Skip to main content
SpringerLink
Log in

Isolation of a new repetitive DNA sequence from Secale africanum enables targeting of Secale chromatin in wheat background

  • Published:
Euphytica Aims and scope Submit manuscript

Abstract

A genome specific DNA sequence that detects Secale africanum chromatin incorporated into wheat was developed in this study. Random amplified polymorphic DNA (RAPD) analysis was used to search for genome specific DNA sequences of S. africanum in lines, R111, “mianyang11” (MY11) and wheat-rye 1RS/1BL translocations R25 and R57. A high copy rye-specific DNA segment pSaD15940 of the S. africanum genome was obtained. The sequence of pSaD15 did not show any significant homology to other reported sequences in databases and it is therefore a new repetitive sequence of Secale. PCR primers were designed for pSaD15940, which amplify a clear 887 bp fragment in S. africanum but not in any wheat. The primers also amplified an 887 bp fragment in other accessions of rye, Chinese Spring-Imperial rye chromosome additions and a diverse range of material carrying different rye chromosomes or chromosomal segments. In situ hybridization showed that probe pSaD15940 was specifically hybridized throughout all rye chromosomes arms except for the terminal regions. The advantage of the rye-specific probe developed herein compared to those of previous reports is that it has been shown to be widely applicable to other Secale species. The probe will be useful as a molecular marker for the introgression of S. africanum and other rye chromosome segments into the wheat genome.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4

Similar content being viewed by others

References

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

    Article  PubMed  CAS  Google Scholar 

  • Alves E, Ballesteros I, Linacero R, Vazquez AM (2005) RYS1, a foldback transposon, is activated by tissue culture and shows preferential insertion points into the rye genome. Theor Appl Genet 111:431–436

    Article  PubMed  CAS  Google Scholar 

  • Appels R, Dennis ES, Smyth DR, Peacock WJ (1981) Two repeated DNA sequences from the heterochromatic region of rye (Secale cereal) chromosomes. Chromosoma 84:265–277

    Article  CAS  Google Scholar 

  • Appels R, Driscoll C, Peacock WJ (1978) Hetero-chromatin and highly repeated DNA sequences in rye (Secale cereal). Chromosoma 70:67–89

    Article  CAS  Google Scholar 

  • Aragon-Alcaide L, Miller T, Schwarzacher T, Reader S, Moore G (1996) A cereal centromere sequence. Chromosoma 105:261–268

    PubMed  CAS  Google Scholar 

  • Bedbrook JR, Jones J, O’Dell M, Thompson R, Flavell RB (1980a) A molecular description of telomeric heterochromatin in Secale species. Cell 19:540–560

    Article  Google Scholar 

  • Bedbrook JR, O’Dell M, Flavell RB (1980b) Amplification of rearranged sequences in cereal plant. Nature (London) 288:133–137

    Article  CAS  Google Scholar 

  • Brunell MS, Lukaszewski AJ, Whitkus R (1999) Development of arm specific RAPD markers for rye chromosome 2R in wheat. Crop Sci 39:1702–1706

    Article  CAS  Google Scholar 

  • Cheng ZJ, Murata M (2003) A centromeric tandem repeat family originating from a part of Ty3/gypsy-retroelement in wheat and its relatives. Genetics 164:665–672

    PubMed  CAS  Google Scholar 

  • Chikmawati T, Skovmand B, Gustafson JP (2005) Phylogenetic relationships among Secale species revealed by amplified fragment length polymorphisms. Genome 48:792–801

    PubMed  CAS  Google Scholar 

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

    Article  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

    Article  PubMed  CAS  Google Scholar 

  • Francis HA, Leitch AR, Koebner MDR (1995) Conversion of a RAPD-generated PCR product, containing a novel dispersed repetitive element, into a fast and robust assay for the presence of rye chromatin in wheat. Theor Appl Genet 90:636–642

    Article  Google Scholar 

  • Francki MG (2001) Identification of Bilby, a diverged centromeric Ty1-copia retrotransposon family from cereal rye (Secale cereale L.). Genome 44:266–274

    Article  PubMed  CAS  Google Scholar 

  • Graybosch RA (2001) Uneasy Unions: quality effects of rye chromatin transfer to wheat. J Cereal Sci 33:3–16

    Article  CAS  Google Scholar 

  • Gu YQ, Coleman-Derr D, Kong X, Anderson OD (2004) Rapid genome evolution revealed by comparative sequence analysis of orthologous regions from four Triticeae genomes. Plant Physiol 135:459–470

    Article  PubMed  CAS  Google Scholar 

  • Guidet F, Rogowsky P, Taylor C, Song W, Langridge P (1991) Cloning and characterization of a new rye-specific repeated sequence. Genome 34:81–87

    Google Scholar 

  • Heslop-Harrison JS (2000) Comparative genome organization in plants: from sequence and markers to chromatin and chromosomes. Plant Cell 12:617–636

