Skip to main content

Plastid genome characterisation in Brassica and Brassicaceae using a new set of nine SSRs

Theoretical and Applied Genetics volume 113, pages 1221–1231 (2006)Cite this article

Abstract

We report a new set of nine primer pairs specifically developed for amplification of Brassica plastid SSR markers. The wide utility of these markers is demonstrated for haplotype identification and detection of polymorphism in B. napus, B. nigra, B. oleracea, B. rapa and in related genera Arabidopsis, Camelina, Raphanus and Sinapis. Eleven gene regions (ndhB-rps7 spacer, rbcL-accD spacer, rpl16 intron, rps16 intron, atpB-rbcL spacer, trnE-trnT spacer, trnL intron, trnL-trnF spacer, trnM-atpE spacer, trnR-rpoC2 spacer, ycf3-psaA spacer) were sequenced from a range of Brassica and related genera for SSR detection and primer design. Other sequences were obtained from GenBank/EMBL. Eight out of nine selected SSR loci showed polymorphism when amplified using the new primers and a combined analysis detected variation within and between Brassica species, with the number of alleles detected per locus ranging from 5 (loci MF-6, MF-1) to 11 (locus MF-7). The combined SSR data were used in a neighbour-joining analysis (SMM, D DM distances) to group the samples based on the presence and absence of alleles. The analysis was generally able to separate plastid types into taxon-specific groups. Multi-allelic haplotypes were plotted onto the neighbour joining tree. A total number of 28 haplotypes were detected and these differentiated 22 of the 41 accessions screened from all other accessions. None of these haplotypes was shared by more than one species and some were not characteristic of their predicted type. We interpret our results with respect to taxon differentiation, hybridisation and introgression patterns relating to the ‘Triangle of U’.

This is a preview of subscription content, access via your institution.

Access options

Buy single article

Instant access to the full article PDF.

USD 39.95

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

Fig. 1

References

  • Balloux F, Lugon-Moulin N (2002) The estimation of population differentiation with microsatellite markers. Mol Ecol 11:155–165

    PubMed  Article  Google Scholar 

  • Bornet B, Branchard M (2004) Use of ISSR fingerprints to detect microsatellites and genetic diversity in several related Brassica taxa and Arabidopsis thaliana. Hereditas 140:245–248

    PubMed  CAS  Article  Google Scholar 

  • Cavell AC, Lydiate DJ, Parkin IAP, Dean C, Trick M (1998) Colinearity between a 30-centimorgan segment of Arabidopsis thaliana chromosome 4 and duplicated regions within the Brassica napus genome. Genome 41:62–69

    PubMed  CAS  Article  Google Scholar 

  • Chung S-M, Staub JE (2003) The development and evaluation of consensus chloroplast primer pairs that possess highly variable sequence regions in a diverse array of plant taxa. Theor Appl Genet 107:757–767

    PubMed  CAS  Article  Google Scholar 

  • Chung S-M, Staub JE, Fazio G (2003) Inheritance of chilling injury: a maternally inherited trait in cucumber. J Am Soc Hort Sci 128:526–530

    CAS  Google Scholar 

  • Coyne S (2002) Transformation and marker gene removal strategies for the plastid genome of Brassica napus. PhD Thesis, Smurfit Institute of Genetics, University of Dublin, Trinity College, pp 172

  • Cronn R, Wendel JF (2003) Cryptic trysts, genomic mergers and plant speciation. New Phytol 161:133–142

    Article  Google Scholar 

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

    Google Scholar 

  • Doyle JJ, Morgante M, Tingey SV, Powell W (1998) Size homoplasy in chloroplast microsatellites of wild perennial relatives of soybean (Glycine subgenus Glycine). Mol Biol Evol 15:215–218

    PubMed  CAS  Google Scholar 

  • Erickson LR, Strauss NA, Beversdorf WB (1983) Restriction patterns reveal origins of chloroplast genomes in Brassica amphidiploids. Theor Appl Genet 65:201–206

