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Genomic reshuffling in advanced lines of hexaploid tritordeum

Genetic Resources and Crop Evolution volume 64, pages 1331–1353 (2017)Cite this article

Abstract

Genomic restructuring was detected in newly synthesized tritordeum by molecular and cytogenetic tools. Genomic stability is expected for advanced tritordeum lines (HchHchAABB; 2n = 42) with multiple generations of self-fertilization. This study intends to confirm or decline this hypothesis by characterizing three advanced tritordeum lines and their parental species using cytogenetics, inter-simple sequence repeat (ISSR) and retrotransposon-based markers. Mitotic chromosomes of each tritordeum line were hybridized with six synthetic oligonucleotide probes using non-denaturing fluorescence in situ hybridization. Polymorphic hybridization patterns and structural rearrangements involving SSR regions were detected. The same chromosome spreads were re-hybridized with genomic DNA of Hordeum chilense Roem. et Schult. and the 45S ribosomal DNA (rDNA) sequence pTa71. These FISH experiments allowed for parental genome discrimination, identification of nucleolar chromosomes, and detection of structural rearrangements, mostly involving rDNA loci. The chromosomes bearing SSR hybridization signals and/or chromosomes involved in structural rearrangements were identified. ISSR, retrotransposon-microsatellite amplified polymorphism, inter-retrotransposon amplified polymorphism and inter-primer binding site markers evidenced genomic reshuffling in all tritordeum lines relative to their parents. Line HT28 was considered the most genetically stable. This work demonstrated that cytogenetic and molecular monitoring of tritordeum is needed, even after several self-fertilization generations, to guarantee the selection of the most stable lines for improvement and sustainable agriculture.

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References

  • Ahirmar R, Verma RC (2015) Colchicine induced asynaptic chromosomal behaviour at meiosis in Allium cepa L. The Nucleus 58:47–51

    Article  Google Scholar 

  • Alkhimova AG, Heslop-Harrison JS, Shchapova AI, Vershinin AV (1999) Rye chromosome variability in wheat-rye addition and substitution lines. Chromosome Res 7:205–212

    CAS  PubMed  Article  Google Scholar 

  • Alkhimova OG, Mazurok NA, Potapova TA, Zakian SM, Heslop-Harrison JS et al. (2004) Diversity patterns of the tandem repeats organization in rye chromosomes. Chromosoma 113:42–52

    CAS  PubMed  Article  Google Scholar 

  • Alvarez JB, Ballesteros J, Sillero JA, Martin LM (1992) Tritordeum: a new crop of potential importance in the food industry. Hereditas 116:193–197

    Article  Google Scholar 

  • Atienza SG, Ballesteros J, Martín A, Hornero-Mendez D (2007) Genetic variability of carotenoid concentration and degree of esterification among tritordeum (×Tritordeum Ascherson et Graebner) and durum wheat accessions. J Agric Food Chem 55:4244–4251

    CAS  PubMed  Article  Google Scholar 

  • Badaeva ED, Dedkova OS, Gay G, Pukhalskyi VA, Zelenin AV, Bernard S, Bernard M (2007) Chromosomal rearrangements in wheat: their types and distribution. Genome 50:907–926

    CAS  PubMed  Article  Google Scholar 

  • Bálint AF, Kovács G, Sutka J (2000) Origin and taxonomy of wheat in the light of recent research. Acta Agron Hung 48:301–313

    Article  Google Scholar 

  • Ballesteros J, Ramirez MC, Martínez C, Atienza SG, Martín A (2005) Registration of HT621, a high carotenoid content tritordeum germplasm line. Crop Sci 45:2662–2663

    Article  Google Scholar 

  • Beckmann JS, Weber JL (1992) Survey of human and rat microsatellites. Genomics 12:627–631

    CAS  Article  Google Scholar 

  • Belay G, Merker A (1998) Cytogenetics analysis of a spontaneous 5B/6B translocation in tetraploid wheat landraces from Ethiopia, and implications for breeding. Plant Breed 117:537–542

    Article  Google Scholar 

  • Bento M, Pereira HS, Rocheta M, Gustafson P, Viegas W, Silva M (2008) Polyploidization as a retraction force in plant genome evolution: sequence rearrangements in Triticale. PLoS ONE 3:e1402. doi:10.1371/journal.pone.0001402

