Genetic architecture of flowering time in maize as inferred from quantitative trait loci meta-analysis and synteny conservation with the rice genome

Genetics

Volumn 168, Issue 4, 2004, Pages 2169-2185

  Chardon, Fabien ^a   Virlon, Bérangère ^a   Moreau, Laurence ^a   Falque, Matthieu ^a   Joets, Johann ^a   Decousset, Laurent ^b   Murigneux, Alain ^b   Charcosset, Alain ^a  

^a INRA Institut National de la Recherche Agronomique   (France)

^b Biogemma   (France)

Author keywords

[No Author keywords available]

Indexed keywords

ARABIDOPSIS; ARTICLE; FLOWERING; GENE MAPPING; GENETIC MODEL; MAIZE; META ANALYSIS; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; QUANTITATIVE TRAIT LOCUS; RESTRICTION FRAGMENT LENGTH POLYMORPHISM; RICE; STATISTICS; SYNTENY; UNINDEXED SEQUENCE;

CHROMOSOME MAPPING; FLOWERING TOPS; GENETIC MARKERS; ORYZA SATIVA; QUANTITATIVE TRAIT LOCI; SYNTENY; ZEA MAYS;

ARABIDOPSIS; EMBRYOPHYTA; JAPONICA; ZEA MAYS;

EID: 11244255494     PISSN: 00166731     EISSN: None     Source Type: Journal    
DOI: 10.1534/genetics.104.032375     Document Type: Article

References (79)

