Skip to main content
SpringerLink
Log in

Validation of in silico-predicted genic SNPs in white clover (Trifolium repens L.), an outbreeding allopolyploid species

  • Original Paper
  • Published:
Molecular Genetics and Genomics Aims and scope Submit manuscript

Abstract

White clover (Trifolium repens L.) is an obligate outbreeding allotetraploid forage legume. Gene-associated SNPs provide the optimum genetic system for improvement of such crop species. An EST resource obtained from multiple cDNA libraries constructed from numerous genotypes of a single cultivar has been used for in silico SNP discovery and validation. A total of 58 from 236 selected sequence clusters (24.5%) were fully validated as containing polymorphic SNPs by genotypic analysis across the parents and progeny of several two-way pseudo-testcross mapping families. The clusters include genes belonging to a broad range of predicted functional categories. Polymorphic SNP-containing ESTs have also been used for comparative genomic analysis by comparison with whole genome data from model legume species, as well as Arabidopsis thaliana. A total of 29 (50%) of the 58 clusters detected putative ortholoci with known chromosomal locations in Medicago truncatula, which is closely related to white clover within the Trifolieae tribe of the Fabaceae. This analysis provides access to translational data from model species. The efficiency of in silico SNP discovery in white clover is limited by paralogous and homoeologous gene duplication effects, which are resolved unambiguously by the transmission test. This approach will also be applicable to other agronomically important cross-pollinating allopolyploid plant species.

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

Similar content being viewed by others

References

  • Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 3:525–539

    Google Scholar 

  • Andersen JR, Lübberstedt T (2003) Functional markers in plants. Trends Plant Sci 8:554–560

    Article  PubMed  CAS  Google Scholar 

  • Attwood SS (1940) Genetics of cross-incompatibility among self-incompatible plants of Trifolium repens. J Am Soc Agron 32:955–968

    Google Scholar 

  • Barker G, Batley J, O’Sullivan H, Edwards KJ, Edwards D (2003) Redundancy based detection of sequence polymorphisms in expressed sequence tag data using autoSNP. Bioinformatics 19:421–422

    Article  PubMed  CAS  Google Scholar 

  • Barrett B, Griffiths A, Schreiber M, Ellison N, Mercer C, Bouton J, Ong B, Forster J, Sawbridge T, Spangenberg G, Bryan G, Woodfield D (2004) A microsatellite map of white clover (Trifolium repens L.). Theor Appl Genet 109:596–608

    PubMed  CAS  Google Scholar 

  • Barrett BA, Baird IJ, Woodfield DR (2005) A QTL analysis of white clover seed production. Crop Sci 5:1844–1850

    Article  CAS  Google Scholar 

  • Batley J, Barker G, O’Sullivan H, Edwards KJ, Edwards D (2003) Mining for single nucleotide polymorphisms and insertions/deletions in maize expressed sequence tag data. Plant Physiol 32:84–91

    Article  CAS  Google Scholar 

  • Brennan AC, Harris SA, Hiscock SJ (2006) The population genetics of sporophytic self-incompatibility in Senecio squalidus L. (Asteraceae): S allele diversity across the British range. Evolution 60:213–224

    Article  PubMed  CAS  Google Scholar 

  • Buetow KH, Edmonson MN, Cassidy AB (1999) Reliable identification of large numbers of candidate SNPs from public EST data. Nat Genet 21:323–325

    Article  PubMed  CAS  Google Scholar 

  • Burke J, Davison D, Hide W (1999) d2-cluster: a validated method for clustering EST and full-length cDNA sequences. Genome Res 9:1135–1142

    Article  PubMed  CAS  Google Scholar 

  • Caradus JR, Woodfield DR (1997) World checklist of white clover varieties II. NZ J Agric Res 40:115–206

    Google Scholar 

  • Chapman R, Erwin TA, Jewell EG, Love CG, Lim GAC, Li X, Mongin M, Spangenberg G, Edwards D (2006) An integrative bioinformatics system for DNA sequence, gene expression, molecular genetic marker, trait and population data. Plant and animal genome XIV, San Diego, p 851

    Google Scholar 

  • Cogan NOI, Abberton MT, Smith KF, Kearney G, Marshall AH, Williams A, Michaelson-Yeates TPT, Bowen C, Jones ES, Vecchies AC, Forster JW (2006a) Individual and multi-environment combined analyses identify QTLs for morphogenetic and reproductive development traits in white clover (Trifolium repens L.). Theor Appl Genet 112:1401–1415

