Genome mapping of white clover (Trifolium repens L.) and comparative analysis within the Trifolieae using cross-species SSR markers

Theoretical and Applied Genetics

Volumn 114, Issue 8, 2007, Pages 1367-1378

  Zhang, Yan ^a   Sledge, Mary K ^a   Bouton, Joe H ^a  

^a PLANT BIOLOGY DIVISION   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOMARKERS; CHROMOSOMES; DNA; GROWTH KINETICS; POLYMORPHISM;

GENETIC LINKAGE MAP; GENOME MAPPING; SIMPLE SEQUENCE REPEAT (SSR);

GENETIC ENGINEERING;

PRIMER DNA;

ALFALFA; ARTICLE; BARREL MEDIC; CHROMOSOME MAP; CLOVER; COMPARATIVE STUDY; DNA SEQUENCE; GENETIC LINKAGE; GENETIC MARKER; GENETICS; GENOME; SPECIES DIFFERENCE; VARIABLE NUMBER OF TANDEM REPEAT;

CHROMOSOME MAPPING; DNA PRIMERS; GENETIC MARKERS; GENOME, PLANT; LINKAGE (GENETICS); MEDICAGO SATIVA; MEDICAGO TRUNCATULA; MINISATELLITE REPEATS; SEQUENCE ANALYSIS, DNA; SPECIES SPECIFICITY; TRIFOLIUM;

DESMODIUM; GLYCINE MAX; MEDICAGO SATIVA; MEDICAGO TRUNCATULA; TRIFOLIEAE; TRIFOLIUM PRATENSE; TRIFOLIUM REPENS;

EID: 34248326866     PISSN: 00405752     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00122-007-0523-3     Document Type: Article

References (51)

