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FISH karyotype comparison between Ab- and A-genome chromosomes using oligonucleotide probes

  • Plant Genetics • Original Paper
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Abstract

Triticum boeoticum (2n = 2x = 14, AbAb) contains beneficial traits for common wheat improvement. The discrimination of Ab-genome chromosomes from A-genome chromosomes is an important step in gene transfer from T. boeoticum to common wheat. In this study, fluorescence in situ hybridization (FISH) analysis using nine oligonucleotide probes revealed high divergence between chromosomes of the common wheat germplasm Crocus and T. boeoticum accession G52. The combination of Oligo-pTa535-HM and Oligo-pSc119.2-HM can differentiate Ab and A chromosomes within homologous groups 2, 4, 5, and 6; chromosomes 2Ab and 6Ab can be identified by using (ACT)7, (CTT)7, and (GAA)7. The probes Oligo-pTa713 and (ACT)7 can be utilized for the identification of chromosomes 1Ab and 3Ab, respectively. Probes (CAG)7 and (CAC)7 can be applied in the identification of 7Ab. Moreover, probe combinations consisting of Oligo-pTa535-HM and (AAC)7 with (ACT)7 or (CTT)7 and of Oligo-pTa535-HM and Oligo-pTa713 with (CAC)7 or (CTT)7 will help discriminate the Ab-genome chromosomes of T. boeoticum. These probes are being used as potential markers to select common wheat Crocus-T. boeoticum G52 alien chromosome lines. Moreover, FISH patterns are highly divergent between Ab- and A-genome chromosomes, indicating that obvious chromosome structural variations arose during wheat evolution.

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References

  • Adonina IG, Goncharov NP, Badaeva ED, Sergeeva EM, Petrash NV, Salina EA (2015) (GAA)n microsatellite as an indicator of the a genome reorganization during wheat evolution and domestication. Comp Cytogenet 9:533–547

    PubMed  PubMed Central  Google Scholar 

  • Anker CC, Niks RE (2001) Prehaustorial resistance to wheat leaf rust in Triticum monococcum (s.s.). Euphytica 117:209–215

    Google Scholar 

  • Badaeva ED, Amosova AV, Goncharov NP, Macas J, Ruban AS, Grechishnikova IV, Zoshchuk SA, Houben A (2015) A set of cytogenetic markers allows the precise identification of all A-genome chromosomes in diploid and polyploid wheat. Cytogenet Genome Res 146:71–79

    PubMed  Google Scholar 

  • Badaeva ED, Ruban AS, Zoshchuk SA, Surzhikov SA, Knüpffer H, Kilian B (2016) Molecular cytogenetic characterization of Triticum timopheevii chromosomes provides new insight on genome evolution of T. zhukovskyi. Plant Syst Evol 302:943–956

    Google Scholar 

  • Beliveau BJ, Joyce EF, Apostolopoulos N, Yilmaz F, Fonseka CY, McCole RB, Changa YM, Lia JB, Senaratnea TN, Williamsa BR, Rouillard J, Wu C (2012) Versatile design and synthesis platform for visualizing genomes with Oligopaint FISH probes. Proc Natl Acad Sci U S A 109:21301–21306

    CAS  PubMed  PubMed Central  Google Scholar 

  • Carmona FE, Bustos AD, Jouve N, Cuadrado A (2013) Cytogenetic diversity of SSR motifs within and between Hordeum species carrying the H genome: H. vulgare L. and H. bulbosum L. Theor Appl Genet 126:949–961

    PubMed  Google Scholar 

  • Castagna R, Borghi B, Huen M, Salamini F (1995) Integrated approach to einkorn wheat breeding. In Hulled wheats. Promoting the conservation and use of underutilized and neglected crops 4. In: Proceedings Wrst Intl. workshop on Hulled wheat, Castelvecchio Pascoli, Tuscany, Italy. IPGRI, Rome, Italy, pp 21–22

  • Contento A, Hslop-Harrison JS, Schwarzacher T (2005) Diversity of a major repetitive DNA sequence in diploid and polyploid Triticeae. Cytogenet Genome Res 109:34–42

    CAS  PubMed  Google Scholar 

  • Cuadrado A, Jouve N (2002) Evolutionary trends of different repetitive DNA sequences during speciation in the genus Secale. J Hered 93:339–345

    CAS  PubMed  Google Scholar 

  • Cuadrado A, Schwarzacher T (1998) The chromosomal organization of simple sequence repeats in wheat and rye genomes. Chromosoma 107:587–594

    CAS  PubMed  Google Scholar 

  • Cuadrado A, Cardoso M, Jouve N (2008) Physical organisation of simple sequence repeats (SSRs) in Triticeae: structural, functional and evolutionary implications. Cytogenet Genome Res 120:210–219