    Article  CAS  Google Scholar 

  • Cogan NOI, Ponting RC, Vecchies AC, Drayton MC, George J, Dobrowolski MP, Sawbridge TI, Spangenberg GC, Smith KF, Forster JW (2006b) Gene-associated single nucleotide polymorphism (SNP) discovery in perennial ryegrass (Lolium perenne L.). Mol Genet Genomics 276:101–112

    Article  CAS  Google Scholar 

  • Coles ND, Coleman CE, Christensen SA, Jellen EN, Stevens MR, Bonifacio A, Rojas-Beltran JA, Fairbanks DJ, Maughan PJ (2005) Development and use of an expressed sequenced tag library in quinoa (Chenopodium quinoa Willd.) for the discovery of single nucleotide polymorphisms. Plant Sci 168:439–447

    Article  CAS  Google Scholar 

  • Doyle JJ, Luckow MA (2003) The rest of the iceberg. Legume diversity and evolution in a phylogenetic context. Plant Physiol 131:900–910

    Article  PubMed  CAS  Google Scholar 

  • Drayton MC, Ponting RC, Vecchies AC, Wilkinson TC, George J, Cogan NOI, Bannan NR, Smith KF, Spangenberg GC, Forster JW (2005) Gene-associated single nucleotide polymorphism discovery in white clover (T. repens L.). In: Humphreys MO (ed) Molecular breeding for the genetic improvement of forage crops and turf. Wageningen Academic Publishers, Netherlands, p 170

    Google Scholar 

  • Ellison NW, Liston A, Steiner JJ, Williams WM, Taylor NL (2006) Molecular phylogenetics of the clover genus (Trifolium—Leguminosae). Mol Phylogenet Evol 39:688–705

    Article  PubMed  CAS  Google Scholar 

  • Forster JW, Jones ES, Kölliker R, Drayton MC, Dupal MP, Guthridge KM, Smith KF, (2001) DNA profiling in outbreeding forage species. In: Henry R (ed) Plant genotyping—the DNA fingerprinting of plants. CABI Press, pp 299–320

  • Forster JW, Jones ES, Batley J, Smith KF (2004) Molecular marker-based genetic analysis of pasture and turf grasses. In: Hopkins A, Wang Z-Y, Sledge M, Barker RE (eds) Molecular breeding of forage and turf. Kluwer, Dordrecht, pp 197–239

    Chapter  Google Scholar 

  • George J, Cogan NOI, Smith KF, Spangenberg GC, Forster JW (2006a) Genetic map integration and comparative genome organisation of white clover (Trifolium repens L.) with model legume species. In: Proceedings of the Third International Legume Genetics and Genomics Conference, Brisbane, April 2006, p 68

  • George J, Dobrowolski MP, van Zijll de Jong E, Cogan NOI, Smith KF, Forster JW (2006b) Assessment of genetic diversity in cultivars of white clover (Trifolium repens L.) detected by simple sequence repeat polymorphism. Genome 49:919–930

    Article  CAS  Google Scholar 

  • Grattapaglia D, Sederoff R (1994) Genetic linkage maps of Eucalyptus grandis and Eucalyptus urophylla using a pseudo-testcross: mapping strategy and RAPD markers. Genetics 137:1121–1137

    PubMed  CAS  Google Scholar 

  • Guthridge KM, Dupal MD, Kölliker R, Jones ES, Smith KF, Forster JW (2001) AFLP analysis of genetic diversity within and between populations of perennial ryegrass (Lolium perenne L.). Euphytica 122:191–201

    Article  CAS  Google Scholar 

  • Huang X, Madan A (1999) CAP3: a DNA sequence assembly program. Genome Res 9:868–877

    Article  PubMed  CAS  Google Scholar 

  • Jones ES, Hughes LJ, Drayton MC, Abberton MT, Michaelson-Yeates TPT, Bowen C, Forster JW (2003) An SSR and AFLP molecular marker-based genetic map of white clover (Trifolium repens L.) Plant Sci 165:447–479

    Article  CAS  Google Scholar 

  • Kölliker R, Jones ES, Drayton MC, Dupal MP, Forster JW (2001) Development and characterisation of simple sequence repeat (SSR) markers for white clover (Trifolium repens L.). Theor Appl Genet 102:416–424

    Article  Google Scholar 

  • Kota R, Rudd S, Facius A, Kolesov G, Thiel T, Zhang H, Stein N, Mayer K, Graner A (2003) Snipping polymorphisms from large EST collections in barley (Hordeum vulgare L.). Mol Gen Genomics 270:24–33

    Article  CAS  Google Scholar 

  • Kulikova O, Gualtieri G, Geurts R, Kim DJ, Cook DR, Huguet T, de Jong JH, Fransz PF, Bisseling T (2001) Integration of the FISH pachytene and genetic maps of Medicago truncatula. Plant J 27:49–58

