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

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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.

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References

  • Albert PS, Gao Z, Danilova TV, Birchler JA (2010) Diversity of chromosomal karyotypes in maize and its relatives. Cytogenet Genome Res 129:6–16

    CAS  PubMed  Google Scholar 

  • Benson G (1999) Tandem Repeats Finder: a program to analyze DNA sequences. Nuc Acids Res 27:573–580

    CAS  Google Scholar 

  • Cuadrado Á, Jouve N (2010) Chromosomal detection of simple sequence repeats (SSRs) using nondenaturing FISH (ND-FISH). Chromosoma 119:495–503

    PubMed  Google Scholar 

  • Cuadrado Á, Vitellozzi F, Jouve N, Ceoloni C (1997) Fluorescence in situ hybridization with multiple repeated DNA probes applied to the analysis of wheat–rye chromosome pairing. Theor Appl Genet 94:347–355

    CAS  Google Scholar 

  • Dawadundup (2009) Development and molecular characterization of wheat-Thinopyrum bessarabicum alien chromosome lines involving 4J and 5J. Master’s thesis, Nanjing Agricultural University, Nanjing. [In Chinese with English abstract.]

  • Doležel J, Číhalíková J, Lucretti S (1992) A high-yield procedure for isolation of metaphase chromosomes from root tips of Vicia faba L. Planta 188:93–98

    PubMed  Google Scholar 

  • Du P, Zhuang LF, Wang YZ, Yuan L, Wang Q, Wang DR, Dawadondup, Tan LJ, Shen J, Xu HB, Zhao H, Chu CG, Qi ZJ (2017) Development of oligonucleotides and multiplex probes for quick and accurate identification of wheat and Thinopyrum bessarabicum chromosomes. Genome 60:93–103

    CAS  PubMed  Google Scholar 

  • Du P, Li L, Liu H, Fu L, Qin L, Zhang Z, Dai X, Huang B, Dong W, Tang F, Zhuang L, Han Y, Qi Z, Zhang X (2018) High-resolution chromosome painting with repetitive and single-copy oligonucleotides in Arachis species identifies structural rearrangements and genome differentiation. BMC Plant Biol 18:240

    CAS  PubMed  PubMed Central  Google Scholar 

  • Gaál E, Valárik M, Molnár I, Farkas A, Linc G (2018) Identification of COS markers specific for Thinopyrum elongatum chromosomes preliminary revealed high level of macrosyntenic relationship between the wheat and Th. elongatum genomes. PLoS One 13:e0208840

    PubMed  PubMed Central  Google Scholar 

  • Gill B, Friebe B, Endo T (1991) Standard karyotype and nomenclature system for description of chromosome bands and structural aberrations in wheat (Triticum aestivum). Genome 34:830–839

    Google Scholar 

  • Grewal S, Yang C, Edwards SH, Scholefield D, Ashling S, Burridge AJ, Burridge AJ, King IP, King J (2018) Characterisation of Thinopyrum bessarabicum chromosomes through genome-wide introgressions into wheat. Theor Appl Genet 131:389–406

  • Han Y, Zhang T, Thammapichai P, Weng Y, Jiang J (2015) Chromosome-specific painting in Cucumis species using bulked oligonucleotides. Genetics 200:771–779

    PubMed  PubMed Central  Google Scholar 

  • Hassani HS, King IP, Reader SM, Caligari PDS, Miller TE (2010) Can Tritipyrum, a new salt tolerant potential amphiploid, be a successful cereal like Triticale? J Agr Sci Tech 2:177–195

    Google Scholar 

  • Heniko S, Ahmad K, Malik HS (2001) The centromere paradox: stable inheritance with rapidly evolving DNA. Science 293:1098–1102

    Google Scholar 

  • Hsiao C, Wang RRC, Dewey DR (1986) Karyotype analysis and genome relationships of 22 diploid species in the tribe Triticeae. Can J Genet Cytol 28:109–120

