision: Accept
On 28 Dec, 2020
Version (no preprint)
Posted 22 Dec, 2020
Editorial decision: Minor revision
On 22 Dec, 2020
Editor assigned
On 21 Dec, 2020
Submission checks complete
On 21 Dec, 2020
Editor invited
On 21 Dec, 2020
This version was not preprinted
Version 2
Posted 02 Dec, 2020
No comments provided
Editorial decision: Minor revision
On 18 Dec, 2020
Review #2 received
Received 16 Dec, 2020
Reviewer #2 agreed
On 25 Nov, 2020
Reviewers invited
Invitations sent on 25 Nov, 2020
Reviewer #1 agreed
On 25 Nov, 2020
Review #1 received
Received 25 Nov, 2020
Editor assigned
On 17 Nov, 2020
Submission checks complete
On 17 Nov, 2020
Editor invited
On 17 Nov, 2020
No comments provided
Editorial decision: Minor revision
On 29 Oct, 2020
Reviewer #4 agreed
On 21 Oct, 2020
Reviewer #3 agreed
On 20 Oct, 2020
Review #2 received
Received 06 Oct, 2020
Review #1 received
Received 06 Oct, 2020
Reviewer #2 agreed
On 15 Sep, 2020
Reviewer #1 agreed
On 08 Sep, 2020
Reviewers invited
Invitations sent on 07 Sep, 2020
Editor assigned
On 23 Aug, 2020
Submission checks complete
On 22 Aug, 2020
Editor invited
On 22 Aug, 2020
First submitted
On 20 Aug, 2020
Metrics
Comments: 0
PDF Downloads: ...
HTML Views: ...
Subject Areas
Epigenetics & Genomics
License:
This work is licensed under a CC BY 4.0 License. Read Full License
View the published article at BMC Genomics.
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 result indicated that the B genome might be more sensitive to the “genome shock” and more changeable during wheat polyplodization.
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.
Figure 1
Figure 1
Figure 2
Figure 2
Figure 3
Figure 3
Figure 4
Figure 4
Figure 5
Figure 5
Figure 6
Figure 6
Figure 7
Figure 7
This is a list of supplementary files associated with this preprint. Click to download.
- Additionalfile1.xlsx
Additional file 1. SSR sequence dynamics observed between wheat and its diploid progenitors.
- Additionalfile1.xlsx
Additional file 1. SSR sequence dynamics observed between wheat and its diploid progenitors.
- Additionalfile2.xlsx
Additional file 2. SSR sequence dynamics observed between wheat and its tetroploid progenitors.
- Additionalfile2.xlsx
Additional file 2. SSR sequence dynamics observed between wheat and its tetroploid progenitors.
- Additionalfile3.tif
Additional file 3. Physical mapping of (AAC)n on chromosomes of wheat and its diploid progenitors by using the web server B2DSC (http://mcgb.uestc.edu.cn/b2dsc) with default parameters for the blast and filter steps [27]. Yellow bars, the distribution of Oligo-CCS1 corresponding to the positions of centromeres of wheat. Blue-to-red bars, the number of HSPs per Mbp of SSR sequences (20 repeat units).
- Additionalfile3.tif
Additional file 3. Physical mapping of (AAC)n on chromosomes of wheat and its diploid progenitors by using the web server B2DSC (http://mcgb.uestc.edu.cn/b2dsc) with default parameters for the blast and filter steps [27]. Yellow bars, the distribution of Oligo-CCS1 corresponding to the positions of centromeres of wheat. Blue-to-red bars, the number of HSPs per Mbp of SSR sequences (20 repeat units).
- Additionalfile4.tif
Additional file 4. Physical mapping of (AAG)n on chromosomes of wheat and its diploid progenitors by B2DSC, using default parameters for the blast and filter steps. Yellow bars, the distribution of Oligo-CCS1 corresponding to the positions of centromeres of wheat. Blue-to-red bars, the number of HSPs per Mbp of SSR sequences (20 repeat units).
- Additionalfile4.tif
Additional file 4. Physical mapping of (AAG)n on chromosomes of wheat and its diploid progenitors by B2DSC, using default parameters for the blast and filter steps. Yellow bars, the distribution of Oligo-CCS1 corresponding to the positions of centromeres of wheat. Blue-to-red bars, the number of HSPs per Mbp of SSR sequences (20 repeat units).
- Additionalfile5.tif
Additional file 5. Physical mapping of (AGC)n on chromosomes of wheat and its diploid progenitors by B2DSC, using default parameters for the blast and filter steps. Yellow bars, the distribution of Oligo-CCS1 corresponding to the positions of centromeres of wheat. Blue-to-red bars, the number of HSPs per Mbp of SSR sequences (20 repeat units).
- Additionalfile5.tif
Additional file 5. Physical mapping of (AGC)n on chromosomes of wheat and its diploid progenitors by B2DSC, using default parameters for the blast and filter steps. Yellow bars, the distribution of Oligo-CCS1 corresponding to the positions of centromeres of wheat. Blue-to-red bars, the number of HSPs per Mbp of SSR sequences (20 repeat units).
- Additionalfile6.tif
Additional file 6. Physical mapping of (AG)n on chromosomes of wheat and its diploid progenitors by B2DSC, using default parameters for the blast and filter steps. Yellow bars, the distribution of Oligo-CCS1 corresponding to the positions of centromeres of wheat. Blue-to-red bars, the number of HSPs per Mbp of SSR sequences (20 repeat units).
- Additionalfile6.tif
Additional file 6. Physical mapping of (AG)n on chromosomes of wheat and its diploid progenitors by B2DSC, using default parameters for the blast and filter steps. Yellow bars, the distribution of Oligo-CCS1 corresponding to the positions of centromeres of wheat. Blue-to-red bars, the number of HSPs per Mbp of SSR sequences (20 repeat units).
- Additionalfile7.xlsx
Additional file 7. The accession list of wheat and its progenitor materials in this study.
- Additionalfile7.xlsx
Additional file 7. The accession list of wheat and its progenitor materials in this study.
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