    Article  PubMed  CAS  Google Scholar 

  • Labate JA, Baldo AM (2005) Tomato SNP discovery by EST mining and resequencing. Mol Breed 16:343–349

    Article  CAS  Google Scholar 

  • Lopez C, Piégu B, Cooke R, Delseny M, Tohme J, Verdier V (2005) Using cDNA and genomic sequences as tools to develop SNP strategies in cassava (Manihot esculenta Crantz). Theor Appl Genet 110:425–431

    Article  PubMed  CAS  Google Scholar 

  • Love CG, Batley J, Edwards D (2003) Applied computational tools for crop genome research. J Plant Biotech 5:193–105

    Google Scholar 

  • Morales M, Roig E, Monforte AJ, Arús P, Garcia-Mas J (2004) Single-nucleotide polymorphisms detected in expressed sequence tags of melon (Cucumis melo L.). Genome 47:352–360

    Article  PubMed  CAS  Google Scholar 

  • Ogihara Y, Hasegawa K, Tsuijimoto H (1994) High-resolution cytological mapping of the long arm of chromosome 5A in common wheat using a series of deletion lines induced by gametocidal (Gc) genes of Aegilops speltoides. Mol Gen Genomics 244:253–259

    CAS  Google Scholar 

  • Pérez-Collazos E, Catalán P (2006) Palaeopolyploidy, spatial structure and conservation genetics of the narrow steppe plant Vella pseudocytisus subsp. paui (Vellinae, Cruciferae). Ann Bot 97:635–647

    Article  PubMed  Google Scholar 

  • Picoult-Newberg L, Ideker TE, Pohl MG, Taylor SL, Donaldson MA, Nickerson DA, Boyce-Jacino M (1999) Mining SNPs from EST databases. Genome Res 9:167–176

    PubMed  CAS  Google Scholar 

  • Ritter E, Gebhardt C, Salamini F (1990) Estimation of recombination frequencies and construction of linkage maps from crosses between heterozygous parents. Genetics 125:645–654

    PubMed  CAS  Google Scholar 

  • Rogers ME, Noble CL, Halloran GM, Nicolas ME (1997) Selecting for salt tolerance in white clover (Trifolium repens): chloride ion exclusion and its heritability. New Phytol 135:645–654

    Article  CAS  Google Scholar 

  • Rostocks N, Mudie S, Cardle L, Russell J, Ramsay L, Booth A, Svensson JT, Wanamaker SI, Walia H, Rodriguez EM, Hedley PE, Liu H, Morris J, Close TJ, Marshall DF, Waugh R (2005) Genome-wide SNP discovery and linkage analysis in barley based on genes responsive to abiotic stress. Mol Gen Genomics 274:515–527

    Article  CAS  Google Scholar 

  • Sawbridge T, Ong E-K, Binnion C, Emmerling M, Meath K, Nunan K, O’Neill M, O’Toole F, Simmonds J, Wearne K, Winkworth A, Spangenberg G (2003a) Generation and analysis of expressed sequence tags in white clover (Trifolium repens L.)Plant Sci 165:1077–1087

    Article  CAS  Google Scholar 

  • Sawbridge T, Ong E-K, Binnion C, Emmerling M, McInnes R, Meath K, Nguyen N, Nunan K, O’Neill M, O’Toole F, Rhodes C, Simmonds J, Tian P, Wearne K, Webster T, Winkworth A, Spangenberg G (2003b) Generation and analysis of expressed sequence tags in perennial ryegrass (Lolium perenne L.). Plant Sci 165:1089–1100

    Article  CAS  Google Scholar 

  • Schmid KJ, Sörensen TR, Stracke R, Törjerk O, Altmann T, Mitchell-Olds T, Weisshaar B (2003) Large-scale identification and analysis of genome-wide single-nucleotide polymorphisms for mapping in Arabidopsis thaliana. Genome Res 13:1250–1257

    Article  PubMed  Google Scholar 

  • Somers DJ, Kirkpatrick R, Moniwa M, Walsh A (2003) Mining single-nucleotide polymorphisms from hexaploid wheat ESTs. Genome 49:431–437

    Article  Google Scholar 

  • Sorrells ME, Wilson WA (1997) Direct classification and selection of superior alleles for crop improvement. Crop Sci 37:691–697

    Article  Google Scholar 

  • Spangenberg G, Forster JW, Edwards D, John U, Mouradov A, Emmerling M, Batley J, Felitti S, Cogan NOI, Smith KF, Dobrowolksi MP (2005a) Future directions in the molecular breeding of forage and turf. In: Humphreys MO (ed) Molecular breeding for the genetic improvement of forage crops and turf. Wageningen Academic Publishers, Netherlands, pp 83–97

