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A microsatellite map of white clover

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Abstract

The white clover (Trifolium repens) nuclear genome (n=2x=16) is an important yet under-characterised genetic environment. We have developed simple sequence repeat (SSR) genetic markers for the white clover genome by mining an expressed sequence tag (EST) database and by isolation from enriched genomic libraries. A total of 2,086 EST-derived SSRs (EST-SSRs) were identified among 26,480 database accessions. Evaluation of 792 EST-SSR primer pairs resulted in 566 usable EST-SSRs. Of these, 335 polymorphic EST-SSRs, used in concert with 30 genomic SSRs, detected 493 loci in the white clover genome using 92 F1 progeny from a pair cross between two highly heterozygous genotypes—364/7 and 6525/5. Map length, as estimated using the joinmap algorithm, was 1,144 cM and spanned all 16 homologues. The R (red leaf) locus was mapped to linkage group B1 and is tightly linked to the microsatellite locus prs318c. The eight homoeologous pairs of linkage groups within the white clover genome were identified using 96 homoeologous loci. Segregation distortion was detected in four areas (groups A1, D1, D2 and H2). Marker locus density varied among and within linkage groups. This is the first time EST-SSRs have been used to build a whole-genome functional map and to describe subgenome organisation in an allopolyploid species, and T. repens is the only Trifolieae species to date to be mapped exclusively with SSRs. This gene-based microsatellite map will enable the resolution of quantitative traits into Mendelian characters, the characterisation of syntenic relationships with other genomes and acceleration of white clover improvement programmes.

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References

  • Adams KL, Cronn R, Percifield R, Wendel JF (2003) Genes duplicated by polyploidy show unequal contributions to the transcriptome and organ-specific reciprocal silencing. Proc Natl Acad Sci USA 100:4649–4654

    Article  CAS  PubMed  Google Scholar 

  • Ane J, Levy J, Thoquet P, Klikova O, de Billy F, Penmetsa V, Kim D, Debelle F, Rosenburg C, Cook D, Bisseling T, Huguet T, Dearie J (2002) Genetic and cytogenetic mapping of DMI1, DMI2 and DMI3 genes of Medicago truncatula involved in Nod factor transduction, nodulation, and mycorrhization. Mol Plant Microbe Interact 15:1108–1118

    PubMed  Google Scholar 

  • Areshchenkova T, Ganal M (2002) Comparative analysis of polymorphism and chromosomal location of tomato microsatellite markers isolated from different sources. Theor Appl Genet 104:229–235

    Article  Google Scholar 

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

    Google Scholar 

  • Atwood SS, Hill HD (1940) The regularity of meiosis in microsporocytes of Trifolium repens. Am J Bot 27:730–735

    Google Scholar 

  • Atwood SS, Sullivan JT (1943) Inheritance of a cyanogenic glucoside and its hydrolysing enzyme in Trifolium repens. J Hered 34:311–320

    Google Scholar 

  • Awadalla P, Ritland K (1997) Microsatellite variation and evolution in the Mimulus guttatus species complex with a contrasting mating system. Mol Biol Evol 14:1023–1034

    CAS  PubMed  Google Scholar 

  • Badr A, Sayed-Ahmed H, El-Shanshouri A, Watson LE (2002) Ancestors of white clover (Trifolium repens L.) as revealed by isozyme polymorphisms. Theor Appl Genet 106:143–148

    CAS  PubMed  Google Scholar 

  • Band MR, Larson JH, Rebeiz M, Green CA, Heyen DW, Donovan J, Windish R, Steining C, Mahyuddin P, Womack JE, Lewin HA (2000) An ordered comparative map of the cattle and human genomes. Genome Res 10:1359–68

    CAS  PubMed  Google Scholar 

  • Bennett MD, Leitch IJ (2003) Angiosperm DNA C-values database (release 4.0, January 2003) http://www.rbgkew.org.uk/cval/homepage.html

  • Brouwer DJ, Osborn TC (1999) A molecular marker linkage map of tetraploid alfalfa (Medicago sativa L.). Theor Appl Genet 99:1194–1200

    Article  CAS  Google Scholar 

  • Brownstein M, Carpten J, Smith J (1996) Modulation of non-templated nucleotide addition by Taq DNA polymerase: primer modifications that facilitate genotyping. BioTechniques 20:1004–1010

    CAS  PubMed  Google Scholar 

  • Caradus JR, Clifford PTP, Chapman DF, Cousins GR, Williams WM, Miller JE (1997) Breeding and description of grasslands sustain. N Z J Agric Res 40:1–7

    Google Scholar 

  • Carnahan HL, Hill HD, Hanson AA, Brown KG (1955) Inheritance and frequencies of leaf markings in white clover. J Hered 46:109–114