1. ABLER, B. S. B., M. D. EDWARDS and C. W. STUBER, 1991 Isoenzymatic identification of quantitative trait loci in crosses of elite maize inbreds. Crop Sci. 31: 267-274.
2. ALTSCHUL, S. F., T. L. MADDEN, A. A. SCHAEFFER, J. ZHANG, Z. ZHANG et al., 1997 Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25: 3389-3402.
3. ARCADE, A., A. LABOURDETTE, M. FALQUE, B. MANGIN, F. CHARDON et al., 2004 BioMercator: integrating genetic maps and QTL towards discovery of candidate genes. Bioinformatics 20: 2324-2326.
4. AUSTIN, D. F., and M. LEE, 1996 Genetic resolution and verification of quantitative trait loci for flowering and plant height with recombinant inbred lines of maize. Genome 39: 957-968.
5. BASU, D., K. DEHESH, H. J. SCHNEIDER-POETSCH, S. E. HARRINGTON, S. R. MCCOUCH et al., 2000 Rice PHYC gene: structure, expression, map position and evolution. Plant Mol. Biol. 41: 27-42.
6. BEAVIS, W. D., O. S. SMITH, D. GRANT and R. FINCHER, 1994 Identification of quantitative trait loci using a small sample of topcrossed and F4 progeny from maize. Crop Sci. 34: 882-896.
7. BENJAMINI, Y., and Y. HOCHBERG, 1995 Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Stat. Soc. B 57: 289-300.
8. BENNETZEN, J. L., and D. A. LAURIE, 1993 Grasses as a single genetic system: genome analysis, colinearity and compatibility. Trends Genet. 9: 259-261.
9. BENSEN, R. J., G. S. JOHAL, V. C. CRANE, J. T. TOSSBERG, P. S. SCHNABLE et al., 1995 Cloning and characterization of the maize An1 gene. Plant Cell 7: 75-84.
10. BLANC, G., L. MOREAU, B. MANGIN and A. CHARCOSSET, 2003 QTL detection in connected populations of maize. 12th Meeting of the EUCARPIA Section of Biometrics in Plant Breeding, Spain, p. 55.
11. BLAZQUEZ, M. A., 2000 Flower development pathways. J. Cell Sci 113: 3547-3548.
12. BOHN, M., M. M. KHAIRALLAH, D. GONZALEZ-DE-LEON, D. A. HOISINGTON, H. F. UTZ et al., 1996 QTL mapping in tropical maize: I. Genomic regions affecting leaf feeding resistance to sugarcane borer and other traits. Crop Sci. 36: 1352-1361.
13. BOHN, M., B. SCHULZ, R. KREPS, D. KLEIN and A. MELCHINGER, 2000 QTL mapping for resistance against the European corn borer (Ostrinia nubilalis H.) in early maturing European dent germ-plasm. Theor. Appl. Genet. 1001: 907-917.
14. BOMBLIES, K., R. L. WANG, B. A. AMBROSE, R. J. SCHMIDT, R. B. MEELEY et al., 2003 Duplicate FLORICAULA/LEAFY homologs zfl1 and zfl2 control inflorescence architecture and flower patterning in maize. Development 130: 2385-2395.
15. BOUCHEZ, A., F. HOSPITAL, M. CAUSSE, A. GALLAIS and A. CHARCOSSET, 2002 Marker-assisted introgression of favorable alleles at quantitative trait loci between maize elite lines. Genetics 162: 1945-1959.
16. CARDINAL, A. J., M. LEE, N. SHAROPOVA, W. L. WOODMAN-CLIKEMAN and M. J. LONG, 2001 Genetics mapping and analysis of quantitative trait loci for resistance to stalk tunneling by the European corn borer in maize. Crop Sci. 41: 835-845.
17. CHANDLER, V. L., and V. BRENDEL, 2002 The Maize Genome Sequencing Project. Plant Physiol. 130: 1594-1597.
18. CHRISTENSEN, A. H., and P. H. QUAIL, 1989 Structure and expression of a maize phytochrome-encoding gene. Gene 85: 381-390.
19. COLASANTI, J., Z. YUAN and V. SUNDARESAN, 1998 The indeterminate gene encodes a zinc finger protein and regulates a leaf-generated signal required for the transition to flowering in maize. Cell 93: 593-603.
20. DABNEY, A., and J. D. STOREY, 2003 QVALUE. University of Washington, Seattle.
21. DANILEVSKAYA, O., P. HERMON, D. SHIRBROUN, E. BRUGGEMANN, M. MUSZYNSKI et al., 2003 Functional analysis of the maize FT/TFL homologs reveals potential players in the floral transition, Abstract 490 in Plant Biology 2003, edited by S. ROSENBERRY. ASPB, Rockville, MD.
22. DARVASI, A., and M. SOLLER, 1997 A simple method to calculate resolving power and confidence interval of QTL map location. Behav. Genet. 27: 125-132.
23. DEHESH, K., J. M. TEPPERMAN, A. H. CHRISTENSEN and P. QUAIL, 1991 phyB is evolutionarily conserved and constitutively expressed in rice seedling shoots. Mol. Gen. Genet. 225: 305-313.
24. DELVIN, B., K. ROEDER and L. WASSERMAN, 2003 False discovery or missed discovery? Heredity 91: 537-538.
25. DEVOS, K. M., and M. D. GALE, 1997 Comparative genetics in the grasses. Plant Mol. Biol. 35: 3-15.
26. DUNFORD, R. P., M. YANO, N. KURATA, T. SASAKI, G. HUESTIS et al., 2002 Comparative mapping of the barley Ppd-H1 photoperiod response gene region, which lies close to a junction between two rice linkage segments. Science 161: 825-834.
27. EL-ASSAL, S. E., C. ALONSO-BLANCO, A. J. PEETERS, C. WAGEMAKER, J. L. WELLER et al., 2003 The role of cryptochrome 2 in flowering in Arabidopsis. Plant Physiol. 133: 1-13.
28. FALQUE, M., L. DÉCOUSSET, A. MURIGNEUX, N. DAUTREVAUX, D. DERVINS et al., 2003 Large-scale cDNA mapping for candidate gene approach. Abstract 116 of the 45th Annual Maize Genetics Conference, University of Missouri, Columbia, MO.
