The first genetic maps for subterranean clover (Trifolium subterraneum L.) and comparative genomics with T. pratense L. and Medicago truncatula Gaertn. to identify new molecular markers for breeding

Molecular Breeding

Volumn 30, Issue 1, 2012, Pages 213-226

  Ghamkhar, Kioumars ^a,e   Isobe, Sachiko ^b   Nichols, Phillip G H ^a,c   Faithfull, Troy ^a   Ryan, Megan H ^a   Snowball, Richard ^c   Sato, Shusei ^b   Appels, Rudi ^d  

^a UNIVERSITY OF WESTERN AUSTRALIA   (Australia)

^b KAZUSA DNA RESEARCH INSTITUTE   (Japan)

^c DEPARTMENT OF AGRICULTURE AND FOOD WESTERN AUSTRALIA   (Australia)

^d MURDOCH UNIVERSITY   (Australia)

^e LA TROBE UNIVERSITY   (Australia)

Author keywords

Isoflavone; Legume; Marker assisted breeding; QTL map; Segmental duplication; Synteny

Indexed keywords

DNA SEQUENCES; FLAVONOIDS; GENOME; PLANTS (BOTANY);

ISOFLAVONES; LEGUME; LINKAGE GROUPS; MARKER-ASSISTED BREEDING; MEDICAGO TRUNCATULA; QTL MAP; RED CLOVER; SEGMENTAL DUPLICATIONS; SUBTERRANEAN CLOVER; SYNTENY;

GENES;

BRASSICACEAE; MEDICAGO TRUNCATULA; TRIFOLIUM; TRIFOLIUM PRATENSE; TRIFOLIUM REPENS; TRIFOLIUM SUBTERRANEUM;

EID: 84861757040     PISSN: 13803743     EISSN: None     Source Type: Journal    
DOI: 10.1007/s11032-011-9612-8     Document Type: Article

References (47)

