Nucleotide diversity and linkage disequilibrium in five Lolium perenne genes with putative role in shoot morphology

Plant Science

Volumn 179, Issue 3, 2010, Pages 194-201

  Brazauskas, Gintaras ^a   Pašakinskiene, Izolda ^a,b   Asp, Torben ^c   Lübberstedt, Thomas ^d  

^a INSTITUTE OF AGRICULTURE   (Lithuania)

^b VILNIUS UNIVERSITY   (Lithuania)

^c DANISH INSTITUTE OF AGRICULTURAL SCIENCES   (Denmark)

^d IOWA STATE UNIVERSITY   (United States)

Author keywords

Linkage disequilibrium; Lolium perenne; Shoot morphology

Indexed keywords

LOLIUM; LOLIUM PERENNE;

EID: 77954311947     PISSN: 01689452     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.plantsci.2010.04.016     Document Type: Article

References (62)

1. Ward S.P., Leyser O. Shoot branching. Curr. Opin. Plant Biol. 2004, 7:73-78.
2. Elgersma A. Seed yield related to crop development and to yield components in nine cultivars of perennial ryegrass (Lolium perenne L.). Euphytica 1990, 49:141-154.
3. Schumacher K., Schmitt T., Rossberg M., Schmitz G., Theres K. The Lateral suppressor (Ls) gene of tomato encodes a new member of the VHIID protein family. Proc. Natl. Acad. Sci. U.S.A. 1999, 96:290-295.
4. Greb T., Clarenz O., Schafer E., Muller D., Herrero R., Schmitz G., Theres K. Molecular analysis of the LATERAL SUPPRESSOR gene in Arabidopsis reveals a conserved control mechanism for axillary meristem formation. Genes Dev. 2003, 17:1175-1187.
5. Li X., Qian Q., Fu Z., Wang Y., Xiong G., Zeng D., Wang X., Liu X., Teng S., Fujimoto H., Yuan M., Luo D., Han B., Li J. Control of tillering in rice. Nature 2003, 422:618-621.
6. Talbert P.B., Adler H.T., Parks D.W., Comai L. The REVOLUTA gene is necessary for apical meristem development and for limiting cell divisions in the leaves and stems of Arabidopsis thaliana. Development 1995, 121:2723-2735.
7. Schmitz G., Tillmann E., Carriero F., Fiore C., Cellini F., Theres K. The tomato Blind gene encodes a MYB transcription factor that controls the formation of lateral meristems. Proc. Natl. Acad. Sci. U.S.A. 2002, 99:1064-1069.
8. Komatsu K., Maekawa M., Ujiie S., Satake Y., Furutani I., Okamoto H., Shimamoto K., Kyozuka J. LAX and SPA: Major regulators of shoot branching in rice. Proc. Natl. Acad. Sci. U.S.A. 2003, 100:11765-11770.
9. Doebley J., Stec A., Hubbard L. The evolution of apical dominance in maize. Nature 1997, 386:485-488.
10. Wang R.L., Stec A., Hey J., Lukensand L., Doebley J. The limits of selection during maize domestication. Nature 1999, 398:236-239.
11. Clark R.M., Linton E., Messing J., Doebley J.F. Pattern of diversity in the genomic region near the maize domestication gene tb1. Proc. Natl. Acad. Sci. U.S.A. 2004, 101:700-707.
12. Clark R.M., Wagler T.N., Quijada P., Doebley J. A distant upstream enhancer at the maize domestication gene tb1 has pleiotropic effects on plant and inflorescent architecture. Nat. Genet. 2006, 38:594-597.
13. Takeda T., Suwa M., Kitano H., Ueguchi-Tanaka M., Ashikari M., Matsuoka M., Ueguchi C. The OsTB1 gene negatively regulates lateral branching in rice. Plant J. 2003, 33:513-520.
14. Lincoln C., Britton J.H., Estelle M. Growth and developmentof the axr1 mutants of Arabidopsis. Plant Cell 1990, 2:1071-1080.