    CAS  Article  Google Scholar 

  • Fay MF, Cowan RS (2001) Plastid microsatellites in Cypripedium calceolus (Orchidaceae): genetic fingerprints from herbarium specimens. Lindleyana 16:151–156

    Google Scholar 

  • Flannery ML (2004) Risk assessment of genetically modified crops in Ireland: investigations of pollen dispersal from oilseed rape (Brassica napus L.) using molecular and pollen trapping techniques. PhD Thesis, Department of Botany, University of Dublin, Trinity College

  • Goldstein DB, Linares AR, Cavalli-Sforza LL, Feldman MW (1995) Genetic absolute dating based on microsatellites and the origin of modern humans. Proc Natl Acad Sci USA 92:6723–6727

    PubMed  CAS  Article  Google Scholar 

  • Halldén C, Gertsson B, Säll T, Lind-Halldén C (1993) Characterization of organellar DNA in alloplasmic lines of Brassica napus L. Plant Breed 111:185–191

    Article  Google Scholar 

  • Hansen LB, Siegismund HR, Jorgensen RB (2003) Progressive introgression between Brassica napus (oilseed rape) and B. rapa. Heredity 91:276–283

    PubMed  CAS  Article  Google Scholar 

  • Harbourne ME, Douglas GC, Waldren S, Hodkinson TR (2005) Characterization and primer development for amplification of chloroplast microsatellite regions of Fraxinus excelsior. J Plant Res 118: 339–341

    PubMed  CAS  Article  Google Scholar 

  • Hodkinson TR, Chase MW, Takahashi C, Leitch IJ, Bennett MD, Renvoize SA (2002) The use of DNA sequencing (ITS and trnL-F), AFLP and fluorescent in situ hybridisation to study allopolyploid Miscanthus (Poaceae). Am J Bot 89:279–286

    CAS  Google Scholar 

  • Jordan W, Courtney MW, Neigel JE (1996) Low levels of interspecific genetic variation at a rapidly evolving chloroplast DNA locus in north American duckweeds (Lemnaceae). Am J Bot 83:430–439

    CAS  Article  Google Scholar 

  • Kresovich S, Szewc-McFadden AK, Bliek SM, McFerson JR (1995) Abundance and characterisation of simple-sequence repeats (SSRs) isolated from a size fractionated genomic library of Brassica napus L. (rapeseed). Theor Appl Genet 91:206–211

    CAS  Article  Google Scholar 

  • Lowe A J, Jones AE, Raybould AF, Trick M, Moule CL, Edwards KJ (2002) Transferability and genome specificity of a new set of microsatellite primers among Brassica species of the U triangle. Mol Ecol Notes 2:7–11

    CAS  Google Scholar 

  • Lowe AJ, Moule C, Trick M, Edwards KJ (2004) Efficient large-scale development of microsatellites for marker and mapping application in Brassica crop species. Theor Appl Genet 108:1103–1112

    PubMed  CAS  Article  Google Scholar 

  • Mabberley DJ (1993) The plant-book: a portable dictionary of the vascular plants. Cambridge University Press, London

    Google Scholar 

  • Martin W, Rujan T, Richly E, Hansen A, Cornelsen S, Lins T, Leister D, Stoebe B, Hasegawa M, Penny D (2002) Evolutionary analysis of Arabidopsis, cyanobacteria and chloroplast genomes reveals plastid phylogeny and thousands of cyanobacterial genes in the nucleus. Proc Natl Acad Sci USA 99:12246–12251

    PubMed  CAS  Article  Google Scholar 

  • Minch E, Ruiz-Linares A, Goldstein D, Feldman M, Cavalli-Sforza LL (1996) Microsat (version 1.5b): a computer program for calculating various statistics on microsatellite allele data

  • Negi MS, Devic M, Delseny M, Lakshmikumaran M (2000) Identification of AFLP fragments linked to seed coat colour in Brassica juncea and conversion to a SCAR marker for rapid selection. Theor Appl Genet 101:146–152

