Skip to main content

Efficient large-scale development of microsatellites for marker and mapping applications in Brassica crop species

Theoretical and Applied Genetics volume 108, pages 1103–1112 (2004)Cite this article

Abstract

A set of 398 simple sequence repeat markers (SSRs) have been developed and characterised for use with genetic studies of Brassica species. Small-insert (250–900 bp) genomic libraries from Brassica rapa, B. nigra, B. oleracea and B. napus, highly enriched for dinucleotide and trinucleotide SSR motifs, were constructed. Screening the clones with a mixture of oligonucleotide repeat probes revealed positive hybridisation to between 75% and 90% of the clones. Of these, 1,230 were sequenced. Primer pairs were designed for 398 SSR clones, and of these, 270 (67.8%) amplified a PCR product of the expected size in their focal and/or closely related species. A further screen of 138 primers pairs that produced a PCR product in B. napus germplasm found that 86 (62.3%) revealed length polymorphisms within at least one line of a test array representing the four Brassica species. The results of this screen were used to identify 56 SSRs and were combined with 41 SSRs that had previously shown polymorphism between the parents of a B. napus mapping population. These 97 SSR markers were mapped relative to a framework of RFLP markers and detected 136 loci over all 19 linkage groups of the oilseed rape genome.

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

Access options

Buy single article

Instant access to the full article PDF.

43,34 €

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

Fig. 1
Fig. 2

References

  • Axelsson T, Bowman CM, Sharpe AG, Lydiate DJ, Lagercrantz U (2000) Amphidiploid Brassica juncea contains conserved progenitor genomes. Genome 43:679–688

    CAS  PubMed  Google Scholar 

  • Bohuon EJR, Keith DJ, Parkin IAP, Sharpe AG, Lydiate DJ (1996) Alignment of the conserved C genomes of Brassica oleracea and Brassica napus. Theor Appl Genet 93:833–839

    CAS  Google Scholar 

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

    Article  CAS  PubMed  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 

  • Edwards KJ, Barker JHA, Daly A, Jones C, Karp A (1996) Microsatellite libraries enriched for several microsatellite sequences in plants. BioTechniques 20:759–760

    Google Scholar 

  • Goldstein DB, Schlötterer C (1999) Microsatellites: evolution and applications. Oxford University Press, Oxford

  • Howell EC, Barker GC, Jones GH, Kearsey MJ, King GJ, Kop EP, Ryder CD, Teakle GR, Vicente JG, Armstrong SJ (2002) Integration of the cytogenetic and genetic linkage maps of Brassica oleracea. Genetics 161:1225–1234

    Google Scholar 

  • Khlestkina EK, Pestsova EG, Salina E, Roder MS, Arbuzova VS, Koval SF, Borner A (2002) Genetic mapping and tagging of wheat genes using RAPD, STS and SSR markers. Cell Mol Biol Lett 7:795–802

    CAS  PubMed  Google Scholar 

  • Kowalski SP, Lan T-H, Feldmann KA, Paterson AH (1994) Comparative mapping of Arabidopsis thaliana and Brassica oleracea chromosomes reveals islands of conserved organization. Genetics 138:1–12

    PubMed  Google Scholar 

  • Lagercrantz U, Lydiate DJ (1995) RFLP mapping in Brassica nigra indicates differing recombination rates in male and female meioses. Genome 38:255–264

    CAS  Google Scholar 

  • Lagercrantz U, Lydiate DJ (1996) Comparative genome mapping in Brassica. Genetics 144:1903–1910

    CAS  PubMed  Google Scholar 

  • Lincoln SE, Daly MJ, Lander ES (1987) MAPMAKER v3.0. A computer programme. Whitehead Institute, Cambridge, Mass.

  • Lionneton E, Ravera S, Sanchez L, Aubert G, Delourme R, Ochatt S (2002) Development of an AFLP-based linkage map and localization of QTLs for seed fatty acid content in condiment mustard (Brassica juncea) Genome 45:1203–1215

  • Lombard V, Delourme R (2001) A consensus linkage map for rapeseed (Brassica napus L.): construction and integration of three individual maps from DH populations. Theor Appl Genet 103:491–507

    CAS  Google Scholar 

  • Lowe AJ, Jones AE, Raybould AF, Trick M, Moule CJ, 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 

  • Lydiate D, Sharpe A, Largercrantz U, Parkin I (1993) Mapping the Brassica genome. Outl Agric 22:85–92

    Google Scholar 

  • Parkin IAP, Sharpe AG, Keith DJ, Lydiate DJ (1995) Identification of the A and C genomes of amphidiploid Brassica napus (oilseed rape). Genome 38:1122–1131

    CAS  Google Scholar 

  • Plieske J, Struss D (2001) Microsatellite markers for genome analysis in Brassica. I. Development in Brassica napus and abundance in Brassicaceae species. Theor Appl Genet 102:689–694

    Article  Google Scholar 

  • Rae SJ, Aldam C, Dominguez I, Hoebrechts M, Barnes SR, Edwards KJ (2002) Development and incorporation of microsatellite markers into the linkage map of sugar beet (Beta vulgaris spp.) Theor Appl Genet 100:1240–1248