    Google Scholar 

  • Huang X, Zhu M, Zhuang L, Zhang S, Wang J, Chen X, Wang D, Chen J, Bao Y, Guo J, Zhang J, Feng Y, Chu C, Du P, Qi Z, Wang H, Chen P (2018) Structural chromosome rearrangements and polymorphisms identified in Chinese wheat cultivars by high-resolution multiplex oligonucleotide FISH. Theor Appl Genet 131:1967–1986

    CAS  PubMed  Google Scholar 

  • Jiang J, Gill B (2006) Current status and the future of fluorescence in situ hybridization (FISH) in plant genome research. Genome 49:1057–1068

    CAS  PubMed  Google Scholar 

  • Jiang J, Friebe B, Gill BS (1994) Recent advances in alien gene transfer in wheat. Euphytica 73:199–212

    Google Scholar 

  • Jurka J, Kapitonov VV, Kohany O, Jurka MV (2007) Repetitive sequences in complex genomes: structure and evolution. Annu Rev Genomics Hum Genet 8:241–259

    CAS  PubMed  Google Scholar 

  • Kato A (1999) Air drying method using nitrous oxide for chromosome counting in maize. Biotech Histochem 74:160–166

    CAS  PubMed  Google Scholar 

  • Kato A, Lamb J, Birchler J (2004) Chromosome painting using repetitive DNA sequences as probes for somatic chromosome identification in maize. Proc Natl Acad Sci USA 101:13554–13559

    CAS  PubMed  Google Scholar 

  • King IP, Orford SE, Cant KA, Reader SM, Miller TE (1996) An assessment of the salt tolerance of wheat/Thinopyrum bessarabicum 5Eb addition and substitution lines. Plant Breed 115:77–78

  • King IP, Forster BP, Law CC, Cant KA, Orford SE, Gorham J, Reader S, Miller TE (1997a) Introgression of salt-tolerance genes from Thinopyrum bessarabicum into wheat. New Phytol 137:75–81

    Google Scholar 

  • King IP, Law CN, Cant KA, Orford SE, Reader SM, Miller TE (1997b) Tritipyrum, a potential new salt-tolerant cereal. Plant Breeding 116:127–132

    Google Scholar 

  • Komuro S, Endo R, Shikata K, Kato A (2013) Genomic and chromosomal distribution patterns of various repeated DNA sequences in wheat revealed by a fluorescence in situ hybridization procedure. Genome 56:131–137

    CAS  PubMed  Google Scholar 

  • Lapitan N (1992) Organization and evolution of higher plant genomes. Genome 35:171–181

    CAS  Google Scholar 

  • Li C (2014) Development and application of molecular markers specific for Thinopyrum bessarabicum Löve based on RNA-seq. Master’s thesis, Nanjing Agricultural University, Nanjing. [In Chinese with English abstract.]

  • Li D, Li T, Wu Y, Zhang X, Zhu W, Wang Y, Zeng J, Xu L, Fan X, Sha L, Zhang H, Zhou Y, Kang H (2018) FISH-based markers enable identification of chromosomes derived from tetraploid Thinopyrum elongatum in hybrid lines. Front Plant Sci 9:526

    PubMed  PubMed Central  Google Scholar 

  • Liu Z (2015) Development and physical mapping of EST-SSR markers identified from transcriptome sequences of Thinopyrum bessarabicum. Master’s thesis, Nanjing Agricultural University, Nanjing. [In Chinese with English abstract.]

  • Mehrotra S, Goyal V (2014) Repetitive sequences in plant nuclear DNA: types, distribution, evolution and function. Genom Proteom Bioinf 12:164–171

    Google Scholar 

  • Mirzaghaderi G, Hassani H, Karimzadeh G (2010) C-banded karyotype of Thinopyrum bessarabicum and identification of its chromosomes in wheat background. Genet Resour Crop Evol 57:319–324

    Google Scholar 

  • Mukai Y, Nakahara Y, Yamamoto M (1993) Simultaneous discrimination of the three genomes in hexaploid wheat by multicolor fluorescence in situ hybridization using total genomic and highly repeated DNA probes. Genome 36:489–494

