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Molecular Breeding

, 39:146 | Cite as

Cytological and molecular characterization of Thinopyrum bessarabicum chromosomes and structural rearrangements introgressed in wheat

  • Jianyong Chen
  • Yuqing Tang
  • Lesha Yao
  • Hao Wu
  • Xinyu Tu
  • Lifang Zhuang
  • Zengjun QiEmail author
Article
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Abstract

Thinopyrum bessarabicum is an important genetic resource for wheat improvement by chromosome engineering. However, the present low-resolution karyotype limits identification of its chromosomes. Oligonucleotide probes to identify tandem repeats provide an efficient way to produce high-resolution karyotypes in many species. In this study, putative tandem repeats were identified using unassembled sequence reads of Th. bessarabicum, and 306 repeat clusters were identified. Among them, 17 had conserved motifs that varied in size from 71 to 856 bp and occupied 0.01% to 1.30% of the genome. Thirty-nine oligonucleotides from 17 clusters were developed, and 21 from 8 clusters produced clear and stable signals in Th. bessarabicum chromosomes. Five tandem repeat clusters were distributed only at the telomeric or subtelomeric regions, and the BSCL242 probe produced signals only on chromosome 7JL. The other three were mainly in intercalary and centromeric regions with a few weak signals in telomeric regions. A new multiplex oligonucleotide probe (ONPM#7) containing 13 oligonucloetides distinguished all wheat and Th. bessarabicum chromosomes after one round of FISH. The high-resolution karyotype of Th. bessarabicum in corresponding with the seven homoeologous group chromosomes of wheat has been developed. Three spontaneous translocations and one isochromosome among Th. bessarabicum chromosomes introgressed into wheat thus have been characterized in combined with molecular marker analysis. The ONPM#7 probe and molecular markers provide powerful tools for engineering transfer of chromosomal segments from Th. bessarabicum to wheat.

Keywords

Fluorescence in situ hybridization Structural chromosome variation Chromosome engineering 

Notes

Acknowledgments

We thank R. McIntosh, University of Sydney, Australia, and Masahiro Kishii, CIMMYT, Mexico, for the English editing of the manuscript.

Author contributions

Project design: ZQ and JC; experimental work: JC, YT, LY, HW, and XT; data analysis: JC, YT, LY, and ZQ; manuscript preparation: JC, YT, LY, LZ, and ZQ. All authors reviewed and approved the manuscript.

Funding information

This project was funded by the Fundamental Research Funds for the Central Universities (Y0201700147). Bioinformatics analyses were supported by the Bioinformatics Center of Nanjing Agricultural University, China.

Compliance with ethical standards

Conflicts of interest

The authors declare that they have no conflicts of interest.

Supplementary material

11032_2019_1054_Fig6_ESM.png (6.9 mb)
Fig. S1

Physical mapping of tandem repeats BSCL5 (a-d), BSCL75 (e-h), BSCL156 (i-l), and BSCL158 (m-p) in Th. bessarabicum. Blue, chromosomes counterstained with DAPI; green, probes modified with FAM; red, probes modified with TAMRA. (PNG 7115 kb)

11032_2019_1054_MOESM1_ESM.tif (56.5 mb)
High resolution image (TIF 57876 kb)
11032_2019_1054_MOESM2_ESM.png (11 kb)
Fig. S2 Idiograms of the genomic organization of six tandem repeats in Th. bessarabicum chromosomes. (PNG 11 kb)
11032_2019_1054_Fig7_ESM.png (6.5 mb)
Fig. S3

Chromosomes of CS-Th. bessarabicum amphiploid after ONPM#7 FISH (a, c) and sequential GISH (b, d). (PNG 6650 kb)

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High resolution image (TIF 26657 kb)
11032_2019_1054_Fig8_ESM.png (1.3 mb)
Fig. S4

Chromosome painting with ONPM#7 and sequential GISH in CS-Th. bessarabicum disomic substitution line DS1J(1B). Arrows indicate chromosome 1J. Images order: chromosomes counterstained with DAPI (blue), chromosome painting with FAM modfied probes (green), chromosome painting with TAMRA modified probes (red), merged figures of blue, green and red, and sequential GISH (green) with Fluorescein-12-dUTP labeled genomic DNA of Th. bessarabicum as probe. (PNG 1356 kb)