    CAS  Article  Google Scholar 

  • Nei M, Li WH (1979) Mathematical model for studying genetic variation in terms of restriction endonucleases. Proc Natl Acad Sci USA 76: 5269–5273

    PubMed  CAS  Article  Google Scholar 

  • Oxelman B, Liden M, Berglund D (1997) Chloroplast rps16 intron phylogeny of the tribe Sileneae (Caryophyllaceae). Plant Syst Evol 206:257–271

    Article  Google Scholar 

  • Palmer JD, Shields CR Cohen DB, Orton TJ (1983) Chloroplast DNA evolution and the origin of amphidiploid Brassica species. Theor Appl Genet 65:181–189

    CAS  Article  Google Scholar 

  • Panda S, Martín JP, Aguinagalde I (2003) Chloroplast and nuclear DNA studies in a few members of the Brassica oleracea L. group using PCR-RFLP and ISSR-PCR markers: a population genetic analysis. Theor Appl Genet 106:1122–1128

    PubMed  CAS  Google Scholar 

  • Powell W, Machray GC, Provan J (1996) Polymorphism revealed by simple sequence repeats. Trends Plant Sci 1:215–222

    Google Scholar 

  • Provan J (2000) Novel chloroplast microsatellites reveal cytoplasmic variation in Arabidopsis thaliana. Mol Ecol 9:2183–2185

    PubMed  CAS  Google Scholar 

  • Provan J, Powell W, Hollingsworth PM (2001) Chloroplast microsatellites: new tools for studies in plant ecology and evolution. Trends Ecol Evol 16:142–147

    PubMed  Article  Google Scholar 

  • Quiros CF, Truco MJ, Hu J (1995) Sequence comparison of two codominant RAPD markers in Brassica nigra: deletions, substitutions and microsatellites. Plant Cell Rep 15:268–270

    CAS  Article  Google Scholar 

  • Rieseberg LH, Soltis DE (1991) Phylogenetic consequences of cytoplasmic gene flow in plants. Evol Trend Plant 5:65–84

    Google Scholar 

  • Samuel R, Pinsker W, Kiehn M (1997) Phylogeny of some species of Cyrtandra (Gesneriaceae) inferred from the atpB-rbcL cpDNA intergene region. Bot Acta 110:503–510

    CAS  Google Scholar 

  • Sato S, Nakamura Y, Kaneko T, Asamizu E, Tabata S (1999) Complete structure of the chloroplast genome of Arabidopsis thaliana. DNA Res 6:283–290

    PubMed  CAS  Article  Google Scholar 

  • Schulte W, Töpfer R, Stracke R, Schell J, Martini N (1997) Multi-functional acetyl-CoA carboxylase from Brassica napus is encoded by a multi-gene family: indication for plastidic localisation of at least one isoform. Proc Natl Acad Sci USA 94:3465–3470

    PubMed  CAS  Article  Google Scholar 

  • Scott SE, Wilkinson MJ (1999) Low probability of chloroplast movement from oilseed rape (Brassica napus) into wild Brassica rapa. Nat Biotechnol 17:390–392

    PubMed  CAS  Article  Google Scholar 

  • Soltis DE, Soltis PS (1993) Molecular data and the dynamic nature of polyploidy. Cr Rev Plant Sci 12:243–273

    CAS  Google Scholar 

  • Soltis DE, Soltis PS (2000) Contributions of plant molecular systematics to studies of molecular evolution. Plant Mol Biol 42:45–75

    PubMed  CAS  Article  Google Scholar 

  • Song KM, Osborn TC, Williams PH (1988) Brassica taxonomy based on nuclear restriction fragment length polymorphisms (RFLPs) 1 Genome evolution of diploid and amphidiploid species. Theor Appl Genet 75:784–794

    CAS  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. Proc Natl Acad Sci 92:7719–7723

