A microsatellite map of white clover

Theoretical and Applied Genetics

Volumn 109, Issue 3, 2004, Pages 596-608

  Barrett, B ^a   Griffiths, A ^a   Schreiber, M ^b   Ellison, N ^a   Mercer, C ^a   Bouton, J ^c   Ong, B ^d   Forster, J ^d   Sawbridge, T ^d   Spangenberg, G ^d   Bryan, G ^a   Woodfield, D ^a  

^a AGRESEARCH GRASSLANDS   (New Zealand)

^b UNIVERSITY OF AUCKLAND   (New Zealand)

^c UNIVERSITY OF GEORGIA   (United States)

^d LA TROBE UNIVERSITY   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHMS; DATABASE SYSTEMS; ESTIMATION; GENES; MAPS;

EXPRESSED SEQUENCE TAG (EST); MICROSATELLITE MAP; SIMPLE SEQUENCE REPEAT (SSR); WHITE CLOVER;

GENETIC ENGINEERING;

TRIFOLIEAE; TRIFOLIUM; TRIFOLIUM REPENS;

EID: 4344668719     PISSN: 00405752     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00122-004-1658-0     Document Type: Article

References (65)

1. 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
2. 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
3. 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
4. Atwood SS (1940) Genetics of cross-incompatibility among self-incompatible plants of Trifolium repens. J Am Soc Agron 32:955-968
5. Atwood SS, Hill HD (1940) The regularity of meiosis in microsporocytes of Trifolium repens. Am J Bot 27:730-735
6. Atwood SS, Sullivan JT (1943) Inheritance of a cyanogenic glucoside and its hydrolysing enzyme in Trifolium repens. J Hered 34:311-320
7. 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
8. 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
9. 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
10. Bennett MD, Leitch IJ (2003) Angiosperm DNA C-values database (release 4.0, January 2003) http://www.rbgkew.org.uk/cval/ homepage.html
11. Brouwer DJ, Osborn TC (1999) A molecular marker linkage map of tetraploid alfalfa (Medicago sativa L.). Theor Appl Genet 99:1194-1200
12. 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
13. 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
14. Carnahan HL, Hill HD, Hanson AA, Brown KG (1955) Inheritance and frequencies of leaf markings in white clover. J Hered 46:109-114
15. Chen CC, Gibson PB (1970) Meiosis in two species of Trifolium and their hybrids. Crop Sci 10:188-189
16. 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
17. 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)
18. Corkill L (1971) Leaf markings in white clover. J Hered 62:307-310
19. Cronn RC, Small RL, Wendel JF (1999) Duplicated genes evolve independently after polyploid formation in cotton. Proc Natl Acad Sci USA 96:14406-14411
20. 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
21. 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
22. 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
23. 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
24. 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
25. 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
26. Gillett JM (1985) Taxonomy and morphology. In: Taylor NL (ed) Clover science and technology. American Society of Agronomy, Madison, Wis., pp 7-69
27. Grattapaglia D, Sederoff R (1994) Genetic linkage maps of Eucalyptus grandis and Eucalyptus urophylla using a pseudotestcross: mapping strategy and RAPD markers. Genetics 137:1121-1137
28. 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
29. 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
30. 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
31. 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
32. 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
33. 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
34. 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
35. 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
36. 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
37. 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
38. 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
39. 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
40. 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
41. 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
42. 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
43. Metzgar D, Bytof J, Wills C (2000) Selection against frameshift mutations limits microsatellite expansion in coding DNA. Genet Res 10:72-80
44. Morgante M, Olivieri AM (1993) PCR-amplified microsatellites as markers in plant genetics. Plant J 3:175-182
45. Morgante M, Hanafey M, Powell W (2002) Microsatellites are preferentially associated with nonrepetitive DNA in plant genomes. Nat Genet 30:194-200
46. Qi X, Stam P, Lindhout P (1996) Comparison and integration of four barley genetic maps. Genome 39:379-394
47. Ramsey L, Macaulay M, Cardle L, Morgante M, Degli lanissevich 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
48. Reinisch A, Dong J, Brubaker CL, Stelly D, Wendel JF, Paterson AH (1994) A detailed RFLP map of Cotton, Gossypium hirsutum x Gossypium barbadense: chromosome organization and evolution in a disomic polyploid genome. Genetics 138:829-847
49. Roder M, Korzun V, Wendchake K, Plaschke J, Tixier M, Leroy P, Ganal M (1998) A microsatellite map of wheat. Genetics 149:2007-2023
50. 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
51. 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
52. 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
53. Schuelke M (2000) An economic method for the fluorescent labeling of PCR fragments. Nat Biotechnol 18:233-234
54. 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
55. 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
56. 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
57. Tasma IM, Shoemaker RC (2003) Mapping flowering time gene homologs in soybean and their association with maturity (E) loci. Crop Sci 43:319-328
58. 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
59. 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
60. 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
61. 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
62. Williams WM (1987) White clover taxonomy and biosystematics. In: Williams WM (ed) White clover. CAB Int, Oxon, pp 323-342
63. 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
64. 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
65. 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