1. 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(3): 596-608.
2. Cannon SB, Sterck L, Rombauts S, Sato S, Cheung F, Gouzy J, Wang X, Mudge J, Vasdewani J, Schiex T, Spannagl M, Monaghan E, Nicholson C, Humphray SJ, Schoof H, Mayer KFX, Rogers J, Quetier F, Oldroyd GE, Debelle F, Cook DR, Retzel EF, Roe BA, Town CD, Tabata S, van de Peer Y, Young ND (2006) Legume genome evolution viewed through the Medicago truncatula and Lotus japonicus genomes. Proc Natl Acad Sci USA 103(40): 14959-14964. doi: 10. 1073/pnas. 0603228103.
3. Chandley AC, McBeath S, Speed RM, Yorston L, Hargreave TB (1987) Pericentric inversion in human chromosome 1 and the risk for male sterility. Br Med J 24(6): 325.
4. Choi H-K, Mun J-H, Kim D-J, Zhu H, Baek J-M, Mudge J, Roe B, Ellis N, Doyle J, Kiss GB, Young ND, Cook DR (2004) Estimating genome conservation between crop and model legume species. Proc Natl Acad Sci USA 101(43): 15289-15294. doi: 10. 1073/pnas. 0402251101.
5. Collins WJ, Cox RI (1984) Oestrogenic activity in forage legumes. In: Barnes RF, Ball PR, Brougham RW, Marten GC, Minson DJ (eds) Forage legumes for energy-efficient animal production, Palmerston North, New Zealand. USDA-ARS: Springfield Virginia, pp 268-276.
6. Faga B (2007) Installing and configuring CMap. Current protocols in bioinformatics. Wiley, London. doi: 10. 1002/0471250953. bi0908s17.
7. Francis CM, Gladstones JS (1983) Exploitation of genetic resources in the selection and breeding of new cultivars of Trifolium subterraneum L. (sensu lato). In: Mclvor JG, Bray RA (eds) Genetic resources of forage plants. CSIRO, Melbourne, pp 2-14.
8. Francis CM, Hume ID (1971) The relationship between lignification and flavonoid production in subterranean clover. Aust J Agric Res 24: 1-5.
9. Francis CM, Millington AJ (1965) Varietal variation in the isoflavone content of subterranean clover: Its estimation by a microtechnique. Aust J Agric Res 16(4): 557-564. doi: 10. 1071/AR9650557.
10. Fridman E, Zamir D (2003) Functional divergence of a syntenic invertase gene family in tomato, potato, and Arabidopsis. Plant Physiol 131(2): 603.
11. George J, Sawbridge TI, Cogan NOI, Gendall AR, Smith KF, Spangenberg GC, Forster JW (2008) Comparison of genome structure between white clover and Medicago truncatula supports homoeologous group nomenclature based on conserved synteny. Genome 51: 905-911.
12. Isobe S, Klimenko I, Ivashuta S, Gau M, Kozlov NN (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.
13. Isobe S, Kolliker R, Hisano H, Sasamoto S, Wada T, Klimenko I, Okumura K, Tabata S (2009) Construction of a consensus linkage map for red clover (Trifolium pratense L.). BMC Plant Biol 9(1): 57.
14. Johnson ME, Viggiano L, Bailey JA, Abdul-Rauf M, Goodwin G, Rocchi M, Eichler EE (2001) Positive selection of a gene family during the emergence of humans and African apes. Nature 413(6855): 514-519.
15. 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 (3): 531-539.
16. 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.). TAG Theor Appl Genet 102(2): 416-424.
17. Kölliker R, Enkeri 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.
18. Kosambi DD (1944) The estimation of map distance from recombination values. Ann Eugen 12(3): 172-175.
19. Kosman E, Leonard KJ (2005) Similarity coefficients for molecular markers in studies of genetic relationships between individuals for haploid, diploid, and polyploid species. Mol Ecol 14(2): 415-424.
20. Li L, Modolo LV, Escamilla-Trevino LL, Achnine L, Dixon RA, Wang X (2007) Crystal structure of Medicago truncatula UGT85H2-insights into the structural basis of a multifunctional (iso)flavonoid glycosyltransferase. J Mol Biol 370(5): 951-963.
21. Liu C-J, Huhman D, Sumner LW, Dixon RA (2003) Regiospecific hydroxylation of isoflavones by cytochrome P450 81E enzymes from Medicago truncatula. The Plant J 36(4): 471-484. doi: 10. 1046/j. 1365-313X. 2003. 01893. x.
22. Manly FF, Cudmore RH, Meer JM (2001) Map Manager QTX, cross-platform software for genetic mapping. Mamm Genome 12: 930-932.
23. Mefford HC, Eichler EE (2009) Duplication hotspots, rare genomic disorders, and common disease. Curr Opin Genet Dev 19(3): 196-204.
24. Morley FHW (1961) Subterranean clover. In: Norman AG (ed) Advances in agronomy, vol 13. Elsevier, Burlington, pp 125-163.