15. Stirnberg P., van De Sande K., Leyser H.M. MAX1 and MAX2 control shoot lateral branching in Arabidopsis. Development 2002, 129:1131-1141.
16. Peng J., Carol P., Richards D.E., King K.E., Cowling R.J., Murphy G.P., Harberd N.P. The Arabidopsis GAI gene defines a signaling pathway that negatively regulates gibberellin responses. Genes Dev. 1997, 11:3194-3205.
17. Peng J., Richards D.E., Hartley N.M., Murphy G.P., Devos K.M., Flintham J.E., Beales J., Fish L.J., Worland A.J., Pelica F., Sudhakar D., Christou P., Snape J.W., Gale M.D., Harberd N.P. 'Green revolution' genes encode mutant gibberellin response modulators. Nature 1999, 400:256-261.
18. Silverstone A.L., Ciampaglio C.N., Sun T. The Arabidopsis RGA gene encodes a transcriptional regulator repressing the gibberellin signal transduction pathway. Plant Cell 1998, 10:155-169.
19. Chandler P.M., Marion-Poll A., Ellis M., Gubler F. Mutants at the Slender1 locus of barley cv. Himalaya. Molecular and physiological characterization. Plant Physiol. 2002, 129:181-190.
20. Ikeda A., Ueguchi-Tanaka M., Sonoda Y., Kitano H., Koshioka M., Futsuhara Y., Matsuoka M., Yamaguchi J. slender rice, a constitutive gibberellin response mutant, is caused by a null mutation of the SLR1 gene, an ortholog of the height-regulating gene GAI/RGA/RHT/D8. Plant Cell 2001, 13:999-1010.
21. Chono M, Honda I., Zeniya H., Yoneyama K., Saisho D., Takeda K., Takatsuto S., Hoshino T., Watanabe Y. A semidwarf phenotype of barley uzu results from a nucleotide substitution in the gene encoding a putative brassinosteroid receptor. Plant Physiol. 2003, 133:1209-1219.
22. Li J., Chory J. A putative leucine-rich repeat receptor kinase involved in brassinosteroid signal transduction. Cell 1997, 90:929-938.
23. Mackay L., Powell W. Methods for linkage disequilibrium mapping in crops. Trends Plant Sci. 2007, 12:57-63.
24. Flint-Garcia S.A., Thornsberry J.M., Buckler E.S. Structure of linkage disequilibrium in plants. Annu. Rev. Plant Biol. 2003, 54:357-374.
25. Remington D.L., Thornsberry J.M., Matsuoka Y., Wilson L.M., Whitt S.R., Doebley J., Kresovich S., Goodman M.M., Buckler E.S. Structure of linkage disequilibrium and phenotypic associations in the maize genome. Proc. Natl. Acad. Sci. U.S.A. 2001, 98:11479-11484.
26. Ching A., Caldwell K.S., Jung M., Dolan M., Smith O.S., Tingey S., Morgante M., Rafalski A.J. SNP frequency, haplotype structure and linkage disequilibrium in elite maize inbred lines. BMC Genet. 2002, 3:19.
27. Andersen J.R, Zein I., Wenzel G., Krützfeldt B., Eder J., Ouzunova M., Lübberstedt T. High levels of linkage disequilibrium and associations with forage quality at a Phenylalanine Ammonia-Lyase locus in European maize (Zea mays L.) inbreds. Theor. Appl. Genet. 2007, 114:307-319.
28. Garris A.J., McCouch S.R., Kresovich S. Population structure and its effect on haplotype diversity and linkage isequilibrium surrounding the xa5 locus of rice (Oryza sativa L.). Genetics 2003, 165:759-769.
29. Rostoks N., Mudie S., Cardle L., Russell J., Ramsay L., Booth A., Svensson J.T., Wanamaker S.I., Walia H., Rodriguez E.M., Hedley P.E., Liu H., Morris J., Close T.J., Marshall D.F., Waugh R. Genome-wide SNP discovery and linkage analysis in barley based on genes responsive to abiotic stress. Mol. Genet. Genomics 2005, 274:515-527.