  • Saal B, Plieske J, Hu J, Quiros CF, Struss D (2001) Microsatellite markers for genome analysis in Brassica. II. Assignment of rapeseed microsatellites to the A and C genomes and genetic mapping in Brassica oleracea L. Theor Appl Genet 102:695–699

    CAS  Google Scholar 

  • Sambrook J, Fritsch EF, Maniatis T (1989) Molecular Cloning: a laboratory manual, 2nd edn. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY

    Google Scholar 

  • Sebastian RL, Howell EC, King GJ, Marshall DF, Kearsey MJ (2000) An integrated AFLP and RFLP Brassica oleracea linkage map from two morphologically distinct doubled-haploid mapping populations. Theor Appl Genet 100:75–81

    CAS  Google Scholar 

  • Sharopova N, McMullen MD, Schultz L, Schroeder S, Sanchez-Villeda H, Gardiner J, Bergstrom D, Houchins K, Melia-Hancock S, Musket T, Duru N, Polacco M, Edwards K, Ruff T, Register JC, Brouwer C, Thompson R, Velasco R, Chin E, Lee M, Woodman-Clikeman W, Long MJ, Liscum E, Cone K, Davis G, Coe EH (2002) Development and mapping of SSR markers for maize. Plant Mol Biol 48: 463–481

    Article  CAS  PubMed  Google Scholar 

  • Sharpe AG, Parkin IAP, Keith DJ, Lydiate DJ (1995) Frequent non-reciprocal translocations in the amphidiploid genome of oilseed rape (Brassica napus). Genome 38:1112–1121

    CAS  Google Scholar 

  • Soltis DE, Soltis PS (1995) The dynamic nature of polyploid genomes. Proc Natl Acad Sci USA 92:8089–8091

    CAS  PubMed  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 USA 92:7719–7723

    CAS  PubMed  Google Scholar 

  • Squirrell J, Hollingsworth PM, Woodhead M, Russell J, Lowe AJ, Gibby M, Powell W (2003) How much effort is required to isolate nuclear microsatellites from plants? Mol Ecol 12:1339–1348

    Article  CAS  PubMed  Google Scholar 

  • Suwabe K, Iketani H, Nunome T, Kage T, Hirai M (2002) Isolation and characterization of microsatellites in Brassica rapa L. Theor Appl Genet 104:1092–1098

    Article  Google Scholar 

  • SzewcMcFadden AKS, 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 

  • Tang S, Yu JK, Slabaugh MB, Shintani DK, Knapp SJ (2002) Simple sequence repeat map of the sunflower genome. Theor Appl Genet 105:1124–1136

    Google Scholar 

  • U N (1935) Genomic analysis of Brassica with special reference to the experimental formation of B. napus and its peculiar mode of fertilization. Jpn J Bot 7:389–452

    Google Scholar 

  • Warwick SI, Black LD, Aguinagalde I (1992) Molecular systematics of Brassica and allied genera (Subtribe Brassicinae, Brassiceae) - chloroplast DNA variation in the genus Diplotaxis. Theor Appl Genet 83:839–850

    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

    Article  CAS  Google Scholar 

  • Westman AL, Kresovich S (1999) Simple sequence repeat (SSR)-based marker variation in Brassica nigra genebank accessions and weed populations. Euphytica 109:85–92

    Article  CAS  Google Scholar 

  • Zane L, Bargelloni L, Patarnello T (2002) Statregies for microsatellite isolation: a review. Mol Ecol 11:1–16

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgements

We would like to thank staff at IACR Long Ashton and the John Innes Centre who provided support and help during laboratory work. This work was primarily funded by a grant (ref D08078) from the Biotechnology and Biological Sciences Research Council. Supporting finance was provided by IACR Long Ashton, John Innes Centre, BBSRC and the Natural Environment Research Council.

Author information

Author notes

  1. K. J. Edwards

    Present address: Functional Genomics Unit, School of Biological Sciences, University of Bristol, Bristol , BS8 1UG, UK

  2. C. Moule

    Present address: Cambridge Institute for Medical Research, Hills Rd, Cambridge , CB2 2XY, UK

  3. A. J. Lowe

    Present address: School of Life Sciences, University of Queensland, QLD 4072, Brisbane, Australia

Affiliations

  1. IACR Long Ashton Research Station, Long Ashton, Bristol, BS41 9AF, UK

    A. J. Lowe, C. Moule & K. J. Edwards

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

    M. Trick

Authors
  1. A. J. Lowe
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. C. Moule
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. M. Trick
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. K. J. Edwards
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to K. J. Edwards.

Additional information

Communicated by O. Savolainen

Electronic Supplementary Material

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Lowe, A.J., Moule, C., Trick, M. et al. Efficient large-scale development of microsatellites for marker and mapping applications in Brassica crop species. Theor Appl Genet 108, 1103–1112 (2004). https://doi.org/10.1007/s00122-003-1522-7

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00122-003-1522-7

Keywords

  • Linkage Group
  • Brassica Species
  • Double Haploid Population
  • Focal Species
  • Genome Species