Journal of Applied Genetics

, Volume 55, Issue 3, pp 313–318 | Cite as

Oligonucleotides replacing the roles of repetitive sequences pAs1, pSc119.2, pTa-535, pTa71, CCS1, and pAWRC.1 for FISH analysis

  • Zongxiang Tang
  • Zujun Yang
  • Shulan FuEmail author
Plant Genetics • Short Communication


Hybrids derived from wheat (Triticum aestivum L.) × rye (Secale cereale L.) have been widely studied because of their important roles in wheat cultivar improvement. Repetitive sequences pAs1, pSc119.2, pTa-535, pTa71, CCS1, and pAWRC.1 are usually used as probes in fluorescence in situ hybridization (FISH) analysis of wheat, rye, and hybrids derived from wheat × rye. Usually, some of these repetitive sequences for FISH analysis were needed to be amplified from a bacterial plasmid, extracted from bacterial cells, and labeled by nick translation. Therefore, the conventional procedure of probe preparation using these repetitive sequences is time-consuming and labor-intensive. In this study, some appropriate oligonucleotide probes have been developed which can replace the roles of repetitive sequences pAs1, pSc119.2, pTa-535, pTa71, CCS1, and pAWRC.1 in FISH analysis of wheat, rye, and hybrids derived from wheat × rye. These oligonucleotides can be synthesized easily and cheaply. Therefore, FISH analysis of wheat and hybrids derived from wheat × rye using these oligonucleotide probes becomes easier and more economical.


Chromosome identification FISH Oligonucleotide probe Rye Wheat 



This work was supported by a grant from the National High Technology Research and Development Program (“863” Program) of China (no. 2011AA100101).