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  • Bento M, Gustafson P, Viegas W, Silva M (2010) Genome merger: from sequence rearrangements in triticale to their elimination in wheat-rye addition lines. Theor Appl Genet 121:489–497

    CAS  PubMed  Article  Google Scholar 

  • Boyko A, Filkowski J, Kovalchuk I (2005) Homologous recombination in plants is temperature and day-length dependent. Mutat Res 572:73–83

    CAS  PubMed  Article  Google Scholar 

  • Cabo S, Carvalho A, Martín A, Lima-Brito J (2014a) Structural rearrangements detected in newly-formed hexaploid tritordeum after three sequential FISH experiments with repetitive DNA sequences. J Genet 93:183–188

    PubMed  Article  Google Scholar 

  • Cabo S, Carvalho A, Rocha L, Martín A, Lima-Brito J (2014b) IRAP, REMAP and ISSR fingerprinting in newly formed hexaploid tritordeum (×Tritordeum Ascherson et Graebner) and respective parental species. Plant Mol Biol Rep 32:761–770

    CAS  Article  Google Scholar 

  • Cabo S, Ferreira L, Carvalho A, Martins-Lopes P, Martín A, Lima-Brito JE (2014c) Potential of Start Codon Targeted (SCoT) markers for DNA fingerprinting of newly synthesized tritordeums and their respective parents. J Appl Genet 55:307–312

    CAS  PubMed  Article  Google Scholar 

  • Cardle L, Ramsay L, Milbourne D, Macaulay M, Marshall D, Waugh R (2000) Computational and experimental characterization of physically clustered simple sequence repeats in plants. Genetics 156:847–853

    CAS  PubMed  PubMed Central  Google Scholar 

  • Carvalho AIF (2004) Emparelhamento meiótico e DNA fingerprint em anfiplóides e híbridos interespecíficos da tribo Triticeae. MCS dissertation, University of Tras-os-Montes and Alto Douro, Vila Real

  • Carvalho A, Matos M, Lima-Brito J, Guedes-Pinto H, Benito C (2005) DNA fingerprint of F1 interspecific hybrids from the Triticeae tribe using ISSRs. Euphytica 143:93–99

    CAS  Article  Google Scholar 

  • Carvalho A, Guedes-Pinto H, Heslop-Harrison JS, Lima-Brito J (2008) Wheat neocentromeres found in F1 triticale × tritordeum hybrids (AABBRHch) after 5-azacytidine treatment. Plant Mol Biol Rep 26:46–52

    CAS  Article  Google Scholar 

  • Carvalho A, Martín A, Heslop-Harrison JS, Guedes-Pinto H, Lima-Brito L (2009) Identification of the spontaneous 7BS/7RL intergenomic translocation in one F1 multigeneric hybrid from the Triticeae tribe. Plant Breed 128:105–108

    CAS  Article  Google Scholar 

  • Carvalho A, Guedes-Pinto H, Lima-Brito J (2013) Polymorphism of the simple sequence repeat (AAC)5 in the nucleolar chromosomes of Old Portuguese wheat cultivars. J Genet 92:583–586

    PubMed  Article  Google Scholar 

  • Charles M, Belcram H, Just J, Huneau C, Viollet A, Couloux A, Segurens B, Carter M, Huteau V, Coriton O, Appels R, Samain S, Chalhoub B (2008) Dynamics and differential proliferation of transposable elements during the evolution of the B and A genomes of wheat. Genetics 180:1071–1086

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  • Chauhan RS, Singh BM (1997) Resistance to Karnal bunt in Hordeum chilense and its amphiploids with Triticum species. Euphytica 96:327–330

    Article  Google Scholar 

  • Chen LZ, Chen JF (2007) Allopolyploid-induced sequence elimination. Genes Genom Genet 1:113–117

    CAS  Google Scholar 

  • Chen L, Lou Q, Zhuang Y, Chen J, Zhang X, Wolukau JN (2007) Cytological diploidization and rapid genome changes of the newly synthesized allotetraploids Cucumis × hytivus. Planta 225:603–614

    CAS  PubMed  Article  Google Scholar 

  • Comai L (2000) Genetic and epigenetic interactions in allopolyploid plants. Plant Mol Biol 43:387–399

    CAS  PubMed  Article  Google Scholar 

  • Comai L, Tyagi AP, Winter K, Holmes-Davis R, Reynolds SH, Stevens Y, Byers B (2000) Phenotypic instability and rapid gene silencing in newly formed Arabidopsis allotetraploids. Plant Cell 12:1551–1567