30. Somers D.J., Banks T., Depauw R., Fox S., Clarke J., Pozniak C., McCartney C. Genome-wide linkage disequilibrium analysis in bread wheat and durum wheat. Genome 2007, 50:557-567.
31. Simko I., Haynes K.G., Jones R.W. Assessment of linkage disequilibrium in potato genome with single nucleotide polymorphism markers. Genetics 2006, 173:2237-2245.
32. Hamblin M.T., Mitchell S.E., White G.M., Gallego J., Kukatla R., Wing R.A., Paterson A.H., Kresovich S. Comparative population genetics of the panicoid grasses: sequence polymorphism, linkage disequilibrium and selection in a diverse sample of Sorghum bicolor. Genetics 2004, 167:471-483.
33. Whitt S.R, Wilson L.M., Tenaillon M.I., Gaut B.S., Buckler E.S. Genetic diversity and selection in the maize starch pathway. Proc. Natl. Acad. Sci. U.S.A. 2002, 99:12959-12962.
34. Xing Y., Frei U., Schejbel B., Asp T., Lübberstedt T. Nucleotide diversity and linkage disequilibrium in 11 expressed resistance candidate genes in Lolium perenne. BMC Plant Biol. 2007, 7:43.
35. Ponting R.C., Drayton M.C., Cogan N.O., Dobrowolski M.P., Spangenberg G.C., Smith K.F., Forster J.W. SNP discovery, validation, haplotype structure and linkage disequilibrium in full-length herbage nutritive quality genes of perennial ryegrass (Lolium perenne L.). Mol. Genet. Genomics 2007, 278:585-597.
36. Skøt L., Humphreys J., Humphreys M.O., Thorogood D., Gallagher J., Sanderson R., Armstead I.P., Thomas I.D. Association of candidate genes with flowering time and water soluble carbohydrate content in Lolium perenne (L.). Genetics 2007, 177:535-547.
37. Cogan N.O.I., Ponting R.C., Vecchies A.C., Drayton M.C., George J., Dobrowolski M.P., Sawbridge T.I., Spangenberg G.C., Smith K.F., Forster J.W. Gene-associated single nucleotide polymorphism (SNP) discovery in perennial ryegrass (Lolium perenne L.). Mol. Genet. Genomics 2006, 276:101-112.
38. Auzanneau J., Huyghe C., Julier B., Barre P. Linkage disequilibrium in synthetic varieties of perennial ryegrass. Theor. Appl. Genet. 2007, 115:837-847.
39. Posselt U.K., Barre P., Brazauskas G., Turner L.B. Comparative analysis of genetic similarity among perennial ryegrass genotypes investigated with AFLPs, ISSRs, RAPDs and SSRs. Czech J. Genet. Plant Breed. 2006, 41:86-93.
40. Saghai-Maroof M.A., Soliman K., Jorgensen R.A., Allard R.W. Ribosomal DNA pacer-length polymorphisms in barley: Mendelian inheritance, chromosomal location and population dynamics. Proc. Natl. Acad. Sci. U.S.A. 1984, 81:8014-8018.
41. Danish Functional Genomics Research Initiative []. http://www.dafgri.dk/.
42. Farrar K., Asp T., Lübberstedt T., Xu M., Thomas A.M., Christiansen C., Humphreys M.O., Donnison I.S. Construction of two Lolium perenne BAC libraries and identification of BACs containing candidate genes for disease resistance and forage quality. Mol. Breed. 2007, 19:15-23.
43. Nei M. Molecular Evolutionary Genetics 1987, Columbia University Press, New York.
44. Watterson G.A. On the number of segregating sites in genetical models without recombination. Theor. Pop. Biol. 1975, 7:256-276.