    CAS  PubMed  Google Scholar 

  • Danilova TV, Friebe B, Gill BS (2012) Single-copy gene fluorescence in situ hybridization and genome analysis: Acc-2 loci mark evolutionary chromosomal rearrangements in wheat. Chromosoma 121:597–611

    CAS  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 

  • Dvorák J, McGuire PE, Cassidy B (1988) Apparent sources of the a genome of wheat inferred from polymorphism in abundance and restriction fragment length of repeated nucleotide sequences. Genome 30:680–689

    Google Scholar 

  • Flavell RB (1986) Repetitive DNA and chromosome evolution in plants. Philos Trans R Soc Lond Ser B Biol Sci 312:227–242

    CAS  Google Scholar 

  • Flavell RB, Bennett MD, Smith JB, Smith DB (1974) Genome size and the proportion of repeated nucleotide sequence DNA in plants. Biochem Genet 12:257–269

    CAS  PubMed  Google Scholar 

  • Fox SE, Geniza M, Hanumappa M, Naithani S, Sullivan C, Preece J, Tiwari VK, Elser J, Leonard JM, Sage A, Gresham C, Kerhornou A, Bolser D, McCarthy F, Kersey P, Lazo GR, Jaiswal P (2014) De novo transcriptome assembly and analyses of gene expression during photomorphogenesis in diploid wheat Triticum monococcum. PLoS One 9:e96855

    PubMed  PubMed Central  Google Scholar 

  • Fu SL, Chen L, Wang YY, Li M, Yang ZJ, Qiu L, Yan BJ, Ren ZL, Tang ZX (2015) Oligonucleotide probes for ND-FISH analysis to identify rye and wheat chromosomes. Sci Rep 5:10552

    PubMed  PubMed Central  Google Scholar 

  • Grewal S, Hubbart-Edwards S, Yang C, Scholefield D, Ashling S, Burridge A, Wilkinson PA, King IP, King J (2018) Detection of T. urartu introgressions in wheat and development of a panel of interspecific introgression lines. Front. Plant Sci 9:1565

    Google Scholar 

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

    PubMed  PubMed Central  Google Scholar 

  • Hao M, Luo JT, Zhang LQ, Yuan ZW, Yang YW, Wu M, Chen WJ, Zheng YL, Zhang HG, Liu DC (2013) Production of hexaploid triticale by a synthetic hexaploid wheat-rye hybrid method. Euphytica 193:347–357

    CAS  Google Scholar 

  • Harjit Singh, Grewal TS, Dhaliwal HS, Pannu PPS, Bagga PPS (1998) Sources of leaf rust and stripe rust resistance in wild relatives of wheat. Crop Improv 25:26–33

    Google Scholar 

  • He Q, Cai Z, Hu T, Liu H, Bao C, Mao W, Jin W (2015) Repetitive sequence analysis and karyotyping reveals centromere-associated DNA sequences in radish (Raphanus sativus L.). BMC Plant Biol 15:105

    CAS  PubMed  PubMed Central  Google Scholar 

  • Heslop-Harrison JS, Schmidt T (1998) Genomes, genes and junk: the large-scale organization of plant genomes. Trends Plant Sci 3:195–199

    Google Scholar 

  • Heun M, Schäfer-Pregl R, Klawan D, Castagna R, Accerbi M, Borghi B, Salamini F (1997) Site of einkorn wheat domestication identified by DNA fingerprinting. Science 278:1312–1314

    CAS  Google Scholar 

  • Hovhannisyan NA, Dulloo MH, Yesayan AH, Knüpffer H, Amri A (2011) Tracking of powdery mildew and leaf rust resistance genes in Triticum boeoticum and T. urartu, wild wheat relatives of common wheat. Czech J Genet Plant Breed 47:45–57

    Google Scholar 

  • Johnson BL, Dahliwal HS (1976) Reproductive isolation of Triticum boeoticum and Triticum urartu and the origin of the tetraploid wheats. Am J Bot 63:1088–1094

    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 

  • Kubaláková M, Kovářová P, Suchánková P, Číhalíková J, Bartoš J, Lucretti S, Watanabe N, Kianian SF, Doležel J (2005) Chromosome sorting in tetraploid wheat and its potential for genome analysis. Genetics 170:823–829

    PubMed  PubMed Central  Google Scholar 

  • Lebedeva TV, Peusha HO (2006) Genetic control of the wheat Triticum monococcum L. resistance to powdery mildew. Genetika 42:71–77

    CAS  PubMed  Google Scholar 

  • Li GR, Gao D, Zhang HG, Li JB, Wang HJ, La SX, Ma JW, Yang ZJ (2016) Molecular cytogenetic characterization of Dasypyrum breviaristatum chromosomes in wheat background revealing the genomic divergence between Dasypyrum species. Mol Cytogenet 9:6