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  • Cuadrado A, Jouve N (2007) The non-random distribution of long clusters of all possible classes of trinucleotide repeats in barley chromosomes. Chromosome Res 15:711–770

    CAS  PubMed  Article  Google Scholar 

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

    PubMed  Article  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  Article  Google Scholar 

  • Cuadrado A, Schwarzacher T, Jouve N (2000) Identification of different chromatin classes in wheat using in situ hybridization with simple sequence repeat oligonucleotides. Theor Appl Genet 101:711–717

    CAS  Article  Google Scholar 

  • Cuadrado A, Cardoso M, Jouve N (2008a) Increasing the physical markers of wheat chromosomes using SSRs as FISH probes. Genome 51:809–815

    CAS  PubMed  Article  Google Scholar 

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

    CAS  PubMed  Article  Google Scholar 

  • Cuadrado A, Golczyk H, Jouve N (2009) A novel, simple and rapid nondenaturing FISH (ND-FISH) technique for the detection of plants telomeres—potential used and possible target structures detected. Chromosome Res 17:755–762

    CAS  PubMed  Article  Google Scholar 

  • Delgado A, Carvalho A, Martín AC, Martín A, Lima-Brito J (2016) Use of the synthetic Oligo-pTa535 and Oligo-pAs1 probes for identification of Hordeum chilense-origin chromosomes in hexaploid tritordeum. Genet Resour Crop Evol 63(6):945–951

    CAS  Article  Google Scholar 

  • Depeiges A, Goubely C, Lenoir A, Cocherel S, Picard G, Raynal M, Grellet F, Delseny M (1995) Identification of the most represented repeated motifs in Arabidopsis thaliana microsatellite loci. Theor Appl Genet 91:160–168

    CAS  PubMed  Article  Google Scholar 

  • Doyle JJ, Doyle JL (1987) A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem Bull 19:11–15

    Google Scholar 

  • Endo TR (1988) Induction of chromosomal structural changes by a chromosome of Aegilops cylindrical L. in common wheat. J Hered 79:366–370

    Article  Google Scholar 

  • Endo TR (1990) Gametocidal chromosomes and their induction of chromosome mutations in wheat. Jpn J Genet 65:135–152

    Article  Google Scholar 

  • Fedoroff N (2000) Transposons and genome evolution in plants. Proc Natl Acad Sci USA 97:7002–7007

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  • Feldman M (2001) The origin of cultivated wheat. In: Bonjean AP, Angus WJ (eds) The world wheat book. A history of wheat breeding. Lavoisier Tech & Doc, Paris, pp 3–56

    Google Scholar 

  • Feldman M, Levy AA (2005) Allopolyploidy: a shaping force in the evolution of wheat genomes. Cytogenet Genome Res 109:250–258

    CAS  PubMed  Article  Google Scholar 

  • Feldman M, Lupton FGH, Miller TE (1995) Wheats. In: Smartt J, Simmonds NW (eds) Evolution of crop plants. Longman Scientific and Technical, Harlow, pp 185–192

    Google Scholar 

  • Feldman M, Liu B, Segal G, Abbo S, Levy AA, Vega JM (1997) Rapid elimination of low-copy DNA sequences in polyploid wheat: a possible mechanism for differentiation of homoeologous chromosomes. Genetics 147:1381–1387

    CAS  PubMed  PubMed Central  Google Scholar 

  • Fu S, Yang M, Fei Y, Tan F, Ren Z, Yan B, Zhang H, Tang Z (2013) Alterations and abnormal mitosis of wheat chromosomes induced by wheat-rye monosomic addition lines. PLoS ONE 8(7):e70483. doi:10.1371/journal.pone.0070483

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  • Fu S, Chen L, Wang Y, Li M, Yang Z, Qiu L, Yan B, Ren Z, Tang Z (2015) Oligonucleotide probes for ND-FISH analysis to identify rye and wheat chromosomes. Sci Rep 5:10552

    PubMed  PubMed Central  Article  Google Scholar 

  • Gerlach WL, Bedbrook JR (1979) Cloning and characterization of ribosomal RNA genes from wheat and barley. Nucleic Acids Res 7:1869–1885

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  • Gernand D, Rutten T, Varshney A, Rubtsova M, Prodanovic S et al (2005) Uniparental chromosome elimination at mitosis and interphase in wheat and pearl millet crosses involves micronucleus formation, progressive heterochromatinization, and DNA fragmentation. Plant Cell 17:2431–2438