25. Nichols PGH (2004) Evolution in sown mixtures of subterranean clover (Trifolium subterraneum L.). University of Western Australia, Perth.
26. Nichols PGH, Collins WJ, Barbetti MJ (1996) Registered cultivars of subterranean clover-their characteristics, origin and identification., vol Bulletin No. 4327. Agriculture Western Australia, South Perth.
27. Nichols PGH, Loi A, Nutt BJ, Evans PM, Craig AD, Pengelly BC, Dear BS, Lloyd DL, Revell CK, Nair RM, Ewing MA, Howieson JG, Auricht GA, Howie JH, Sandral GA, Carr SJ, de Koning CT, Hackney BF, Crocker GJ, Snowball R, Hughes SJ, Hall EJ, Foster KJ, Skinner PW, Barbetti MJ, You MP (2007) New annual and short-lived perennial pasture legumes for Australian agriculture-15 years of revolution. Field Crops Res 104(1-3): 10-23. doi: 10. 1016/j. fcr. 2007. 03. 016.
28. Nichols P, Cocks P, Francis C (2009) Evolution over 16 years in a bulk-hybrid population of subterranean clover (Trifolium subterraneum L.) at two contrasting sites in south-western Australia. Euphytica 169(1): 31-48.
29. Ouyang S, Zhu W, Hamilton J, Lin H, Campbell M, Childs K, Thibaud-Nissen F, Malek RL, Lee Y, Zheng L (2006) The TIGR rice genome annotation resource: improvements and new features. Nucleic Acids Res 35(suppl 1): D883.
30. Parkin IAP, Gulden SM, Sharpe AG, Lukens L, Trick M, Osborn TC, Lydiate DJ (2005) Segmental structure of the Brassica napus genome based on comparative analysis with Arabidopsis thaliana. Genetics. doi: 10. 1534/genetics. 105. 042093.
31. Paterson AH, Bowers JE, Bruggmann R, Dubchak I, Grimwood J, Gundlach H, Haberer G, Hellsten U, Mitros T, Poliakov A (2009) The Sorghum bicolor genome and the diversification of grasses. Nature 457(7229): 551-556.
32. Quinlivan BJ (1961) The effect of constant and fluctuating temperatures on the permeability of the hard seeds of some legume species. Aust J Agric Res 12(6): 1009-1022. doi: 10. 1071/AR9611009.
33. Salisbury PA, Halloran GM (1983) Inheritance of rate of breakdown of seed coat impermeability in subterranean clover (Trifolium subterraneum L.). Euphytica 32(3): 807-819.
34. Salisbury PA, Aitken Y, Halloran GM (1987) Genetic control of flowering time and its component processes in subterranean clover (Trifolium subterraneum L.). Euphytica 36(3): 887-902.
35. Sato S, Isobe S, Asamizu E, Ohmido N, Kataoka R, 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.
36. Slattery HD (1981) Physiological and genetic control of seed coat impermeability in subterranean clover (Trifolium subterraneum L.). University of Western Australia, Perth.
37. Tan BH, Collins WJ (1987) Multi-allelic nature of the locus controlling leaf marking in subterranean clover. Aust J Agric Res 38(3): 547-558. doi: 10. 1071/AR9870547.
38. Taylor GB (2005) Hardseededness in Mediterranean annual pasture legumes in Australia: a review. Aust J Agric Res 56(7): 645-662.
39. Varshney R, Bertioli D, Moretzsohn M, Vadez V, Krishnamurthy L, Aruna R, Nigam S, Moss B, Seetha K, Ravi K, He G, Knapp S, Hoisington D (2009) The first SSR-based genetic linkage map for cultivated groundnut (Arachis hypogaea L.). Theor Appl Genet 118(4): 729-739.
40. Voorrips RE (2002) MapChart: software for the graphical presentation of linkage maps and QTLs. J Hered 93(1): 77-78.
41. Wang X (2011) Structure, function, and engineering of enzymes in isoflavonoid biosynthesis. Func Integr Genomics 11(1): 13-22. doi: 10. 1007/s10142-010-0197-9.
42. Wang J, Drayton MC, George J, Cogan NOI, Baillie RC, Hand ML, Kearney G, Trigg P, Erb S, Wilkinson T, Bannan N, Forster JW, Smith KF (2010) QTL analysis of salt stress tolerance in white clover (Trifolium repens L.). TAG Theor Appl Genet 120: 607-619.
43. 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(4): 1174-1181. doi: 10. 1104/pp. 104. 057034.
44. Zeng ZB (1993) Theoretical basis for separation of multiple linked gene effects in mapping quantitative trait loci. Proc Natl Acad Sci USA 90: 10972-10976.
45. Zeng ZB (1994) Precision mapping of quantitative trait loci. Genetics 136: 1457-1468.
46. Zhang L, Lu HHS, Chung W, Yang J, Li WH (2005) Patterns of segmental duplication in the human genome. Mol Biol Evol 22(1): 135.
47. Zhang Y, Sledge M, Bouton J (2007) Genome mapping of white clover (Trifolium repens L.) and comparative analysis within the Trifolieae using cross-species SSR markers. Theor Appl Genet 114(8): 1367-1378.