    Google Scholar 

  • Spangenberg G, Sawbridge T, Ong EK, Love CG, Erwin TA, Logan EG, Edwards D (2005b) Clover ASTRA: a web-based resource for Trifolium EST analysis. In: Humphreys MO (ed) Molecular breeding for the genetic improvement of forage crops and turf. Wageningen Academic Publishers, Netherlands, p 195

    Google Scholar 

  • Spangenberg G, Sawbridge T, Ong EK, Love CG, Erwin TA, Logan EG, Edwards D (2005c) Ryegrass ASTRA: a web-based resource for Lolium EST analysis. In: Humphreys MO (ed) Molecular breeding for the genetic improvement of forage crops and turf. Wageningen Academic Publishers, Netherlands, p 201

    Google Scholar 

  • Taillon-Miller P, Gu Z, Li Q, Hillier L, Kwok P-Y (1998) Overlapping genomic sequences: a treasure trove of single-nucleotide polymorphisms. Genome Res 8:748–754

    PubMed  CAS  Google Scholar 

  • Williams W (1987) Adaptive variation. In: Baker MJ, Williams WM (eds) White clover. CAC International, Wallingford, pp 299–321

    Google Scholar 

  • Yang WC, Bai X-D, Kabelka E, Eaton C, Kamoun S, van der Knapp E, Francis D (2004) Discovery of single nucleotide polymorphisms in Lycopersicon esculentum by computer aided analysis of expressed sequence tags. Mol Breed 14:21–34

    Article  CAS  Google Scholar 

  • Young ND, Cannon SB, Sato S, Kim D, Cook DR, Town CD, Roe BA, Tabata S. (2005) Sequencing the genespaces of Medicago truncatula and Lotus japonicus. Plant Physiol 137:1174–1181

    Article  PubMed  CAS  Google Scholar 

  • Zhu H, Cannon SB, Young ND, Cook DR (2002) Phylogeny and genomic organisation of the TIR and non-TIR NBS-LRR resistance gene family in Medicago truncatula. Mol Plant Micro Interact 15:529–539

    CAS  Google Scholar 

  • Zhu H, Choi H-K, Cook DR, Shoemaker RC (2005) Bridging model and crop legumes through comparative genomics. Plant Physiol 137:1189–1196

    Article  PubMed  CAS  Google Scholar 

Download references

Acknowledgments

This work was supported by funding from the Victorian Department of Primary Industries, Dairy Australia Ltd., the Geoffrey Gardiner Dairy Foundation, Meat and Livestock Australia Ltd. and the Molecular Plant Breeding Cooperative Research Centre. The authors thank Prof. Michael Hayward for careful critical reading of the manuscript.

Author information

Author notes

  1. T. I. Sawbridge

    Present address: Molecular Bioscience Technologies, Department of Primary Industries and Fisheries, The University of Queensland, St Lucia, QLD, 4072, Australia

Authors and Affiliations

  1. Primary Industries Research Victoria, Victorian AgriBiosciences Centre, La Trobe Research and Development Park, Bundoora, VIC, 3083, Australia

    N. O. I. Cogan, M. C. Drayton, R. C. Ponting, A. C. Vecchies, T. I. Sawbridge, G. C. Spangenberg & J. W. Forster

  2. Primary Industries Research Victoria, Hamilton Centre, Hamilton, VIC, 3300, Australia

    N. R. Bannan & K. F. Smith

  3. Molecular Plant Breeding Cooperative Research Centre, La Trobe Research and Development Park, Bundoora, VIC, 3083, Australia

    N. O. I. Cogan, M. C. Drayton, R. C. Ponting, A. C. Vecchies, N. R. Bannan, T. I. Sawbridge, K. F. Smith, G. C. Spangenberg & J. W. Forster

Authors
  1. N. O. I. Cogan
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. M. C. Drayton
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. R. C. Ponting
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. A. C. Vecchies
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. N. R. Bannan
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. T. I. Sawbridge
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. K. F. Smith
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. G. C. Spangenberg
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. J. W. Forster
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to J. W. Forster.

Additional information

Communicated by W.R. McCombie.

N.O.I. Cogan and M.C. Drayton contributed equally to this work.

Electronic supplementary material

Below are the links to the electronic supplementary materials.

Image file (151 kb)

Image file (170 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Cogan, N.O.I., Drayton, M.C., Ponting, R.C. et al. Validation of in silico-predicted genic SNPs in white clover (Trifolium repens L.), an outbreeding allopolyploid species. Mol Genet Genomics 277, 413–425 (2007). https://doi.org/10.1007/s00438-006-0198-5

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00438-006-0198-5

Keywords

Search

Navigation