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  • Grandbastien M-A (1998) Activation of plant retrotransposons under stress conditions. Trends Plant Sci 3:181–187

    Article  Google Scholar 

  • Han FP, Fedak G, Ouellet T, Liu B (2003) Rapid genomic changes in interspecific and intergeneric hybrids and allopolyploids of Triticeae. Genome 46:716–723

    CAS  PubMed  Article  Google Scholar 

  • Hanson RE, Islam-Faridi MN, Crane CF, Zwick MS, Czeschin DG, Wendel JF, McKnight TD, Price HJ (2000) Ty1-copia-retrotransposon behaviour in a polyploid cotton. Chromosome Res 8:73–76

    CAS  PubMed  Article  Google Scholar 

  • Heslop-Harrison JS, Harrison GE, Leitch IJ (1992) Reprobing of DNA:DNA in situ hybridization preparations. Trends Genet 8:372–373

    CAS  PubMed  Article  Google Scholar 

  • Hua YW, Liu M, Li ZY (2006) Parental genome separation and elimination of cells and chromosomes revealed by AFLP and GISH analyses in a Brassica carinata × Orychophragmus violaceus cross. Ann Bot 97:993–998

    PubMed  PubMed Central  Article  Google Scholar 

  • Jiang J, Friebe B, Gill BS (1994) Chromosome painting of Amigo wheat. Theor Appl Genet 89:811–813

    CAS  PubMed  Google Scholar 

  • Joshi GP, Endo TR, Nasuda S (2013) PCR and sequence analysis of barley chromosome 2H subjected to the gametocidal action of chromosome 2C. Theor Appl Genet 126:2381–2390

    CAS  PubMed  Article  Google Scholar 

  • Kalendar R, Grob T, Regina M, Suoniemi A, Schulman A (1999) IRAP and REMAP: two retrotransposon-base DNA fingerprinting techniques. Theor Appl Genet 98:704–711

    CAS  Article  Google Scholar 

  • Kalendar R, Tanskanen J, Chang W, Antonius K, Sela H, Peleg O, Schulman AH (2008) Cassandra retrotransposons carry independently transcribed 5S RNA. Proc Natl Acad Sci USA 105:5833–5838

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  • Kalendar R, Antonius K, Smýkal P, Schulman AH (2010) iPBS: a universal method for DNA fingerprinting and retrotransposon isolation. Theor Appl Genet 121:1419–1430

    CAS  PubMed  Article  Google Scholar 

  • Katti MV, Ranjekar PK, Gupta VS (2001) Differential distribution of simple sequence repeats in eukaryotic genome sequences. Mol Biol Evol 18:1161–1167

    CAS  PubMed  Article  Google Scholar 

  • King IP, Laurie DA (1993) Chromosome damage in early embryo and endosperm development in crosses involving the preferentially transmitted 4S1chromosome of Aegilops sharonensis. Heredity 70:52–59

    Article  Google Scholar 

  • Koba T, Takumi S, Shimada T (1997) Isolation, identification and characterization of disomic and translocated barley chromosome addition lines of common wheat. Euphytica 96:289–296

    Article  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  Article  Google Scholar 

  • Kota RS, Dvorak J (1998) Genomic instability in wheat induced by chromosome 6BS of Triticum speltoides. Genetics 120:1085–1094

    Google Scholar 

  • Kovalchuk I, Kovalchuk O, Kalck V, Boyko V, Filkowski J, Heinlein M, Hohn B (2003) Pathogen-induced systemic plant signal triggers DNA rearrangements. Nature 423:760–762

    CAS  PubMed  Article  Google Scholar 

  • LaFave MC, Sekelsky J (2009) Mitotic recombination: why? when? how? where? PLoS Genet 5(3):e1000411. doi:10.1371/journal.pgen.1000411

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  • Lagercrantz U, Ellegren H, Andersson L (1993) The abundance of various polymorphic microsatellite motifs differs between plants and vertebrates. Nucleic Acids Res 21:1111–1115

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  • Lan T, Albert VA (2011) Dynamic distribution patterns of ribosomal DNA and chromosomal evolution in Paphiopedilum, a lady’s slipper orchid. BMC Plant Biol 11:126. http://www.biomedcentral.com/1471-2229/11/126. 12 Sept 2011

