• 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 Nat Acad Sci USA 100:4649–4654

  Article PubMed CAS  Google Scholar 

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

  Article PubMed CAS  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

  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 

• Bryan GJ, Stephenson P, Collins A, Kirby J, Smith JB, Gale MD (1999) Low levels of DNA sequence variation among adapted genotypes of hexaploid wheat. Theor Appl Genet 99:192–198

  Article CAS  Google Scholar 

• Caldwell KS, Dvorak J, Lagudah ES, Akhunov E, Luo M-C, Wolters P, Powell W (2004) Sequence polymorphism in polyploid wheat and their D-genome diploid ancestor. Genetics 167:941–947

  Article PubMed CAS  Google Scholar 

• Chen CC, Gibson PB (1970) Chromosome pairing in two interspecific hybrids ofTrifolium. Can J Genet Cytol 12:790–794

  Google Scholar 

• Chen CC, Gibson PB (1971) Karyotypes of fifteenTrifolium species in section Amoria. Crop Sci 11:441–445

  Google Scholar 

• Chen M, Wang QY, Cheng XG, Xu ZS, Li LC, Ye XG, Xia LQ, Ma YZ (2007)GmDREB2, a soybean DRE-binding transcription factor, conferred drought and high-salt tolerance in transgenic plants. Biochem Biophys Res Commun 353:299–305

  Article PubMed CAS  Google Scholar 

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

  Article CAS  Google Scholar 

• Cogan NOI, Drayton MC, Ponting RC, Vecchies AC, Bannan NR, Sawbridge TI, Smith KF, Spangenberg GC, Forster JW (2007) Validation of in silico-predicted genic single nucleotide polymorphism in white clover (Trifolium repens L.). Mol Genet Genom 277:413–425

  Article CAS  Google Scholar 

• Coulondre C, Miller JH, Farabaugh PJ, Gilbert W (1978) Molecular basis of base substitution hotspots inEscherichia coli. Nature 274:775–780

  Article PubMed CAS  Google Scholar 

• Cronn RC, Wendel JF (1998) Simple methods for isolating homoeologous loci from allopolyploid genomes. Genome 41:756–762

  Article CAS  Google Scholar 

• Dobrowolski MP, Forster JW (2007) Chapter 9: Linkage disequilibrium-based association mapping in forage species. In: Oraguzie NC, Rikkerink E, Gardiner SE, De Silva NH (eds) Association mapping in plants. Springer, New York, pp 197–209

  Chapter  Google Scholar 

• Dracatos PM, Cogan NOI, Dobrowolski MP, Sawbridge TI, Spangenberg GC, Smith KF, Forster JW (2008) Discovery and genetic mapping of single nucleotide polymorphisms in candidate genes for pathogen defence response in perennial ryegrass (Lolium perenne L.). Theor Appl Genet 117:203–219

  Article PubMed CAS  Google Scholar 

• Edwards D, Forster JW, Cogan NOI, Batley J, Chagné D (2007) Chapter 4: Single nucleotide polymorphism discovery in plants. In: Oraguzie NC, Rikkerink E, Gardiner SE, De Silva NH (eds) Association mapping in plants. Springer, New York, pp 53–76

  Chapter  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 

• Erwin TA, Jewell EG, Love CG, Lim GAC, Li X, Chapman R, Batley J, Stajich JE, Mongin E, Stupka ER, Spangenberg G, Edwards D (2007) BASC: an integrated bioinformatics system forBrassica research. Nucl Acids Res 35:870–873

  Article  Google Scholar 

• Faville M, Vecchies AC, Schreiber M, Drayton MC, Hughes LJ, Jones ES, Guthridge KM, Smith KF, Sawbridge T, Spangenberg GC, Bryan GT, Forster JW (2004) Functionally-associated molecular genetic marker map construction in perennial ryegrass (Lolium perenne L.). Theor Appl Genet 110:12–32

  Article PubMed CAS  Google Scholar 

• 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 Academic Press, Dordrecht, pp 197–239

  Chapter  Google Scholar 

• Forster JW, Cogan NOI, Dobrowolski MP, Francki MG, Spangenberg GC, Smith KF (2008) Functionally-associated molecular genetic markers for temperate pasture plant improvement. In: Henry RJ (ed) Plant genotyping II: SNP technology. CABI Press, Wallingford, pp 154–187

  Google Scholar 

• Fredman D, White SJ, Potter S, Eichler EE, Den Dunnen JT, Brookes AJ (2004) Complex SNP-related sequence variation in segmental genome duplications. Nat Genet 36:861–866