    Article  PubMed  CAS  Google Scholar 

  • Iqbal MJ, Rayburn AL (1995) Identification of the 1RS rye chromosomal segment in wheat by RAPD analysis. Theor Appl Genet 91:1048–1053

    Article  CAS  Google Scholar 

  • Ito H, Nasuda S, Endo TR (2004) A direct repeat sequence associated with the centromeric retrotransposons in wheat. Genome 47:747–756

    Article  PubMed  CAS  Google Scholar 

  • Jiang HR, Dai DQ, Sun DF (1992) Creation of special germaplasm resources in Triticum. J Sichuan Agric Univ 10:255–259

    Google Scholar 

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

    Article  Google Scholar 

  • Jiang JM, Nasuda SH, Dong FG, Scherrer CW, Woo SS, Wing RA, Gill BS, Ward DC (1996) A conserved repetitive DNA element located in the centromeres of cereal chromosomes. Proc Natl Acad Sci USA 93:14210–14213

    Article  PubMed  CAS  Google Scholar 

  • Katto MC, Endo TR, Nasuda S (2004) A PCR-based marker for targeting small rye segments in wheat background. Genes Genet Syst 79:245–250

    Article  PubMed  CAS  Google Scholar 

  • Kiyotaka N, Hisashi T, Tetsuo S (1999) A novel repetitive sequence, termed the JNK repeat family, located on an extra heterochromatic region of chromosome 2R of Japanese rye. Chromosome Res 6:95–101

    Google Scholar 

  • Ko JM, Do GS, Suh DY, Seo BB, Shin DC, Moon HP (2002) Identification and chromosomal organization of two rye genome-specific RAPD products useful as introgression markers in wheat. Genome 45:157–164

    Article  PubMed  CAS  Google Scholar 

  • Koebner RMD (1995) Generation of PCR-based markers for the detection of rye chromatin in a wheat background. Theor Appl Genet 90:740–745

    Article  Google Scholar 

  • Lapitan NLV, Sears RG, Gill BS (1988) Amplification of repeated DNA sequences in wheat × rye hybrids regenerated from tissue culture. Theor Appl Genet 75:381–388

    Article  CAS  Google Scholar 

  • Lapitan NLV, Sears RG, Rayburn AL, Gill BS (1986) Wheat-rye translocations. J Hered 77:415–419

    Google Scholar 

  • Lee JH, Graybosch RA, Lee DJ (1994) Detection of rye chromosome 2R using the polymerase chain reaction and sequence-specific DNA primers. Genome 37:19–22

    Article  PubMed  CAS  Google Scholar 

  • Lelley T, Josifek KJ, Kaltsikes PJ (1978) Polymorphism in the Giemsa C-banding pattern of rye chromosomes. Can J Genet Cytol 20:307–312

    Google Scholar 

  • Li WL, Zhang P, Feller JP, Friebe B, Gill BS (2004) Sequence composition, organization and evolution of core Triticeae genome. Plant J 40:500–511

    Article  PubMed  CAS  Google Scholar 

  • Liu C, Li GR, Yang ZJ, Feng J, Zhou JP, Ren ZL (2006a) Specific DNA band isolation and SCAR marker construction of rye genome. Acta Bot Boreal-Occident Sin 26:2434–2438

    CAS  Google Scholar 

  • Liu C, Yang ZJ, Feng J, Zhou JP, Chi SH, Ren ZL (2006b) Development of Dasypyrum genome specific marker by using wheat microsatellites. Hereditas (Beijing) 28:1573–1579

    Article  CAS  Google Scholar 

  • Lukaszewski AJ, Gustafson JP (1987) Cytogenetics of Triticale. Plant Breed Rev 5:41–93

    Google Scholar 

  • Mao L, Zhai WX, Hu H, Zhu LH (1994) Cloning and characterization of a repetitive sequence in rye (Secale cereal). Plant Sci 100:51–57

    Article  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

    PubMed  CAS  Google Scholar 

  • Nagaki K, Tsujimoto H, Sasakuma T (1999) A novel repetitive sequence, termed the JNK repeat family, located on an extra heterochromatic region of chromosome 2R of Japanese rye. Chromosome Res 7:95–101

    Article  PubMed  CAS  Google Scholar 

  • Presting GG, Malysheva L, Fuchs J, Schubert I (1998) A TY3-GYPSY retrotransposon-like sequence localizes to the centromeric regions of cereal chromosomes. Plant J 16:721–728

    Article  PubMed  CAS  Google Scholar 

  • Rayburn AL, Gill BS (1985) Use of biltin-labeled probes to map specific DNA sequences on wheat chromosomes. J Hered 76:78–81

    Google Scholar 

  • Rogowsky PM, Manning S, Liu JY, Langridge P (1991) The R173 family of rye-specific repetitive DNA sequences: a structure analysis. Genome 34:88–95