    PubMed  PubMed Central  Google Scholar 

  • Li HY, Liu XJ, Zhang MH, Feng Z, Liu DC, Ayliffe M, Hao M, Ning SZ, Yuan ZW, Yan ZH, Chen XJ, Zhang LQ (2018) Development and identification of new synthetic T. turgidum–T. monococcum amphiploids. Plant Genet Resour C 16(6):555–563

    CAS  Google Scholar 

  • Ling HQ, Zhao S, Liu D, Wang J, Sun H, Zhang C, Fan H, Li D, Dong L, Tao Y, Gao C, Wu H, Lii Y, Cui Y, Guo X, Zheng S, Wang B, Yu K, Liang Q, Yang W, Lou X, Chen J, Feng M, Jian J, Zhang X, Luo G, Jiang Y, Liu J, Wang Z, Sha Y, Zhang B, Wu H, Tang D, Shen Q, Xue P, Zou S, Wang X, Liu X, Wang F, Yang Y, Zn X, Dong Z, Zhang K, Zhang X, Luo MC, Dvorak J, Tong Y, Wang J, Yang H, Li Z, Wang D, Zhang A, Wang J (2013) Draft genome of the wheat A-genome progenitor Triticum urartu. Nature 496:87–90

    CAS  PubMed  Google Scholar 

  • Ling HQ, Ma B, Shi X, Liu H, Dong L, Sun H, Cao Y, Gao Q, Zheng S, Li Y, Yu Y, Du H, Qi M, Li Y, Lu H, Yu H, Cui Y, Wang N, Chen C, Wu H, Zhao Y, Zhang J, Li Y, Zhou W, Zhang B, Hu W, van Eijk MJT, Tang J, Witsenboer HMA, Zhao S, Li Z, Zhang A, Wang D, Liang C (2018) Genome sequence of the progenitor of wheat a subgenome Triticum urartu. Nature 557:424–428

    CAS  PubMed  PubMed Central  Google Scholar 

  • Liu XJ, Zhang MH, Liu X, Li HY, Hao M, Ning SZ, Yuan ZW, Liu DC, Wu BH, Chen XJ, Chen WJ, Zhang LQ (2018) Molecular cytogenetic identification of newly synthetic Triticum kiharae with high resistance to stripe rust. Genet Resour Crop Evol 65(6):1725–1732

    CAS  Google Scholar 

  • McIntyre CL, Pereira S, Moran LB, Appels R (1990) New Secale cereale (rye) DNA derivatives for the detection of rye chromosome segments in wheat. Genome 33:635–640

    CAS  PubMed  Google Scholar 

  • Megyeri M, Farkas A, Varga M, Kovács G, Molnár-Láng M, Molnár I (2012) Karyotypic analysis of Triticum monococcum using standard repetitive DNA probes and simple sequence repeats. Acta Agron Hung 60:87–95

    CAS  Google Scholar 

  • Megyeri M, Mikó P, Farkas A, Molnár-Láng M, Molnár I (2017) Cytomolecular discrimination of the am chromosomes of Triticum monococcum and the A chromosomes of Triticum aestivum using microsatellite DNA repeats. J Appl Genet 58:67–70

    CAS  PubMed  Google Scholar 

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

    Google Scholar 

  • Michikawa A, Yoshida K, Okada M, Sato K, Takumi S (2019) Genome-wide polymorphisms from RNA sequencing assembly of leaf transcripts facilitate phylogenetic analysis and molecular marker development in wild einkorn wheat. Mol Gen Genomics 294:1327–1341

    CAS  Google Scholar 

  • Mikó P, Megyeri M, Farkas A, Molnár I, Molnár-Láng M (2015) Molecular cytogenetic identification and phenotypic description of a new synthetic amphiploid, Triticum timococcum (AtAtGGAmAm). Genet Res Crop Evol 62:55–66

    Google Scholar 

  • Mirzaghaderi G, Houben A, Badaeva E (2014) Molecular-cytogenetic analysis of Aegilops triuncialis and identification of its chromosomes in the background of wheat. Mol Cytogenet 7:91

    PubMed  PubMed Central  Google Scholar 

  • Molnár I, Linc G, Dulai S, Nagy ED, Molnár-Láng M (2007) Ability of chromosome 4H to compensate for 4D in response to drought stress in a newly developed and identified wheat-barley 4H(4D) disomic substitution line. Plant Breed 126:369–374

    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 

  • Pedersen C, Rasmussen SK, Linde-Laursen I (1996) Genome and chromosome identification in cultivated barley and related species of the Triticeae (Poaceae) by in situ hybridization with the GAA-satellite sequence. Genome 39:93–104