1. Aranzana MJ, Pineda A, Cosson P, Dirlewanger E, Ascasibar J, Cipriani G, Ryder CD, Testolin R, Abbott A, King GJ, Iezzoni AF, Arús P (2003) A set of simple-sequence repeat (SSR) markers covering the Prunus genome. Theor Appl Genet 106:819-825
2. Atwood SS, Hill HD (1940) The regularity of meiosis in microsporocytes of Trifolium repens. Am J Bot 27:730-735
3. Barnes S (2002) Comparing Arabidopsis to other flowering plants. Curr Opin Plant Biol 5:128-134
4. 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. Theor Appl Genet 109:596-608
5. Barrett B, Baird I, Woodfield D (2005) A QTL analysis of white clover seed production. Crop Sci 45:1844-1850
6. Bennett MD, Leitch IJ (2003) Angiosperm DNA C-values database (release 4.0, January 2003). http://www.rbgkew.org.uk/cval/homepage.html
7. Bennetzen JL, Ma J (2003) The genetic colinearity of rice and other cereals on the basis of genomic sequence analysis. Curr Opin Plant Biol 6:128-133
8. Bouton JH, Woodfield DR, Caradus JR, Wood DT (2005) Registration of 'Durana' white clover. Crop Sci 45:797
9. Brink GE, Pederson GA, Alison MW, Ball DM, Bouton JH, Rawls RC, Steudemann JA, Venuto BC (1999) Growth of white clover ecotypes, cultivars, and germplasms in the southeastern USA. Crop Sci 39:1809-1814
10. Brouwer DJ, Osborn TC (1999) A molecular marker linkage map of tetraploid alfalfa (Medicago sativa L.). Theor Appl Genet 99:1194-1200
11. Chakravarti A, Lasher LK, Reefer JE (1991) A maximum likelihood method for estimating genome length using genetic linkage data. Genetics 128:175-182
12. Choi HK, Kim D, Uhm T, Limpens E, Lim H, Mun JH, Kalo P, Penmetsa RV, Seres A, Kulikova O, Roe BA, Bisseling T, Kiss GB, Cook DR (2004a) A sequence-based genetic map of Medicago truncatula and comparison of marker colinearity with M. sativa. Genetics 166:1463-1502
13. Choi HK, Mun JH, Kim DJ, Zhu H, Baek JM, Mudge J, Roe B, Ellis N, Doyle J, Kiss GB, Young ND, Cook DR (2004b) Estimating genome conservation between crop and model legume species. Proc Natl Acad Sci USA 101:15289-15294
14. Cogan NO, Abberton MT, Smith KF, Kearney G, Marshall AH, Williams A, Michaelson-Yeates TP, Bowen C, Jones ES, Vecchies AC, Forster JW (2006) 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
15. Delseny M (2004) Re-evaluating the relevance of ancestral shared synteny as a tool for crop improvement. Curr Opin Plant Biol 7:126-131
16. 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
17. Eujayl I, Sledge MK, Wang L, May GD, Chekhovskiy K, Zwonitzer JC, Mian MA (2004) Medicago truncatula EST-SSRs reveal cross-species genetic markers for Medicago spp. Theor Appl Genet 108:414-422
18. Faville MJ, 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
19. Gaitán-Solís E, Duque MC, Edwards KJ, Tohme J (2002) Microsatellite repeats in common bean (Phaseolus vulgaris): isolation, characterization, and cross-species amplification in Phaseolus ssp. Crop Sci 42:2128-2136
20. Gale MD, Devos KM (1998) Comparative genetics in the grasses. Proc Natl Acad Sci USA 95:1971-1974
21. George J, Cogan NOC, Smith KF, Spangenberg GC, Forster JW (2006) Genetic map integration and comparative genome organization of white clover (Trifolium repens L.) with model legume species. Poster 452. In: Abstracts of plant and animal genome XI Conference, San Diego, CA, USA, 14-18 January 2006
22. Gibson PB, Cope WA (1985) White Clover. In: Taylor NL (ed) Clover Science and Technology. ASA, CSSA, SSSA, Madison, pp 471-490
23. Gibson PB, Barnett OW, Pederson GA, McLaughlin MR, Knight WE, Miller JD, Cope WA, Tolin SA (1989) Registration of southern regional virus resistant white clover germplasm. Crop Sci 29:241-242
24. Gonzales MD, Archuleta E, Farmer A, Gajendran K, Grant D, Shoemaker R, Beavis WD, Waugh ME (2005) The Legume Information System (LIS): an integrated information resource for comparative legume biology. Nucleic Acids Res 33(Database issue): D660-D665
25. Grattapaglia D, Sederoff R (1994) Genetic linkage maps of Eucalyptus grandis and Eucalyptus urophylla using a pseudo-test-cross: mapping strategy and RAPD markers. Genetics 137:1121-1137
26. Gustine DL, Voigt PW, Brummer EC, Papadopoulos YA (2002) Genetic variation of RAPD markers for North American white clover collections and cultivars. Crop Sci 42:343-347
27. Gutierrez MV, Vaz Patto MC, Huguet T, Cubero JI, Moreno MT, Torres AM (2005) Cross-species amplification of Medicago truncatula microsatellites across three major pulse crops. Theor Appl Genet 110:1210-1217