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High resolution image (TIF 19305 kb)
11032_2019_1054_Fig9_ESM.png (1.5 mb)
Fig. S5

Chromosome painting in CS-Th. bessarabicum monosomic addition line MA2J with ONPM#7. Arrow indicates chromosome 2J. Images order is the same as Fig. S4. (PNG 1540 kb)

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High resolution image (TIF 20920 kb)
11032_2019_1054_Fig10_ESM.png (1.1 mb)
Fig. S6

Chromosome painting with ONPM#7 and sequential GISH in CS-Th. bessarabicum monosomic addition line MA3J. Arrow indicates chromosome 3J. Images order is the same as Fig. S4. (PNG 1145 kb)

11032_2019_1054_MOESM6_ESM.tif (15.3 mb)
High resolution image (TIF 15707 kb)
11032_2019_1054_Fig11_ESM.png (1.3 mb)
Fig. S7

Chromosome painting with ONPM#7 and sequential GISH in CS-Th. bessarabicum disomic substitution line DS5J(5A). Arrows indicate chromosomes 5J. Images order is the same as Fig. S4. (PNG 1321 kb)

11032_2019_1054_MOESM7_ESM.tif (18.6 mb)
High resolution image (TIF 19000 kb)
11032_2019_1054_Fig12_ESM.png (1.4 mb)
Fig. S8

Chromosome painting with ONPM#7 and sequential GISH in CS-Th. bessarabicum disomic substitution line DS6J(6A). Arrows indicate chromosomes 6J. Images order is the same as Fig. S4. (PNG 1470 kb)

11032_2019_1054_MOESM8_ESM.tif (19.5 mb)
High resolution image (TIF 20003 kb)
11032_2019_1054_Fig13_ESM.png (130 kb)
Fig. S9

Chromosome painting with ONPM#7 and sequential GISH in CS-Th. bessarabicum line M5B/MS5J(5A)/MS7J(7D). Arrow indicates chromosome 7J. Images order is the same as Fig. S4. (PNG 130 kb)

11032_2019_1054_MOESM9_ESM.tif (15 mb)
High resolution image (TIF 15380 kb)
11032_2019_1054_Fig14_ESM.png (3.7 mb)
Fig. S10

Chromosome painting in CS-Th. bessarabicum disomic addition line DA6JS·2JL with ONPM#7. Arrows indicate chromosomes 6JS·2JL. Images order is: chromosome painting (multi-color), and sequential GISH (green). (PNG 3834 kb)

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High resolution image (TIF 10073 kb)
11032_2019_1054_Fig15_ESM.png (3 mb)
Fig. S11

Chromosome painting in CS-Th. bessarabicum disomic addition line DA3JS·4JL with ONPM#7. Arrows indicate chromosomes 3JS·4JL. Images order is the same as Fig. S10. (PNG 3083 kb)

11032_2019_1054_MOESM11_ESM.tif (9.3 mb)
High resolution image (TIF 9483 kb)
11032_2019_1054_Fig16_ESM.png (3.6 mb)
Fig. S12

Chromosome painting in CS-Th. bessarabicum disomic addition line DA4JL·3JS with ONPM#7. Arrows indicate chromosomes 4JL·3JS. Images order is the same as Fig. S10. (PNG 3672 kb)

11032_2019_1054_MOESM12_ESM.tif (9.5 mb)
High resolution image (TIF 9702 kb)
11032_2019_1054_MOESM13_ESM.doc (39 kb)
ESM 1 (DOC 39 kb)
11032_2019_1054_MOESM14_ESM.xls (39 kb)
ESM 2 (XLS 39 kb)

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Copyright information

© Springer Nature B.V. 2019

Authors and Affiliations

  • Jianyong Chen
    • 1
  • Yuqing Tang
    • 1
  • Lesha Yao
    • 1
  • Hao Wu
    • 1
  • Xinyu Tu
    • 1
  • Lifang Zhuang
    • 1
  • Zengjun Qi
    • 1
    Email author
  1. 1.State Key Laboratory of Crop Genetics and Germplasm EnhancementNanjing Agricultural UniversityNanjingChina

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