  Article PubMed CAS  Google Scholar 

• Frugier F, Poirier S, Satiat-Jeunemaître B, Kondorosi A, Crespi M (2000) AKrüppel-like zinc finger protein is involved in nitrogen-fixing root nodule organogenesis. Genes Dev 14:475–482

  PubMed CAS  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. Plant and Animal Genome XIV, San Diego, pp 542

• George J, Dobrowolski MP, 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 PubMed CAS  Google Scholar 

• Griffiths A, Barrett B, Simon D, Anderson C, Somerville D, Lawn J, Warren J, Khan A, Jones C (2007) A consensus map of white clover with in silico alignment toMedicago indicates a translocation. Proc Fifth Intl Symp Molecular Breeding of Forage and Turf, Sapporo July 2007, pp 115

• Huang B, Liu JY (2006) A cotton dehydration-responsive element binding protein functions as a transcriptional repressor of DRE-mediated gene expression. Biochem Biophys Res Commun 343:1023–1031

  Article PubMed CAS  Google Scholar 

• Humphreys MW, Thomas HM, Morgan WG, Meredith MR, Harper JA, Thomas H, Zwierzykowski Z, Ghesquiére M (1995) Discriminating the ancestral progenitors of hexaploidFestuca arundinacea using genomic in situ hybridisation. Heredity 75:171–174

  Article  Google Scholar 

• Jander G, Norris SR, Rounsley SD, Bush DF, Levin IM, Last RL (2002)Arabidopsis map-based cloning in the post-genome era. Plant Physiol 129:440–450

  Article PubMed CAS  Google Scholar 

• Jones ES, Hughes LJ, Drayton MC, Abberton MT, Michaelson-Yeates TPT, Forster JW (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 

• 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 

• Lawless KA, Drayton MC, Hand MC, Ponting RC, Cogan NOI, Sawbridge TI, Smith KF, Spangenberg GC, Forster JW. (2008) Interpretation of SNP haplotype complexity in white clover (Trifolium repens L.), an outbreeding allotetraploid species, Chap 19. In: Yamada T, Spangenberg G (eds) Molecular Breeding of Forage and Turf: The Proceedings of the 5th International Symposium on the Molecular Breeding of Forage and Turf. Springer, New York (in press)

• Lu CM, Yang WY, Zhang WJ, Lu B-R (2005) Identification of SNPs and development of allelic specific PCR markers for high molecular weight glutenin subunitDtx1.5 fromAegilopstauschii through sequence characterisation. J Cereal Sci 41:13–18

  Article CAS  Google Scholar 

• Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, Berka J, Braverman MS, Chen Y-J, Chen Z, Dewell SB, Du L, Fierro JM, Gomes XV, Godwin BC, He W, Helgesen S, Ho CH, Irzyk GP, Jando SC, Alenquer MLI, Jarvie TP, Jirage KB, Kim J-B, Knight JR, Lanza JR, Leamon JH, Lefkowitz SM, Lei M, Li J, Lohman KL, Lu H, Makhijani VB, McDade KE, McKenna MP, Myers EW, Nickerson E, Nobile JR, Plant R, Puc BP, Ronan MT, Roth GT, Sarkis GJ, Simons JF, Simpson JW, Srinivasan M, Tartaro KR, Tomasz A, Vogt KA, Volkmer GA, Wang SH, Wang Y, Weiner MP, Yu P, Begley RF, Rothberg JM (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature 437:376–380

  PubMed CAS  Google Scholar 

• Merchan F, Breda C, Perez Hormaeche J, Sousa C, Kondorosi A, Aguilar OM, Megias M, Crespi M (2003) AKrüppel-lke transcription factor gene is involved in salt stress responses inMedicago spp. Plant and Soil 257:1–9

  Article CAS  Google Scholar 

• Michaelson-Yeates TPT, Marshall A, Abberton MT, Rhodes I (1997) Self-incompatibility and heterosis in white clover (Trifolium repens L.). Euphytica 94:341–348

  Article  Google Scholar 

• Mondragon-Palomino M, Gaut BS (2005) Gene conversion and the evolution of three leucine-rich repeat gene families inArabidopsis thaliana. Mol Biol Evol 22:2444–2456

  Article PubMed CAS  Google Scholar 

• Moore RC, Purugganan MD (2005) The evolutionary dynamics of plant duplicate genes. Curr Op Plant Biol 8:122–128