  • Lee PS, Greenwell PW, Dominska M, Gawel M, Hamilton M, Petes TD (2009) A fine-structure map of spontaneous mitotic crossovers in the yeast Saccharomyces cerevisiae. PLoS Genet 5(3):e1000410. doi:10.1371/journal.pgen.1000410

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  • Leitch IJ, Bennett MD (1997) Polyploidy in angiosperms. Trends Plant Sci 2:470–476

    Article  Google Scholar 

  • Lima-Brito J (1998) Estudos citogenéticos em híbridos multigenéricos de trigo, centeio e cevada. Ph.D. thesis, University of Tras-os-Montes and Alto Douro, Vila Real

  • Liu B, Segal G, Vega JM, Feldman M, Abbo S (1997) Isolation and characterization of chromosome-specific sequences from a chromosome arm genomic library of common wheat. Plant J 11:959–965

    CAS  Article  Google Scholar 

  • Liu B, Vega JM, Feldman M (1998a) Rapid genomic changes in newly synthesized amphiploids of Triticum and Aegilops. II. Changes in low-copy coding DNA sequences. Genome 41:535–542

    CAS  PubMed  Article  Google Scholar 

  • Liu B, Vega JM, Segal G, Abbo S, Rodova M, Feldman M (1998b) Rapid genomic changes in newly synthesized amphiploids of Triticum and Aegilops. I. Changes in low-copy noncoding DNA sequences. Genome 41:272–277

    CAS  Article  Google Scholar 

  • Lucht JM, Mauch-Mani B, Steiner HY, Metraux JP, Ryals J, Hohn B (2002) Pathogen stress increases somatic recombination frequency in Arabidopsis. Nat Genet 30:311–314

    PubMed  Article  Google Scholar 

  • Lukens LN, Pires JC, Leon E, Vogelzang R, Oslach L et al (2006) Patterns of sequence loss and cytosine methylation within a population of newly resynthesized Brassica napus allopolyploids. Plant Physiol 140:336–348

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  • Ma XF, Gustafson JP (2005) Genome evolution of allopolyploids: a process of cytological and genetic diploidization. Cytogenet Genome Res 109:236–249

    CAS  PubMed  Article  Google Scholar 

  • Ma XF, Gustafson JP (2006) Timing and rate of genome variation in triticale following allopolyploidization. Genome 49:950–958

    CAS  PubMed  Article  Google Scholar 

  • Madlung A, Tyagi A, Watson B, Jiang HM, Kagochi T et al. (2005) Genomic changes in synthetic Arabidopsis polyploids. Plant J 41:221–230

    CAS  PubMed  Article  Google Scholar 

  • Martín A (1988) Tritordeum: the first ten years. Rachis 7:2–15

    Google Scholar 

  • Martín A, Sánchez-Monge Laguna E (1982) Cytology and morphology of the amphiploid Hordeum chilense × Triticum turgidum conv. durum. Euphytica 31:261–267

    Article  Google Scholar 

  • Martín A, Martínez-Araque C, Rubiales D, Ballesteros J (1996) Tritordeum: triticale’s new brother cereal. In: Guedes-Pinto H, Darvey N, Carnide VP (eds) Triticale: today and tomorrow. Kluwer, London, pp 57–72

    Chapter  Google Scholar 

  • Martín A, Martín LM, Cabrera A, Ramirez MC, Giménez MJ, Rubiales D, Hernandez P, Ballesteros J (1998) The potential of Hordeum chilense in breeding Triticeae species. In: Jaradat AA (ed) Triticeae III. Science Publish, Washington, pp 377–386

    Google Scholar 

  • Martín A, Alvarez JB, Martín LM, Barro F, Ballesteros J (1999) The development of tritordeum: a novel cereal for food processing. J Cereal Sci 30:85–95

    Article  Google Scholar 

  • Martín AC, Atienza SG, Ramírez MC, Barro F, Martín A (2008) Male fertility restoration of wheat in Hordeum chilense cytoplasm is associated with 6HchS chromosome addition. Aust J Agric Res 59:206–213

    Article  Google Scholar 

  • McClintock B (1978) Mechanisms that rapidly reorganize the [maize] genome. Stadler Genet Sym 10:25–48

    Google Scholar 

  • Mellado-Ortega E, Atienza SG, Hornero-Méndez D (2015) Carotenoid evolution during postharvest storage of durum wheat (Triticum turgidum conv. durum) and tritordeum (×Tritordeum Ascherson et Graebner) grains. J Cereal Sci 62:134–142