    CAS  PubMed  Google Scholar 

  • Novák P, Neumann P, Pech J, Steinhaisl J, Macas J (2013) RepeatExplorer: a Galaxy-based web server for genome-wide characterization of eukaryotic repetitive elements from next-generation sequence reads. Bioinformatics 29:792–793

    PubMed  Google Scholar 

  • Novák P, Ávila Robledillo L, Koblížková A, Vrbová I, Neumann P, Macas J (2017) TAREAN: a computational tool for identification and characterization of satellite DNA from unassembled short reads. Nuc Acids Res 45(12):e111

    Google Scholar 

  • Patokar C, Sepsi A, Schwarzacher T, Kishii M, Heslop-Harrison J (2016) Molecular cytogenetic characterization of novel wheat-Thinopyrum bessarabicum recombinant lines carrying intercalary translocations. Chromosoma 125:163–172

    CAS  PubMed  Google Scholar 

  • Pedersen C, Langridge P (1997) Identification of the entire chromosome complement of bread wheat by two-colour FISH. Genome 40:589–593

    CAS  PubMed  Google Scholar 

  • Pu J, Wang Q, Shen Y, Zhuang L, Li C, Tan M, Bie T, Chu C, Qi Z (2015) Physical mapping of chromosome 4J of Thinopyrum bessarabicum using gamma radiation-induced aberrations. Theor Appl Genet 128:1319–1328

    CAS  PubMed  Google Scholar 

  • Qi Z, Du P, Qian B, Zhuang L, Chen H, Chen T, Shen J, Guo J, Feng Y, Pei Z (2010) Characterization of a wheat-Thinopyrum bessarabicum (T2JS-2BS·2BL) translocation line. Theor Appl Genet 121:589–597

    CAS  PubMed  Google Scholar 

  • Qian B (2007) Chromosome structure of Thinopyrum bessarabicum Löve introduced into common wheat revealed by molecular markers. Master’s thesis, Nanjing Agricultural University, Nanjing. [In Chinese with English abstract.]

  • Ribeiro-Carvalho C, Guedes-Pinto H, Heslop-Harrison JS, Schwarzacher T (2001) Introgression of rye chromatin on chromosome 2D in the Portuguese wheat landrace ‘Barbela’. Genome 44:1122–1128

    CAS  PubMed  Google Scholar 

  • Rychlik W (2007) OLIGO 7 primer analysis software. Methods Mol Biol 402:35

    CAS  PubMed  Google Scholar 

  • Schneider A, Linc G, Molnár-Láng M, Graner A (2003) Fluorescence in situ hybridization polymorphism using two repetitive DNA clones in different cultivars of wheat. Plant Breed 122:396–400

    CAS  Google Scholar 

  • Shen J (2011) Development and molecular cytogenetic characterization of wheat-Thinopyrum bessarabicum alien chromosome lines. Master’s thesis, Nanjing Agricultural University, Nanjing. [In Chinese with English abstract.]

  • Shen Y, Shen J, Dawadondup, Zhuang L, Wang Y, Pu J, Feng Y, Chu C, Wang X, Qi Z (2013) Physical localization of a novel blue-grained gene derived from Thinopyrum bessarabicum. Mol Breeding 31:195–204

    CAS  Google Scholar 

  • Tan (2011) Development and identification of structural variations involving chromosome 1J and 5J of Th. bessarabicum Löve. Master thesis, Nanjing Agricultural University, Nanjing, China. [In Chinese with English abstract.]

  • Tang Z, Yang Z, Fu S (2014) Oligonucleotides replacing the roles of repetitive sequences pAs1, pSc119.2, pTa-535, pTa71, CCS1, and pAWRC.1 for FISH analysis. J Appl Genet 55:313–318

    CAS  PubMed  Google Scholar 

  • Wang RRC (1985) Genome analysis of Thinopyrum bessarabicum and Th. elongatum. Can J Genet Cytol 27:722–728

  • Wang Y (2013) Development and characterization of small segment translocations of Thinopyrum bessarabicum and cytological mapping of interest genes. Master’s thesis, Nanjing Agricultural University, Nanjing. [In Chinese with English abstract.]