  1. Alkhimova AG, Heslop-Harrison JS, Shchapova AI, Vershinin AV (1999) Rye chromosome variability in wheat–rye addition and substitution lines. Chromosome Res 7:205–212PubMedCrossRefGoogle Scholar
  2. Aragón-Alcaide L, Miller T, Schwarzacher T, Reader S, Moore G (1996) A cereal centromeric sequence. Chromosoma 105:261–268PubMedCrossRefGoogle Scholar
  3. Badaeva ED, Badaev NS, Bolsheva NL, Zelenin AV (1986) Chromosome alterations in the karyotype of triticale in comparison with the parental forms. 1. Heterochromatic regions of R genome chromosomes. Theor Appl Genet 72:518–523PubMedCrossRefGoogle Scholar
  4. Contento A, Heslop-Harrison JS, Schwarzacher T (2005) Diversity of a major repetitive DNA sequence in diploid and polyploid Triticeae. Cytogenet Genome Res 109:34–42PubMedCrossRefGoogle Scholar
  5. Cuadrado A, Jouve N (2002) Evolutionary trends of different repetitive DNA sequences during speciation in the genus Secale. J Hered 93:339–345PubMedCrossRefGoogle Scholar
  6. Cuadrado A, Schwarzacher T (1998) The chromosomal organization of simple sequence repeats in wheat and rye genomes. Chromosoma 107:587–594PubMedCrossRefGoogle Scholar
  7. Cuadrado A, 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 94:347–355CrossRefGoogle Scholar
  8. 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 121:597–611PubMedCrossRefGoogle Scholar
  9. Fradkin M, Ferrari MR, Espert SM, Ferreira V, Grassi E, Greizerstein EJ, Poggio L (2013) Differentiation of triticale cultivars through FISH karyotyping of their rye chromosomes. Genome 56:267–272PubMedCrossRefGoogle Scholar
  10. Francki MG (2001) Identification of Bilby, a diverged centromeric Ty1-copia retrotransposon family from cereal rye (Secale cereale L.). Genome 44:266–274PubMedCrossRefGoogle Scholar
  11. Francki MG, Berzonsky WA, Ohm HW, Anderson JM (2002) Physical location of a HSP70 gene homologue on the centromere of chromosome 1B of wheat (Triticum aestivum L.). Theor Appl Genet 104:184–191PubMedCrossRefGoogle Scholar
  12. Fu SL, Tang ZX, Ren ZL (2010) Inter- and intra-genomic transfer of small chromosomal segments in wheat–rye allopolyploids. J Plant Res 123:97–103PubMedCrossRefGoogle Scholar
  13. Fu SL, Sun CF, Yang MY, Fei YY, Tan FQ, Yan BJ, Ren ZL, Tang ZX (2013a) Genetic and epigenetic variations induced by wheat–rye 2R and 5R monosomic addition lines. PLoS One 8(1):e54057. doi: 10.1371/journal.pone.0054057 PubMedCentralPubMedCrossRefGoogle Scholar
  14. Fu SL, Yang MY, Fei YY, Tan FQ, Ren ZL, Yan BJ, Zhang HY, Tang ZX (2013b) Alterations and abnormal mitosis of wheat chromosomes induced by wheat–rye monosomic addition lines. PLoS One 8(7):e70483PubMedCentralPubMedCrossRefGoogle Scholar
  15. Fu SL, Lv ZL, Guo X, Zhang XQ, Han FP (2013c) Alteration of terminal heterochromatin and chromosome rearrangements in derivatives of wheat–rye hybrids. J Genet Genom 40:413–420CrossRefGoogle Scholar
  16. Han FP, Lamb JC, Birchler JA (2006) High frequency of centromere inactivation resulting in stable dicentric chromosomes of maize. Proc Natl Acad Sci U S A 103:3238–3243PubMedCentralPubMedCrossRefGoogle Scholar
  17. 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 193:347–357CrossRefGoogle Scholar
  18. Heckmann S, Macas J, Kumke K, Fuchs J, Schubert V, Ma L, Novák P, Neumann P, Taudien S, Platzer M, Houben A (2013) The holocentric species Luzula elegans shows interplay between centromere and large-scale genome organization. Plant J 73:555–565PubMedCrossRefGoogle Scholar
  19. Houben A, Kynast RG, Heim U, Hermann H, Jones RN, Forster JW (1996) Molecular cytogenetic characterisation of the terminal heterochromatic segment of the B-chromosome of rye (Secale cereale). Chromosoma 105:97–103PubMedCrossRefGoogle Scholar
  20. Ijdo JW, Wells RA, Baldini A, Reeders ST (1991) Improved telomere detection using a telomere repeat probe (TTAGGG)n generated by PCR. Nucleic Acids Res 19:4780PubMedCentralPubMedCrossRefGoogle Scholar
  21. Jones RN, Viegas W, Houben A (2008) A century of B chromosomes in plants: so what? Ann Bot 101:767–775PubMedCentralPubMedCrossRefGoogle Scholar
  22. Ko JM, Seo BB, Suh DY, Do GS, Park DS, Kwack YH (2002) Production of a new wheat line possessing the 1BL.1RS wheat–rye translocation derived from Korean rye cultivar Paldanghomil. Theor Appl Genet 104:171–176PubMedCrossRefGoogle Scholar
  23. 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 56:131–137PubMedCrossRefGoogle Scholar
  24. Kwiatek M, Wiśniewska H, Apolinarska B (2013) Cytogenetic analysis of Aegilops chromosomes, potentially usable in triticale (X Triticosecale Witt.) breeding. J Appl Genet 54:147–155PubMedCentralPubMedCrossRefGoogle Scholar
  25. Lukaszewski AJ (2008) Unexpected behavior of an inverted rye chromosome arm in wheat. Chromosoma 117:569–578PubMedCrossRefGoogle Scholar
  26. Ma XF, Fang P, Gustafson JP (2004) Polyploidization-induced genome variation in triticale. Genome 47:839–848PubMedCrossRefGoogle Scholar
  27. Manzanero S, Puertas MJ, Jiménez G, Vega JM (2000) Neocentric activity of rye 5RL chromosome in wheat. Chromosome Res 8:543–554PubMedCrossRefGoogle Scholar
  28. Manzanero S, Vega JM, Houben A, Puertas MJ (2002) Characterization of the constriction with neocentric activity of 5RL chromosome in wheat. Chromosoma 111:228–235PubMedCrossRefGoogle Scholar
  29. Molnár I, Cifuentes M, Schneider A, Benavente E, Molnár-Láng M (2011) Association between simple sequence repeat-rich chromosome regions and intergenomic translocation breakpoints in natural populations of allopolyploid wild wheats. Ann Bot 107:65–76PubMedCentralPubMedCrossRefGoogle Scholar
  30. Molnár-Láng M, Cseh A, Szakács É, Molnár I (2010) Development of a wheat genotype combining the recessive crossability alleles kr1kr1kr2kr2 and the 1BL.1RS translocation, for the rapid enrichment of 1RS with new allelic variation. Theor Appl Genet 120:1535–1545PubMedCrossRefGoogle Scholar
  31. Pedersen C, Langridge P (1997) Identification of the entire chromosome complement of bread wheat by two-colour FISH. Genome 40:589–593PubMedCrossRefGoogle Scholar
  32. Ren TH, Yang ZJ, Yan BJ, Zhang HQ, Fu SL, Ren ZL (2009) Development and characterization of a new 1BL.1RS translocation line with resistance to stripe rust and powdery mildew of wheat. Euphytica 169:207–213CrossRefGoogle Scholar
  33. 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 44:1122–1128PubMedCrossRefGoogle Scholar
  34. 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 122:396–400CrossRefGoogle Scholar
  35. Schwarzacher T (2003) DNA, chromosomes, and in situ hybridization. Genome 46:953–962PubMedCrossRefGoogle Scholar
  36. 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 116:825–834PubMedCrossRefGoogle Scholar
  37. Tang ZX, Fu SL, Ren ZL, Zhou JP, Yan BJ, Zhang HQ (2008) Variations of tandem repeat, regulatory element, and promoter regions revealed by wheat–rye amphiploids. Genome 51:399–408PubMedCrossRefGoogle Scholar
  38. Tang ZX, Fu SL, Ren ZL, Zhang HQ, Yang ZJ, Yan BJ (2009) Characterization of three wheat cultivars possessing new 1BL.1RS wheat–rye translocations. Plant Breed 128:524–527CrossRefGoogle Scholar
  39. Valenzuela NT, Perera E, Naranjo T (2013) Identifying crossover-rich regions and their effect on meiotic homologous interactions by partitioning chromosome arms of wheat and rye. Chromosome Res 21:433–445PubMedCrossRefGoogle Scholar

Copyright information

© Institute of Plant Genetics, Polish Academy of Sciences, Poznan 2014

Authors and Affiliations

  1. 1.State Key Laboratory of Plant Breeding and GeneticsSichuan Agricultural UniversityWenjiang, ChengduPeople’s Republic of China
  2. 2.School of Life Science and TechnologyUniversity of Electronic Science and Technology of ChinaChengduPeople’s Republic of China

Personalised recommendations