    Google Scholar 

  • Chen CC, Gibson PB (1970) Meiosis in two species of Trifolium and their hybrids. Crop Sci 10:188–189

    Google Scholar 

  • Cho Y, Ishii T, Temnykg S, Chen X, Lipovich L, McCouch S, Park W, Ayres N, Cartinhour S (2000) Diversity of microsatellites derived from genomic libraries and GenBank sequences in rice (Oryza sativa). Theor Appl Genet 100:713–722

    CAS  Google Scholar 

  • Choi HK, Kim D, Uhm T, Limpens E, Lim H, Kalo P, Penmetsa R, Seres A, Kulikova O, Bisseling T, Kiss GB, Cook D (2004) A sequence-based map of Medicago truncatula and comparison of marker co-linearity with Medicago sativa. Genetics 166 (in press)

  • Corkill L (1971) Leaf markings in white clover. J Hered 62:307–310

    Google Scholar 

  • Cronn RC, Small RL, Wendel JF (1999) Duplicated genes evolve independently after polyploid formation in cotton. Proc Natl Acad Sci USA 96:14406–14411

    Article  CAS  PubMed  Google Scholar 

  • Davis GL, McMullen MD, Baysdorfer C, Musket T, Grant D, Staebell M, Xu G, Polacco M, Koster L, Melia-Hancock S, Houchins K, Chao S, Coe EH Jr (1999) A maize map standard with sequenced core markers, grass genome reference points and 932 expressed sequence tagged sites (ESTs) in a 1736-locus map. Genetics 152:1137–1172

    CAS  PubMed  Google Scholar 

  • Decroocq V, Favé M, Hagen L, Bordenave L, Decroocq S (2002) Development and transferability of apricot and grape EST microsatellite markers across taxa. Theor Appl Genet 106:912–922

    PubMed  Google Scholar 

  • Dvorak J, Luo M-C, Yang Z-L (1997) Restriction fragment length polymorphism and divergence in the genomic regions of high and low recombination in self-fertilizing and cross-fertilizing aegilops species. Genetics 148:423–434

    Google Scholar 

  • Eujayl I, Sorrells M, Baum M, Wolters P (2002) Isolation of EST-derived microsatellite markers for genotyping the A and B genomes of wheat. Theor Appl Genet 104:399–407

    CAS  Google Scholar 

  • Eujayl I, Sledge M, Wang L, May G, Chekhovskiy K, Zwonitzer JC, Mian M (2004) Medicago truncatula EST-SSRs reveal cross species genetic markers for Medicago spp. Theor Appl Genet 108:414–422

    Article  CAS  PubMed  Google Scholar 

  • Fulton T, Van der Hoeven R, Eannetta N, Tanksley S (2002) Identification, analysis, and utilization of conserved ortholog set markers for comparative genomics in higher plants. Plant Cell 14:1457–1467

    Google Scholar 

  • Gillett JM (1985) Taxonomy and morphology. In: Taylor NL (ed) Clover science and technology. American Society of Agronomy, Madison, Wis., pp 7–69

  • 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

    CAS  PubMed  Google Scholar 

  • Griffiths AG, Barrett BA, Ellison N, Sawbridge T, Spangenburg G, Bryan GJ, Schreiber M (2002) Getting out there: transportability of white clover EST and genomic DNA-derived microsatellites. In: McComb J (ed) Proc 12th Australasian Plant Breed Conf. Perth, Australia, pp 69–72

  • Gualtieri G, Kulikova O, Limpens E, Kim DJ, Cook DR, Bisselin T, Geurts R (2002) Microsynteny between pea and Medicago truncatula in the SYM2 region. Plant Mol Biol 50:225–235

    CAS  Google Scholar 

  • He C, Poysa V, Yu K (2003) Development and characterization of simple sequence repeat (SSR) markers and their use in determining relationships among Lycopersicon esculentum cultivars. Theor Appl Genet 106:363–373

    CAS  PubMed  Google Scholar 

  • Holton T, Christopher J, McClure L, Harker N, Henry R (2002) Identification and mapping of polymorphic SSR markers from expressed gene sequences of barley and wheat. Mol Breed 9:63–71

    CAS  Google Scholar 

  • Isobe S, Klimenko I, Ivashuta S, Gau M, Kozlov N (2003) First RFLP linkage map of red clover (Trifolium pratense L.) based on cDNA probes and its transferability to other red clover germplasm. Theor Appl Genet 108:105–112

    Article  CAS  PubMed  Google Scholar 

  • Jiang C, Wright R, El-Zik K, Paterson AH (1998) Polyploid formation created unique avenues for response to selection in Gossypium (cotton). Proc Natl Acad Sci USA 95:4419–4424