  • Wang H, Dai K, Xiao J, Yuan C, Zhao R, Doležel J, Wang X (2017) Development of intron targeting (IT) markers specific for chromosome arm 4VS of Haynaldia villosa by chromosome sorting and next-generation sequencing. BMC Genomics 18:167

    PubMed  PubMed Central  Google Scholar 

  • William M, Mujeeb-Kazi A (1993) Thinopyrum bessarabicum: biochemical and cytological markers for the detection of genetic introgression in its hybrid derivatives with Triticum aestivum L. Theor Appl Genet 86:365–370

    CAS  PubMed  Google Scholar 

  • William M, Mujeeb-Kazi A (1995) Biochemical and molecular diagnostics of Thinopyrum bessarabicum chromosomes in Triticum aestivum germplasm. Theor Appl Genet 90:952–956

    CAS  PubMed  Google Scholar 

  • Yang J, Liu Z, Chen J, Wang Y, Zhuang L, Qi Z (2018) Accurate characterization of Wheat-Thinopyrum bessarabicum alien chromosome translocations using oligonucleotide multiplex painting combined with genomic in situ hybridization and molecular marker analysis. J Triticeae Crops 38:253–261. [In Chinese with English abstract.]

  • Zhang P, Li W, Fellers J, Friebe B, Gill BS (2004) BAC-FISH in wheat identifies chromosome landmarks consisting of different types of transposable elements. Chromosoma 112:288–299

    CAS  PubMed  Google Scholar 

  • Zhang X, Wei X, Xiao J, Yuan C, Wu Y, Cao A, Xing L, Chen P, Zhang S, Wang X, Wang H (2017) Whole genome development of intron targeting (IT) markers specific for Dasypyrum villosum chromosomes based on next-generation sequencing technology. Mol Breed 37:115

    CAS  Google Scholar 

  • Zhang S, Zhu M, Shang Y, Wang J, Dawadundup, Zhuang L, Zhang J, Chu C, Qi Z (2019) Physical organization of repetitive sequences and chromosome diversity of barley revealed by fluorescence in situ hybridization (FISH). Genome. https://doi.org/10.1139/gen-2018-0182

  • Zhu M, Du P, Zhuang L, Chu C, Zhao QZ (2017) A simple and efficient non-denaturing FISH method for maize chromosome differentiation using single-strand oligonucleotide probes. Genome 60:657–664

    CAS  PubMed  Google Scholar 

  • Zhuang L, Qi Z, Ying J, Chen P, Liu D (2003) Development and identification of a set of Triticum aestivum-Thinopyrum bessarabicum disomic alien addition lines. Acta Genetica Sin 30:919–925. [In Chinese with English abstract.]

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Acknowledgments

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

Funding

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.

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Authors and Affiliations

  1. State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China

    Jianyong Chen, Yuqing Tang, Lesha Yao, Hao Wu, Xinyu Tu, Lifang Zhuang & Zengjun Qi

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  1. Jianyong Chen
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  2. Yuqing Tang
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  3. Lesha Yao
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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.

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Correspondence to Zengjun Qi.

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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)

High resolution image (TIF 57876 kb)

Fig. S2

Idiograms of the genomic organization of six tandem repeats in Th. bessarabicum chromosomes. (PNG 11 kb)

Fig. S3

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

High resolution image (TIF 26657 kb)

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)

High resolution image (TIF 19305 kb)

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)

High resolution image (TIF 20920 kb)

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)

High resolution image (TIF 15707 kb)

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)

High resolution image (TIF 19000 kb)

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)

High resolution image (TIF 20003 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)

High resolution image (TIF 15380 kb)

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)

High resolution image (TIF 10073 kb)

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)

High resolution image (TIF 9483 kb)

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)

High resolution image (TIF 9702 kb)

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Chen, J., Tang, Y., Yao, L. et al. Cytological and molecular characterization of Thinopyrum bessarabicum chromosomes and structural rearrangements introgressed in wheat. Mol Breeding 39, 146 (2019). https://doi.org/10.1007/s11032-019-1054-8

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