45. Rozas J., Sanchez-DelBarrio J.C., Messeguer X., Rozas R. DnaSP: DNA polymorphsim analyses by the coalscent and other methods. Bioinformatics 2003, 19:2496-2497.
46. Tajima F. Statistical method for testing the neutral mutational hypothesis by DNA polymorphism. Genetics 1989, 123:585-595.
47. Lewontin R.C. The interaction of selection and linkage. I. General considerations: heterotic models. Genetics 1964, 49:49-67.
48. Hill W.G., Robertson A. Linkage disequilibrium in finite populations. Theor. Appl. Genet. 1968, 38:226-231.
49. Sokal R.R., Rohlf F.J. Biometry 1981, W. H. Freeman and Company, New York. second ed.
50. Hill T., Lewicki P. Statistics Methods and Applications 2006, StatSoft, Tulsa, OK.
51. Thakur J.K., Tyagi A.K., Khurana J.P. OsIAA1, an Aux/IAA cDNA from rice, and changes in its expression as influenced by auxin and light. DNA Res. 2001, 8:193-203.
52. Mockaitis K, Estelle M. Auxin receptors and plant development: a new signaling paradigm. Annu. Rev. Cell Dev. Biol. 2008, 24:55-80.
53. Cubas P., Lauter N., Doebley J., Coen E. The TCP domain: a motif found in proteins regulating plant growth and development. Plant J. 1999, 18:215-222.
54. Studer B., Jensen L.B., Hentrup S., Brazauskas G., Kolliker R., Lubberstedt T. Genetic characterisation of seed yield and fertility traits in perennial ryegrass (Lolium perenne L.). Theor. Appl. Genet. 2008, 117:781-791.
55. Borevitz J.O., Hazen S.P., Michael T.P., Morris G.P., Baxter I.R., Hu T.T., Chen H., Werner J.D., Nordborg M., Salt D.E., Kay S.A., Chory J., Weigel D., Jones J.D.G., Ecker J.R. Genome-wide patterns of single-feature polymorphism in Arabidopsis thaliana. Proc. Natl. Acad. Sci. U.S.A. 2007, 104:12057-12062.
56. Ingvarsson P.K. Nucleotide polymorphism and linkage disequilibrium within and among natural populations of european aspen (Populus tremula L., Salicaceae). Genetics 2005, 169:945-953.
57. Brown G.R., Gill G.P., Kuntz R.J., Langley C.H., Neale D.B. Nucleotide diversity and linkage disequilibrium in loblolly pine. Proc. Natl. Acad. Sci. U.S.A. 2004, 101:15255-15260.
58. Nordborg M. Linkage disequilibrium, gene trees and selfing: an ancestral recombination graph with partial self-fertilization. Genetics 2000, 154:923-929.
59. Nordborg M, Borevitz J.O., Bergelson J., Berry C.C., Chory J., Hagenblad J., Kreitman M., Maloof J.N., Noyes T., Oefner P.J., Stahl E.A., Weigel D. The extent of linkage disequilibrium in Arabidopsis thaliana. Nat. Genet. 2002, 30:190-193.
60. Nordborg M., Hu T.T., Ishino Y., Jhaveri J., Toomajian C., et al. The pattern of polymorphism in Arabidopsis thaliana. PLoS Biol. 2005, 3:196.
61. Weber A., Clark R.M., Vaughn L., de Jesus Sanchez-Gonzalez J., Yu J., Yandell B.S., Bradbury P., Doebley J. Major regulatory genes in maize contribute to standing variation in Teosinte (Zea mays ssp. parviglumis). Genetics 2007, 177:2349-2359.
62. Yamamuro C., Ihara Y., Wu X., Noguchi T., Fujioka S., Takatsuto S., Ashikari M., Kitano H., Matsuoka M. Loss of function of a rice brassinosteroid insensitive1 homolog prevents internode elongation and bending of the lamina joint. Plant Cell 2000, 12:1591-1606.