    CAS  Article  Google Scholar 

  • Metzgar D, Bytof J, Wills C (2000) Selection against frameshift mutations limits microsatellite expansion in coding DNA. Genome Res 10:72–80

    CAS  PubMed  PubMed Central  Google Scholar 

  • Millán T, Martín A, de Haro A (1988) Field trial of tritordeum. Cereal Res Commun 16:31–38

    Google Scholar 

  • Molinier J, Oakeley EJ, Niederhauser O, Kovalchuk I, Hohn B (2005) Dynamic response of plant genome to ultraviolet radiation and other genotoxic stresses. Mutat Res 571:235–247

    CAS  PubMed  Article  Google Scholar 

  • Molinier J, Ries G, Zipfel C, Hohn B (2006) Transgeneration memory of stress in plants. Nature 442:1046–1049

    CAS  PubMed  Article  Google Scholar 

  • Molnár-Láng M, Linc G, Friebe BR, Sutka J (2000) Detection of wheat-barley translocations by genomic in situ hybridization in derivatives of hybrids multiplied in vitro. Euphytica 112:117–123

    Article  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  Article  Google Scholar 

  • Nasuda S, Friebe B, Gill BS (1998) Gametocidal Genes induce chromosome breakage in the interphase prior to the mitotic cell division of the male gametophyte in wheat. Genetics 149:1115–1124

    CAS  PubMed  PubMed Central  Google Scholar 

  • Ozkan H (2000) Genomic changes in newly synthesized amphiploids of Aegilops and Triticum. Ph.D. Thesis, University of Cukurova, Adana, Turkey

  • Ozkan H, Levy A, Feldman M (2001) Allopolyploidy-induced rapid genome evolution in the wheat (Aegilops-Triticum) group. Plant Cell 13:1735–1747

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  • Ozkan H, Tuna M, Arumuganathan K (2003) Nonadditive changes in genome size during allopolyploidization in the wheat (Aegilops-Triticum) group. J Heredity 94(3):260–264

    CAS  Article  Google Scholar 

  • Padilla JA, Martin A (1986) Aneuploidy in hexaploid tritordeum. Cereal Res Commun 14:341–346

    Google Scholar 

  • Pavia I, Carvalho A, Rocha L, Gaspar MJ, Lima-Brito J (2014) Physical location of SSR regions and cytogenetics instabilities in Pinus sylvestris chromosomes revealed by ND-FISH. J Genet 93:567–571

    PubMed  Article  Google Scholar 

  • Peterhans A, Schlüpmann H, Basse C, Paszkowski J (1990) Intrachromosomal recombination in plants. EMBO J 9:3437–3445

    CAS  PubMed  PubMed Central  Google Scholar 

  • Richter KS, Kleinow T, Jeske H (2014) Somatic homologous recombination in plants is promoted by a geminivirus in a tissue-selective manner. Virology 452–453:287–296

    PubMed  Article  CAS  Google Scholar 

  • Ries G, Heller W, Puchta H, Sandermann H, Seidlitz HK, Hohn B (2000) Elevated UV-B radiation reduces genome stability in plants. Nature 406:98–101

    CAS  PubMed  Article  Google Scholar 

  • Rosa M, von Harder M, Cigliano RA, Schlögelhofer P, Scheid OM (2013) The Arabidopsis SWR1 chromatin-remodeling complex is important for DNA repair, somatic recombination and meiosis. Plant Cell 25:1990–2001

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  • Rosato M, Moreno-Saiz JC, Galián JA, Rosseló JA (2015) Evolutionary site-number changes of ribosomal DNA loci during speciation: complex scenarios of ancestral and more recent polyploid events. AoB Plants 7:135. doi:10.1093/aobpla/plv135

    Article  CAS  Google Scholar 

  • Rubiales D, Ballesteros J, Martín A (1991) The reaction of ×Tritordeum and its Triticum spp. and Hordeum chilense parents to rust diseases. Euphytica 54:75–81

    Article  Google Scholar 

  • Sachs L (1952) Chromosome mosaics in experimental amphiploids in the Triticeae. Heredity 6:157–170

    Article  Google Scholar 

  • Salina EA, Ozkan H, Feldman M, Shumny VK (2000) Subtelomeric repeat reorganization in synthesized amphiploids of wheat. In: Proceedings of the international conference on biodiversity and dynamics of systems in north Eurasia, Novosibirsk, Russia, pp 102–105