    PubMed  CAS  Article  Google Scholar 

  • Swofford DL (2000) PAUP4*: Phylogenetic analysis using parsimony (* and other methods), version 4.0b10. Sinauer Associates, Massachusetts

    Google Scholar 

  • Szewc-McFadden AK, Kresovich S, Bliek SM, Mitchell SE, McFerson JR (1996) Identification of polymorphic, conserved simple sequence repeats (SSRs) in cultivated Brassica species. Theor Appl Genet 93:534–538

    CAS  Google Scholar 

  • Taberlet P, Gielly L, Pautou G, Bouvet J (1991) Universal primers for amplification of three non-coding regions of chloroplast DNA. Plant Mol Biol 17:1105–1109

    PubMed  CAS  Article  Google Scholar 

  • The Arabidopsis Genome Initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408:796–815

    Article  Google Scholar 

  • Thiel T (2003) MISA—Microsatellite identification tool. http://www.pgrc.ipk-gatersleben.de/misa/

  • UN (1935) Genome analysis in Brassica with special reference to the experimental formation of B. napus and peculiar mode of fertilisation. Jpn J Bot 7:389–452

    Google Scholar 

  • UKCropNet (2003) Brassica Database. http://www.ukcrop.net/perl/ace/search/BrassicaDB

  • Warwick SI, Black LD (1991) Molecular systematics of Brassica and allied genera (subtribe Brassicinae, Brassiceae) -chloroplast genome and cytodeme congruence. Theor Appl Genet 82:81–92

    CAS  Article  Google Scholar 

  • Westman AL, Kresovich S (1998) The potential for cross-taxa simple-sequence repeat (SSR) amplification between Arabidopsis thaliana L. and crop Brassicas. Theor Appl Genet 96:272–281

    CAS  Article  Google Scholar 

  • Yang Y-W, Tseng P-F, Tai P-Y, Chang C-J (1998) Phylogenetic position of Raphanus in relation to Brassica species based on 5S rRNA spacer sequence data. Bot Bull Acad Sin 39:153–160

    CAS  Google Scholar 

  • Yang YW, Tai PY, Chen Y, Li WH (2002) A study of the phylogeny of Brassica rapa, B. nigra, Raphanus sativus, and their related genera using noncoding regions of chloroplast DNA. Mol Phylogenet Evol 23:268–275

    PubMed  CAS  Article  Google Scholar 

Download references

Acknowledgments

MLF was supported by a Teagasc PhD Walsh Fellowship. TAK and SC were supported by EU contract LSHG-CT-2003–503238 (PLASTOMICS).

Author information

Authors and Affiliations

  1. Department of Botany, School of Natural Sciences, Trinity College, University of Dublin, Dublin, D2, Ireland

    M. L. Flannery, F. J. G. Mitchell, N. Salamin, P. Dowding & T. R. Hodkinson

  2. Smurfit Institute of Genetics, Trinity College, University of Dublin, Dublin, D2, Ireland

    S. Coyne & T. A. Kavanagh

  3. Teagasc Crop Research Centre, Oak Park, Carlow, Ireland

    M. L. Flannery & J. I. Burke

  4. Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland

    N. Salamin

Authors
  1. M. L. Flannery
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. F. J. G. Mitchell
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. S. Coyne
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. T. A. Kavanagh
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. J. I. Burke
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. N. Salamin
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. P. Dowding
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. T. R. Hodkinson
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to T. R. Hodkinson.

Additional information

Communicated by H. C. Becker.

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Flannery, M.L., Mitchell, F.J.G., Coyne, S. et al. Plastid genome characterisation in Brassica and Brassicaceae using a new set of nine SSRs. Theor Appl Genet 113, 1221–1231 (2006). https://doi.org/10.1007/s00122-006-0377-0

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00122-006-0377-0

Keywords

  • Plastid Genome
  • Brassica Species
  • Mononucleotide Repeat
  • trnL Intron
  • Rps16 Intron