    CAS  PubMed  Google Scholar 

  • Jones E, Hughes L, Drayton M, Abberton M, Michaelson-Yeats T, Bowen C, Forster J (2003) An SSR and AFLP molecular marker-based genetic map of white clover (Trifolium repens L.). Plant Sci 165:531–539

    Article  CAS  Google Scholar 

  • Julier B, Flajoulot S, Barre P, Cardinet G, Santoni S, Huguet T, Huyghe C (2003) Construction of two genetic linkage maps in cultivated tetraploid alfalfa (Medicago sativa) using microsatellite and AFLP markers. BMC Plant Biol 3:9

    Article  PubMed  Google Scholar 

  • Kalo P, Endre G, Zimanyi L, Csanadi G, Kiss GB (2000) Construction of an improved linkage map of diploid alfalfa (Medicago sativa). Theor Appl Genet 100:641–657

    Article  Google Scholar 

  • Kantety RV, La Rota M, Matthews DE, Sorrells M (2002) Data mining for simple sequence repeats in expressed sequence tags from barley, maize, rice, sorghum and wheat. Plant Mol Biol 48:501–510

    Article  CAS  PubMed  Google Scholar 

  • Kolliker 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 

  • Lan TH, DelMonte TA, Reischmann KP, Hyman J, Kowalski SP, McFerson J, Kresovich S, Paterson AH (2000) An EST-enriched comparative map of Brassica oleracea and Arabidopsis thaliana. Genome Res 10:776–788

    CAS  PubMed  Google Scholar 

  • Li YC, Korol AB, Fahima T, Beiles A, Nevo E (2002) Microsatellites: genomic distribution, putative functions and mutational mechanisms: a review. Mol Ecol 11:2453–2465

    Article  CAS  PubMed  Google Scholar 

  • Matthews BF, Devine TE, Weisemann JM, Beard HS, Lewers KS, MacDonald MH, Park Y-B, Maiti R, Lin J-J, Kuo J, Pedroni MJ, Cregan PB, Saunders JA (2001) Incorporation of sequenced cDNA and genomic markers into the soybean genetic map. Crop Sci 41:516–521

    CAS  Google Scholar 

  • Mercer CF, van den Bosch J, Miller K (1999) The effectiveness of recurrent selection of white clover (Trifolium repens) for resistance to New Zealand populations of clover cyst nematode (Heterodera trifolii). Nematology 1:449–455

    Article  Google Scholar 

  • Metzgar D, Bytof J, Wills C (2000) Selection against frameshift mutations limits microsatellite expansion in coding DNA. Genet Res 10:72–80

    CAS  Google Scholar 

  • Morgante M, Olivieri AM (1993) PCR-amplified microsatellites as markers in plant genetics. Plant J 3:175–182

    CAS  PubMed  Google Scholar 

  • Morgante M, Hanafey M, Powell W (2002) Microsatellites are preferentially associated with nonrepetitive DNA in plant genomes. Nat Genet 30:194–200

    Article  CAS  PubMed  Google Scholar 

  • Qi X, Stam P, Lindhout P (1996) Comparison and integration of four barley genetic maps. Genome 39:379–394

    CAS  Google Scholar 

  • Ramsey L, Macaulay M, Cardle L, Morgante M, Degli Ianissevich S, Maestri E, Powell W, Waugh R (1999) Intimate association of microsatellite repeats with retrotransposons and other dispersed repetitive elements in barley. Plant J 17:415–425

    CAS  PubMed  Google Scholar 

  • Reinisch A, Dong J, Brubaker CL, Stelly D, Wendel JF, Paterson AH (1994) A detailed RFLP map of Cotton, Gossypium hirsutum × Gossypium barbadense: chromosome organization and evolution in a disomic polyploid genome. Genetics 138:829–847

    CAS  PubMed  Google Scholar 

  • Roder M, Korzun V, Wendchake K, Plaschke J, Tixier M, Leroy P, Ganal M (1998) A microsatellite map of wheat. Genetics 149:2007–2023

    PubMed  Google Scholar 

  • Sanwen H, Baoxi Z, Milbourne D, Cardle L, Guimei Y, Jiazhen G (2000) Development of pepper SSR markers from sequence databases. Euphytica 117:163–167

    Article  Google Scholar 

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

    Article  CAS  Google Scholar 

  • Schnabel E, Kulikova O, Penmetsa R, Bisseling T, Cook D, Frugoli J (2003) An integrated physical, genetic and cytogenetic map around the sunn locus of Medicago truncatula. Genome 46:665–672

    Article  CAS  PubMed  Google Scholar 

  • Schuelke M (2000) An economic method for the fluorescent labeling of PCR fragments. Nat Biotechnol 18:233–234