  • Scheid OM, Jakovleva L, Afsar K, Maluszynska J, Paszkowski J (1996) A change in ploidy can modify epigenetic silencing. Proc Natl Acad Sci USA 93:7114–7119

    Article  Google Scholar 

  • Schmidt T, Boblenz K, Metzlaff M, Kaemmer D, Weising K, Kahl G (1993) DNA fingerprinting in sugar beet (Beta vulgaris)—identification of double-haploid breeding lines. Theor Appl Genet 85:653–657

    CAS  PubMed  Google Scholar 

  • Schwarzacher T, Heslop-Harrison JS (2000) Practical in situ hybridization. BIOS Scientific Publishers Limited, Oxford, UK, ISBN 185996138 X

  • Schwarzacher T, Leitch AR, Bennett MD, Heslop-Harrison JS (1989) In situ localization of parental genomes in a wild hybrid. Ann Bot 64:315–324

    Article  Google Scholar 

  • See DR (2007) Genomic targeting and mapping of a gametocidal gene in wheat. MCS dissertation, Kansas State University

  • Shaked H, Kashkush K, Ozkan H, Feldman M, Levy AA (2001) Sequence elimination and cytosine methylation are rapid and reproducible responses of the genome to wide hybridization and allopolyploidy in wheat. Plant J 13:1749–1759

    CAS  Google Scholar 

  • Singh M, Barman AS (2013) Chromosome breakages associated with 45S ribosomal DNA sequences in spotted snakehead fish Channa punctatus. Mol Biol Rep 40:723–729

    CAS  PubMed  Article  Google Scholar 

  • Song K, Lu P, Tang K, Osborn TC (1995) Rapid genome change in synthetic polyploids of Brassica and its implications for polyploid evolution. Trends Ecol Evol 9:348–352

    Google Scholar 

  • Subramanian S, Mishra RK, Singh L (2003) Genome-wide analysis of microsatellite repeats in humans: their abundance and density in specific genomic regions. Genome Biol 4:R13. doi:10.1186/gb-2003-4-2-r13

    PubMed  PubMed Central  Article  Google Scholar 

  • Tahmasebi S, Heidari B, Paknivat H, Dadkhodaie A (2015) Consequences of 1BL/1RS translocation on agronomic and physiological traits in wheat. Cereal Res Commun. doi:10.1556/0806.43.2015.016

    Google Scholar 

  • Tang ZX, Fu SL, Yan BJ, Zhang HQ, Ren ZL (2012) Unequal chromosome division and inter-genomic translocation occurred in somatic cells of wheat-rye allopolyploid. J Plant Res 125:283–290

    PubMed  Article  Google Scholar 

  • Tang Z, Li M, Chen L, Wang Y, Ren Z et al. (2014a) New types of wheat chromosomal structural variations in derivatives of wheat-rye hybrids. PLoS ONE 9(10):e110282. doi:10.1371/journal.pone.0110282

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  • Tang Z, Yang Z, Fu S (2014b) 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  Article  Google Scholar 

  • Tautz D, Schlötterer C (1994) Simple sequences. Curr Opin Genet Dev 4:832–837

    CAS  PubMed  Article  Google Scholar 

  • Teo CH, Tan SH, Ho CL, Faridah QZ, Othman YR, Heslop-Harrison JS, Kalendar R, Schulman AH (2005) Genome constitution and classification using retrotransposon-based markers in the orphan crop banana. J Plant Biol 48:96–105

    CAS  Article  Google Scholar 

  • Toth G, Gaspari Z, Jurka J (2000) Microsatellites in different eukaryotic genomes: survey and analysis. Genome Res 10:967–981

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  • Tsujimoto H, Noda K (1990) Mutation of five marker genes in wheat by gametocidal gene of Ae. speltoides, Gc1a. Wheat Inf Serv 71:6–9

    Google Scholar 

  • Tsujimoto H, Tsunewaki K (1983) Genetic analyses on a gametocidal gene originated from Aegilops aucheri. In: Proceedings of the 6th international wheat genetics symposium, Kyoto, Japan, pp 1077–1081

  • Tsujimoto H, Tsunewaki K (1984) Gametocidal genes in wheat and its relatives. I. Genetic analysis in common wheat of a gametocidal gene derived from Aegilops speltoides. Can J Genet Cytol 26:78–84