    Google Scholar 

  • Rogowsky PM, Liu JY, Manning S, Taylor C, Langridge P (1992) Structural heterogeneity in the R173 family of rye-specific repetitive DNA sequences. Plant Mol Biol 20:95–102

    Article  PubMed  CAS  Google Scholar 

  • Saal B, Wricke G (1999) Development of simple sequence repeat markers in rye (Secale cereale L.). Genome 42:964–972

    Article  PubMed  CAS  Google Scholar 

  • Sharma HC, Gill BS (1983) Current status of wide hybridization in wheat. Euphytica 32:17–31

    Article  Google Scholar 

  • Singh RJ, Robbelen G (1977) Identification by Giemsa technique of the translocations separating cultivated rye from three wild species of Secale. Chromosoma (Berl) 59:217–225

    Article  Google Scholar 

  • Van Campenhout S, Volckaert G (1999) The fortuitous cloning of retroelement-like sequences from wheat and rye as by-products of a specific polymerase chain reaction. DNA Seq 10:173–178

    PubMed  Google Scholar 

  • Vershinin AV, Schwarzacher T, Heslop-Harrison JS (1995) The large-scale genomic organization of repetitive DNA family at the telomeres of rye chromosomes. Plant Cell 7:1823–1833

    Article  PubMed  CAS  Google Scholar 

  • Wan XQ, Yang ZJ, Feng J, Liu Y, Ren ZL (2005) Generation of a rye chromosomes specific PCR-based marker. Southwest China J Agric Sci 18(suppl):50–53

    Google Scholar 

  • Wang J, Wang XP, Ji J, Wang ZG, An TG, Li JM, Zhang ZQ (2006) Creation of novel wheat-rye 1BS/1RS translocation lines and characterization by molecular cytogenetics. Acta Agron Sin 32:30–33

    Google Scholar 

  • Yang ZJ, Ren ZL (2000) Genetic specification on rye chromatin transferred to wheat line 85-DH5304. J Sichuan Agric Univ 18:109–112

    Google Scholar 

  • Yang ZJ, Li GR, Ren ZL (2001a) Identification of a Triticum durum-Secale africanum amphiploid and its crossability with common wheat. J Genet Breed 5:45–50

    Google Scholar 

  • Yang ZJ, Li GR, Jiang HR, Ren ZL (2001b) Expression of nucleolus, endosperm storage proteins and disease resistance in an amphiploid between Aegilops tauschii and Secale silvestre. Euphytica 119:317–321

    Article  Google Scholar 

  • Yang ZJ, Li GR, Jiang HR, Ren ZL (2001c) Intergenomic interaction of Nucleolus, gliadin and disease resistance in a Triticum aestivum-Secale africanum amphiploid. J Sichuan Agric Univ 19:340–343

    Google Scholar 

  • Zhou JP, Yang ZJ, Feng J, Tang ZX, Ren ZL (2005) Isolation and identification of rye special DNA sequences. Southwest China J Agric Sci 18:598–602

    Google Scholar 

Download references

Acknowledgements

We are thankful to the National Natural Science Foundation of China (No. 30671288 and 30671136), Program for New Century Excellent Talents in University (NCET-06-0810) and the Science and Technology Committee of Sichuan Province, China for their financial support. We particular thank Dr I. Dundas (The University of Adelaide, Australia), Prof. B. Friebe (Kansas State University, USA), Dr. S.M. Reader (John Innes Center, Britain) and NPGS for kindly providing seeds. We are grateful to Dr I. Dundas for his helpful comments on the manuscript.

Author information

Authors and Affiliations

  1. School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 610054, Sichuan, P.R. China

    Cheng Liu, Zu-Jun Yang, Guang-Rong Li, Zi-Xian Zeng, Yong Zhang, Jian-Ping Zhou, Zhao-Hui Liu & Zheng-Long Ren

  2. Key Laboratory for Plant Genetics and Breeding, Sichuan Agricultural University, Ya’an city, 625014, Sichuan, P.R. China

    Zheng-Long Ren

  3. Industrial Crop Breeding and Cultivation Institute, Sichuan Academy of Agriculture Sciences, Jianyang, 641400, Sichuan, P.R. China

    Zhao-Hui Liu

Authors
  1. Cheng Liu
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Zu-Jun Yang
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Guang-Rong Li
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Zi-Xian Zeng
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Yong Zhang
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Jian-Ping Zhou
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Zhao-Hui Liu
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Zheng-Long Ren
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding authors

Correspondence to Cheng Liu, Zu-Jun Yang or Zheng-Long Ren.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Liu, C., Yang, ZJ., Li, GR. et al. Isolation of a new repetitive DNA sequence from Secale africanum enables targeting of Secale chromatin in wheat background. Euphytica 159, 249–258 (2008). https://doi.org/10.1007/s10681-007-9484-5

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10681-007-9484-5

Keywords

Search

Navigation