28. Herrmann D, Boller B, Studer B, Widmer F, Kolliker R (2006) QTL analysis of seed yield components in red clover (Trifolium pratense L.). Theor Appl Genet 112:536-545
29. Jaiswal P, Ni J, Yap I, Ware D, Spooner W, Youens-Clark K, Ren L, Liang C, Zhao W, Ratnapu K, Faga B, Canaran P, Fogleman M, Hebbard C, Avraham S, Schmidt S, Casstevens TM, Buckler ES, Stein L, McCouch S (2006) Gramene: a bird's eye view of cereal genomes. Nucleic Acids Res 34(Database issue):D717-D723
30. 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
31. 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
32. Kalo P, Seres A, Taylor SA, Jakab J, Kevei Z, Kereszt A, Endre G, Ellis TH, Kiss GB (2004) Comparative mapping between Medicago sativa and Pisum sativum. Mol Genet Genomics 272:235-246
33. Kölliker R, Jones ES, Jahufer MZZ, Forster JW (2001a) Bulked AFLP analysis for the assessment of genetic diversity in white clover (Trifolium repens L.). Euphytica 121:305-315
34. Kölliker R, Jones ES, Drayton MC, Dupal MP, Forster JW (2001b) Development and characterisation of simple sequence repeat (SSR) markers for white clover (Trifolium repens L.). Theor Appl Genet 102:416-424
35. Kölliker R, Enkerli J, Widmer F (2006) Characterization of novel microsatellite loci for red clover (Trifolium pratense L.) from enriched genomic libraries. Mol Ecol Notes 6:50-53
36. 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
37. Mian MA, Saha MC, Hopkins AA, Wang ZY (2005) Use of tall fescue EST-SSR markers in phylogenetic analysis of cool-season forage grasses. Genome 48:637-647
38. Morgante M, Hanafey M, Powell W (2002) Microsatellites are preferentially associated with nonrepetitive DNA in plant genomes. Nat Genet 30:194-200
39. Paterson AH, Freeling M, Sasaki T (2005) Grains of knowledge: genomics of model cereals. Genome Res 15:1643-1650
40. Peakall R, Gilmore S, Keys W, Morgante M, Rafalski A (1998) Cross-species amplification of soybean (Glycine max) simple sequence repeats (SSRs) within the genus and other legume genera: implications for the transferability of SSRs in plants. Mol Biol Evol 15:1275-1287
41. Sato S, Isobe S, Asamizu E, Ohmido N, Nakamura Y, Kaneko T, Sakurai N, Okumura K, Klimenko I, Sasamoto S, Wada T, Watanabe A, Kohara M, Fujishiro T, Tabata S (2005) Comprehensive structural analysis of the genome of red clover (Trifolium pratense L.). DNA Res 12:301-364
42. Schuelke M (2000) An economic method for the fluorescent labeling of PCR fragments. Nat Biotechnol 18:233-234
43. Sledge MK, Ray IM, Jiang G (2005) An expressed sequence tag SSR map of tetraploid alfalfa (Medicago sativa L.). Theor Appl Genet 111:980-992
44. Sorrells ME, La Rota M, Bermudez-Kandianis CE, Greene RA, Kantety R, Munkvold JD, Miftahudin, Mahmoud A, Ma X, Gustafson PJ, Qi LL, Echalier B, Gill BS, Matthews DE, Lazo GR, Chao S, Anderson OD, Edwards H, Linkiewicz AM, Dubcovsky J, Akhunov ED, Dvorak J, Zhang D, Nguyen HT, Peng J, Lapitan NL, Gonzalez-Hernandez JL, Anderson JA, Hossain K, Kalavacharla V, Kianian SF, Choi DW, Close TJ, Dilbirligi M, Gill KS, Steber C, Walker-Simmons MK, McGuire PE, Qualset CO (2003) Comparative DNA sequence analysis of wheat and rice genomes. Genome Res 13:1818-1827
45. Taylor NL, Quarles RF, Anderson MK (1980) Methods of overcoming interspecific barriers in Trifolium. Euphytica 29:441-450
46. Van Ooijen JW, Voorrips RE (2001) JoinMap® 3.0, Software for the calculation of genetic linkage maps. Plant Research International, Wageningen
47. Wang ML, Gillaspie AG, Newman ML, Dean RE, Pittman RN, Morris JB, Pederson GA (2004) Transfer of simple sequence repeat (SSR) markers across the legume family for germplasm characterization and evaluation. Plant Genet Res 2:107-119
48. Williams CG, Goodman MM, Stuber CW (1995) Comparative recombination distances among Zea mays L. inbreds, wide crosses and interspecific hybrids. Genetics 141:1573-1581
49. Williams WM (1987) White clover taxonomy and biosystematics. In: Williams WM (ed) White Clover. CAB International, Oxon, pp 323-342
50. Wipf L, Cooper DC (1938) Chromosome numbers in nodules and roots of red clover, common vetch and garden pea. Proc Natl Acad Sci USA 24:87-91
51. Zhu H, Choi HK, Cook DR, Shoemaker RC (2005) Bridging model and crop legumes through comparative genomics. Plant Physiol 137:1189-1196