    Article  Google Scholar 

  • Tu YQ, Sun J, Ge XH, Li ZY (2009) Chromosome elimination, addition and introgression in intertribal partial hybrids between Brassica rapa and Isatis indigotica. Ann Bot 103:1039–1048

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  • Varshney RK, Thiel T, Stein N, Langridge P, Graner A (2002) In silico analysis of frequency and distribution of microsatellites in ESTs of some cereal species. Cell Mol Biol Lett 7:537–546

    CAS  PubMed  Google Scholar 

  • Villegas D, Casadesús J, Atienza SG, Martos V, Maalouf F, Karam F, Aranjuelo I, Nogués S (2010) Tritordeum, wheat and triticale yield components under multi-local mediterranean drough conditions. Field Crops Res 116:68–74

    Article  Google Scholar 

  • Wallace RB, Johnson MJ, Hirose T, Miyake T, Kawashima EH, Itakura K (1981) The use of synthetic oligonucleotides as hybridization probes. II. Hybridization of oligonucleotides of mixed sequence to rabbit β-globin DNA. Nucleic Acids Res 9:879–894

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  • Wegscheider E, Benjak A, Forneck A (2009) Clonal variation in Pinot noir revealed by S-SAP involving universal retrotransposon-based sequences. Am J Enol Vitic 60:104–109

    CAS  Google Scholar 

  • Wendel JF, Schnabel A, Seelanan T (1995) Bidirectional interlocus concerted evolution following allopolyploid speciation in cotton (Gossypium). Proc Natl Acad Sci USA 92:280–284

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  • Wessler SR (1996) Plant retrotransposons: turned on by stress. Curr Biol 6:959–961

    CAS  PubMed  Article  Google Scholar 

  • Zhao XP, Si Y, Hanson RE, Crane CF, Price HJ, Stelly DM, Wendel JF, Paterson NH (1998) Dispersed repetitive DNA has spread to new genomes since polyploid formation in cotton. Genome Res 8:479–492

    CAS  PubMed  Article  Google Scholar 

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Acknowledgments

This work was partially supported by the HY-WHEAT project—International Consortium (P-KBBE/AGRGPL/0002/2010), funded by the Portuguese Foundation for Science and Technology (“Fundação para a Ciência e a Tecnologia” [FCT]), the “Programa Operacional de Factores Competitividade” (COMPETE), “Quadro de Referência Estratégico Nacional 2007–2013” (QREN), and “Fundo Europeu de Desenvolvimento Regional” (FEDER) of the European Union, and also by the project AGL2013-43329-R funded by the “Ministerio de Economía y Competitividad” of Spain.

Authors’ contribution

The authors have made the following declarations regarding their contributions: Conceived and designed the experiments: JLB and AC. Performed the experiments: AD and AC. Analyzed the data: AD, AC, JLB. Contributed with plant material/reagents/analysis tools: ACM, AM, JLB. Contributed to the writing of the manuscript: all authors.

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    Authors and Affiliations

    1. University of Tras-os-Montes and Alto Douro, 5001-801, Vila Real, Portugal

      Andreia Delgado

    2. BioISI – Biosystems and Integrative Sciences Institute, Faculty of Sciences, University of Lisbon, C8 BDG Campo Grande, Lisbon, Portugal

      Ana Carvalho & José Lima-Brito

    3. CSIC – Consejo Superior de Investigaciones Científicas, Córdoba, Spain

      Azahara Carmen Martín & Antonio Martín

    4. John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK

      Azahara Carmen Martín

    5. Department of Genetics and Biotechnology, University of Tras-os-Montes and Alto Douro, 5001-801, Vila Real, Portugal

      José Lima-Brito

    Authors
    1. Andreia Delgado
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    2. Ana Carvalho
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    3. Azahara Carmen Martín
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    4. Antonio Martín
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    5. José Lima-Brito
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    Correspondence to José Lima-Brito.

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    Andreia Delgado and Ana Carvalho have contributed equally to this work.

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    Delgado, A., Carvalho, A., Martín, A.C. et al. Genomic reshuffling in advanced lines of hexaploid tritordeum. Genet Resour Crop Evol 64, 1331–1353 (2017). https://doi.org/10.1007/s10722-016-0439-3

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    Keywords

    • Allopolyploidy
    • Non-denaturing fluorescence in situ hybridization (ND-FISH)
    • Retrotransposon-based markers
    • Structural rearrangements
    • Tritordeum