  Article CAS  Google Scholar 

• Nakashima K, Shinwari ZK, Sakuma Y, Seki M, Miura S, Shinozaki K, Yamaguchi-Shinozaki K (2000) Organization and expression of twoArabidopsisDREB2 genes encoding DRE-binding proteins involved in dehydration- and high-salinity-responsive gene expression. Plant Mol Biol 42:657–665

  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 ofAegilops speltoides. Mol Genet Genom 244:253–259

  CAS  Google Scholar 

• Olsen KM, Sutherland BL, Small LL (2007) Molecular evolution of theLi/li chemical defence polymorphism in white clover (Trifolium repens L.). Mol Ecol 16:4180–4193

  Article PubMed CAS  Google Scholar 

• Ponting RC, Drayton MD, Cogan NOI, Dobrowolski MP, Smith KF, Spangenberg GC, Forster JW (2007) SNP discovery, validation, haplotype structure and linkage disequilibrium in full-length herbage nutritive quality genes of perennial ryegrass (Lolium perenne L.). Mol Genet Genom 278:589–597

  Google Scholar 

• Rickert A, Premstaller A, Gebhardt C, Oefner PJ (2002) Genotyping of SNPs in a polyploidy genome by pyrosequencing. BioTechniques 32:592–603

  PubMed CAS  Google Scholar 

• Robertson M, Chandler PM (1994) A dehydrin-cognate protein from pea (Pisum sativum L.) with an atypical pattern of expression. Plant Mol Biol 26:805–816

  Article PubMed CAS  Google Scholar 

• Romo S, Labrador E, Dopico B (2001) Water stress-regulated gene expression inCicer arietinum seedlings and plants. Plant Physiol Biochem 39:1017–1026

  Article CAS  Google Scholar 

• Ross P, Hall L, Haff LA (2000) Quantitative approach to single-nucleotide polymorphism analysis using MALDI-TOF mass spectrometry. BioTechniques 29: 620–6, 628–629

  Google Scholar 

• Russell J, Booth A, Fuller J, Harrower B, Hedley P, Machray G, Powell W (2004) A comparison of sequence-based polymorphism and haplotype content in transcribed and anonymous regions of the barley genome. Genome 47:389–398

  Article PubMed 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 (2003) Generation and analysis of expressed sequence tags in white clover (Trifolium repens L.). Plant Sci 165:1077–1087

  Article CAS  Google Scholar 

• Senanayake YDA, Bringhurst RS (1967) Origin ofFragaria polyploids. I. Cytological analysis. Am J Bot 54:221–228

  Article  Google Scholar 

• Simko I (2004) One potato, two potato: haplotype association mapping in autotetraploids. Trends Plant Sci 9:441–448

  Article PubMed CAS  Google Scholar 

• Small RL, Wendel JF (2000) Copy number lability and evolutionary dynamics of theAdh gene family in diploid and tetraploid cotton (Gossypium). Genetics 155:1913–1926

  PubMed CAS  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

  Google Scholar 

• Spangenberg GC, Forster JW, Edwards D, John U, Mouradov A, Emmerling M, Batley J, Felitti S, Cogan NOI, Smith KF, Dobrowolski MP (2005) 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 

• Tombolato DCM, Zhang K, Davis TM, Folta Km (2008) Implementation of gene pair haplotypes provides evidence of the subgenome composition of cultivated strawberry (Fragaria × ananassa). Plant and Animal Genome XVI, San Diego, January 2008, pp 666

• Wang XS, Zhu HB, Jin GL, Liu HL, Wu WR, Zhu J (2007) Genome-scale identification and analysis of LEA genes in rice (Oryza sativa L.). Plant Sci 172:414–420

  Article CAS  Google Scholar 

• Wendel JF (2000) Genome evolution in polyploids. Plant Mol Biol 42:225–249

  Article PubMed CAS  Google Scholar 

• Wilhelm J, Pingoud A (2003) Real-time polymerase chain reaction. Chembiochem 4:1120–1128

  Article PubMed CAS  Google Scholar 

• Zhang Y, Sledge MK, Bouton JH (2007) Genome mapping of white clover (Trifolium repens L.) and comparative analysis within the Trifolieae using cross-species SSR markers. Theor Appl Genet 114:1367–1378

  Article PubMed CAS  Google Scholar 

• Zhu YL, Song QJ, Hyten DL, Van Tassell CP, Matukumalli LK, Grimm DR, Hyatt SM, Fickus EW, Young ND, Cregan PB (2003) Single-nucleotide polymorphisms in soybean. Genetics 163:1123–1134

  PubMed CAS  Google Scholar 

Download references