    CAS  PubMed  Google Scholar 

  • Rogers WJ, Miller TE, Payne PI, Seekings JA, Sayers EJ, Holt LM, Law CN (1997) Introduction to bread wheat (Triticum aestivum L.) and assessment for bread-making quality of alleles from T. boeoticum Boiss. Ssp. thaoudar at Glu-A1 encoding two high-molecular-weight subunits of glutenin. Euphytica 93:19–29

    CAS  Google Scholar 

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

    CAS  Google Scholar 

  • Sepsi A, Molnár I, Szalay D, Molnár-Láng M (2008) Characterization of a leaf rust resistant wheat–Thinopyrum ponticum partial amphiploid BE-1 using sequential multicolor GISH and FISH. Theor Appl Genet 116:825–834

    CAS  PubMed  Google Scholar 

  • Takumi S, Nasuda S, Liu YG, Tsunewaki K (1993) Wheat phylogeny determined by RFLP analysis of nuclear DNA. 1. Einkorn wheat. Jpn J Genet 68:73–79

    Google Scholar 

  • Tang ZX, Yang ZJ, Fu SL (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 

  • Tang SY, Qiu L, Xiao ZQ, Fu SL, Tang ZX (2016) New oligonucleotide probes for ND-FISH analysis to identify barley chromosomes and to investigate polymorphisms of wheat chromosomes. Genes 7:118

    PubMed Central  Google Scholar 

  • Tautz D (1989) Hypervariability of simple sequences as a general source for polymorphic markers. Nucleic Acids Res 17:6463–6471

    CAS  PubMed  PubMed Central  Google Scholar 

  • Vasu K, Harjit-Singh, Chhuneja P, Singh S, Dhaliwal HS (2000) Molecular tagging of Karnal bunt resistance genes of Triticum monococcum transferred to Triticum aestivum L. Crop Improv 27:33–42

    Google Scholar 

  • Xiao ZQ, Tang SY, Qiu L, Tang ZX, Fu SL (2017) Oligonucleotides and ND-FISH displaying different arrangements of tandem repeats and identification of Dasypyrum villosum chromosomes in wheat backgrounds. Molecules 22:973

    PubMed Central  Google Scholar 

  • Zhang RQ, Zhang MY, Wang XE, Chen PD (2014) Introduction of chromosome segment carrying the seed storage protein genes from chromosome 1V of Dasypyrum villosum showed positive effect on bread-making quality of common wheat. Theor Appl Genet 127:523–533

    CAS  Google Scholar 

  • Zhao LB, Ning SZ, Yu JJ, Hao M, Zhang LQ, Yuan ZW, Zheng YL, Liu DC (2016) Cytological identification of an Aegilops variabilis chromosome carrying stripe rust resistance in wheat. Breed Sci 66:522–529

    CAS  PubMed  PubMed Central  Google Scholar 

  • Zhao LB, Ning SZ, Yi YJ, Zhang LQ, Yuan ZW, Wang JR, Zheng YL, Hao M, Liu DC (2018) Fluorescence in situ hybridization karyotyping reveals the presence of two distinct genomes in the taxon Aegilops tauschii. BMC Genomics 19:3

    PubMed  PubMed Central  Google Scholar 

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Funding

This research was financially supported by the National Natural Science Foundation of China (31671682, 31671689).

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Authors and Affiliations

  1. State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China

    Dengcai Liu & Lianquan Zhang

  2. Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China

    Zhen Feng, Minghu Zhang, Xin Liu, Dongyu Liang, Xiaojuan Liu, Ming Hao, Dengcai Liu, Shunzong Ning, Zhongwei Yuan, Bo Jiang, Xuejiao Chen, Xue Chen & Lianquan Zhang

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  1. Zhen Feng
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  2. Minghu Zhang
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  3. Xin Liu
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Fig. S1

Photomicrographs showing the distribution of several probes on metaphase chromosomes of the T. boeoticum accession G52. a Oligo-pTa535-HM (green), b (CAG)7 (green), c (GAA)7 (green), d (AAC)7 (red), e (CTT)7 (red), f Oligo-pTa713 (red), g (CAC)7 (green), h (ACT)7 (red). (PNG 2118 kb)

Fig. S2

Photomicrographs showing the distribution of several probes on metaphase chromosomes of the common wheat germplasm Crocus. a Oligo-pTa535-HM (green), Oligo-pSc119.2-HM (red), b (CAG)7 (green), c (GAA)7 (green), d (AAC)7 (red), e (CTT)7 (red), f (ACT)7 (red), g Oligo-pTa713 (red), h (CAC)7 (green). (PNG 2468 kb)

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Feng, Z., Zhang, M., Liu, X. et al. FISH karyotype comparison between Ab- and A-genome chromosomes using oligonucleotide probes. J Appl Genetics 61, 313–322 (2020). https://doi.org/10.1007/s13353-020-00555-7

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