    Article  CAS  PubMed  Google Scholar 

  • Scott KD, Eggler P, Seaton G, Rossetto M, Ablett EM, Lee LS, Henry RJ (2000) Analysis of SSRs derived from grape ESTs. Theor Appl Genet 100723–726

  • 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 Jr (2002) Development and mapping of SSR markers for maize. Plant Mol Biol 48:463–81

    Article  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 

  • Tasma IM, Shoemaker RC (2003) Mapping flowering time gene homologs in soybean and their association with maturity (E) loci. Crop Sci 43:319–328

    CAS  Google Scholar 

  • Temnykh S, DeClerck G, Lukashova A, Leonard L, Cartinhour S, McCouch S (2001) Computational and experimental analysis of microsatellites in rice (Oryza sativa L.): frequency, length variation, transposon associations and genetic marker potential. Genet Res 11:1441–1452

    Article  CAS  Google Scholar 

  • Thoquet P, Gherardi M, Journet EP, Kereszt A, Ane JM, Prosperi JM, Huguet T (2002) The molecular genetic linkage map of the model legume Medicago truncatula: an essential tool for comparative legume genomics and the isolation of agronomically important genes. BMC Plant Biol 2:1

    Article  PubMed  Google Scholar 

  • Thornsberry J, Goodman M, Doebley J, Kresovich S, Nielsen D, Buckler E (2001) Dwarf8 polymorphisms associate with variation in flowering time. Nat Genet 28:286–289

    Article  CAS  PubMed  Google Scholar 

  • Vigouroux Y, Jaqueth JS, Matsuoka Y, Smith OS, Beavis WD, Smith JSC, Doebley J (2002) Rate and pattern of mutation at microsatellite loci in maize. Mol Biol Evol 19:1251–1260

    CAS  PubMed  Google Scholar 

  • Williams WM (1987) White clover taxonomy and biosystematics. In: Williams WM (ed) White clover. CAB Int, Oxon, pp 323–342

  • Wu J, Maehara T, Shimokawa T, Yamamoto S, Harada C, Takazaki Y, Ono N, Mukai Y, Koike K, Yazaki J, Fujii F, Shomura A, Ando T, Kono I, Waki K, Yamamoto K, Yano M, Matsumoto T, Sasaki T (2002) A comprehensive rice transcript map containing 6591 expressed sequence tag sites. Plant Cell 14:525–535

    CAS  PubMed  Google Scholar 

  • Zhu H, Cannon S, Young N, Cook D (2002) Phylogeny and genomic organization of the TIR and non-TIR NBS-LRR Resistance Gene Family in Medicago truncatula. Mol Plant Microbe Interact 15:529–539

    CAS  PubMed  Google Scholar 

  • Zhu H, Kim DJ, Baek JM, Choi HK, Ellis LC, Kuester H, McCombie WR, Peng HM, Cook DR (2003) Syntenic relationships between Medicago truncatula and Arabadopsis reveal extensive divergence of genome organization. Plant Physiol 131:1018–1026

    Article  CAS  PubMed  Google Scholar 

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Acknowledgements

The authors recognise the technical contributions of Greig Cousins, Kenyon Moore, Benjamin Franzmayr and Deborah Knox. Funds were provided by the New Zealand Foundation for Research, Science, and Technology under contract no. C10X0203. Mapped and novel EST-SSRs are available via Material Transfer Agreement for research purposes or via license for commercial purposes.

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Authors and Affiliations

  1. AgResearch Limited, Grasslands Research Centre, Private Bag 11008, Palmerston North, New Zealand

    B. Barrett, A. Griffiths, N. Ellison, C. Mercer, G. Bryan & D. Woodfield

  2. AgResearch Joint Bioinformatics, Institute School of Biological Sciences, University of Auckland, 3a Symonds St, Private Bag 92-019, Auckland, New Zealand

    M. Schreiber

  3. Department of Agronomy, University of Georgia, Athens, GA 30602, USA

    J. Bouton

  4. Department of Primary Industries Plant Biotechnology Centre, La Trobe University, Bundoora, Victoria, 3086, Australia

    B. Ong, J. Forster, T. Sawbridge & G. Spangenberg

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  1. B. Barrett
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  2. A. Griffiths
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  3. M. Schreiber
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  4. N. Ellison
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  5. C. Mercer
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  9. T. Sawbridge
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  11. G. Bryan
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Correspondence to B. Barrett.

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Communicated by C. Möllers

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Barrett, B., Griffiths, A., Schreiber, M. et al. A microsatellite map of white clover. Theor Appl Genet 109, 596–608 (2004). https://doi.org/10.1007/s00122-004-1658-0

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