29. GAUT, B. S., 2002 Evolutionary dynamics of grass genomes. New Phytol. 154: 15-28.
30. GOFF, S. A., D. RICKE, T. H. LAN, G. PRESTING, R. WANG et al., 2002 A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science 296: 92-100.
31. GOFFINET, B., and S. GERBER, 2000 Quantitative trait loci: a meta-analysis. Genetics 155: 463-473.
32. GROH, S., M. M. KHAIRALLAH, D. GONZALEZ-DE-LEON, M. WILLCOX, C. JIANG et al., 1998 Comparison of QTLs mapped in RILs and their test-cross progenies of tropical maize for insect resistance and agronomic traits. Plant Breed. 117: 193-202.
33. HAYAMA, R., S. YOKOI, S. TAMAKI, M. YANO and K. SHIMAMOTO, 2003 Adaptation of photoperiodic control pathways produces short-day flowering in rice. Nature 422: 719-722.
34. IRISH, E. E., and T. M. NELSON, 1991 Identification of multiple stages in the conversion of maize meristems from vegetative to floral development. Development 112: 891-898.
35. IZAWA, T., T. OIKAWA, S. TOKUTOMI, K. OKUNO and K. SHIMAMOTO, 2000 Phytochromes confer the photoperiodic control of flowering in rice (a short-day plant). Plant J. 22: 391-399.
36. IZAWA, T., Y. TAKAHASHI and M. YANO, 2003 Comparative biology comes into bloom: genomic and genetic comparison of flowering pathways in rice and Arabidopsis. Curr. Opin. Plant Biol. 6: 113-120.
37. KEARSEY, M. J., and A. G. FARQUHAR, 1998 QTL analysis in plants: Where are we now? Heredity 80: 137-142.
38. KOESTER, R. P., P. H. Sisco and C. W. STUBER, 1993 Identification of quantitative trait loci controlling days to flowering and plant height in two nearisogenic lines of maize. Crop Sci. 33:1209-1216.
39. KOJIMA, S.,Y. TAKAHASHI, Y. KOBAYASHI, L. MONNA, T. SASAKI et al., 2002 Hd3a, a rice ortholog of the Arabidopsis FT gene, promotes transition to flowering downstream of Hd1 under short-day conditions. Plant Cell Physiol. 43: 1096-1105.
40. KOORNNEEF, M., C. ALONSO-BLANCO, A. J. PEETERS and W. SOPPE, 1998 Genetic control of flowering time in Arabidopsis. Annu. Rev. Plant Physiol. Plant Mol. Biol. 49: 345-370.
41. LAURIE, D. A., 1997 Comparative genetics of flowering time. Plant Mol. Biol. 35: 167-177.
42. LEE, M., N. SHAROPOVA, W. D. BEAVIS, D. GRANT, M. KATT et al., 2002 Expanding the genetic map of maize with the intermated B73 × Mol7 (IBM) population. Plant Mol. Biol. 48: 453-461.
43. LIN, Y. R., K. F. SCHERTZ and A. H. PATERSON, 1995 Comparative analysis of QTLs affecting plant height and maturity across the poacea, in reference to an interspecific sorghum population. Genetics 141: 391-411.
44. LÜBBERSTEDT, T., A. MELCHINGER, C. C. SCHÖN, H. F. UTZ and D. KLEIN, 1997 Qtl mapping in testcrosses of European flint lines of maize: I. Comparison of different testers for forage yield traits. Crop Sci. 37: 921-931.
45. LYNCH, M., and B. WALSH, 1998 Genetics and Analysis of Quantitative Traits. Sinauer Associates, Sunderland, MA.
46. MCSTEEN, P., D. LAUDENCIA-CHINGCUANCO and J. COLASANTI, 2000 A floret by any other name: control of meristem identity in maize. Trends Plant Sci. 5: 61-66.
47. MECHIN, V., O. ARGILLIER, Y. HÉBERT, E. GUINGO, L. MOREAU et al., 2001 Genetic analysis and QTL mapping of cell wall digestibility and lignification in silage maize. Crop Sci. 41: 690-697.
48. MICHAELS, S. D., and R. M. AMASINO, 2001 Loss of FLOWERING LOCUS C activity eliminates the late-flowering phenotype of FRIGIDA and autonomous pathway mutations but not responsiveness to vernalization. Plant Cell 13: 935-941.
49. MILLAR, A. J., 2004 Input signals to the plant circadian clock. J. Exp. Bot. 55: 277-283.
50. MOREAU, L., 1998 Contribution méthodologique et expérimentale à l'étude de la sélection assistée par marqueurs: application au maïs. Ph.D. Thesis, Institut National Agronomique, Paris-Grignon.
51. MURAKAMI, M., M. ASHIKARI, K. MIURA, T. YAMASHINO and T. MIZUNO, 2003 The evolutionarily conserved OsPRR quintet: rice pseudo-response regulators implicated in circadian rhythm. Plant Cell Physiol. 44: 1229-1236.
52. OGAS, J., 1998 Dissecting the gibberellin response pathway. Curr. Biol. 8: R165-R167.
53. PATERSON, A. H., Y. R. LIN, Z. LI, K. F. SCHERTZ, J. F. DOEBLEY et al., 1995 Convergent domestication of cereal crops by independent mutations at corresponding genetic loci. Science 269: 1714-1718.
54. PATERSON, A. H., J. E. BOWERS, D. G. PETERSON, J. C. ESTILL and B. A. CHAPMAN, 2003 Structure and evolution of cereal genomes, Curr. Opin. Genet. Dev. 13: 644-650.
55. PENG, J., D. E. RICHARDS, N. M. HARTLEY, G. P. MURPHY, K. M. DEVOS et al., 1999 'Green revolution' genes encode mutant gibberellin response modulators. Nature 400: 256-261.
56. RAGOT, M., P. H. SISCO, D. HOISINGTON and C. W. STUBER, 1995 Molecular-marker-mediated characterization of favourable exotic alleles at quantitative trait loci in maize. Crop Sci. 35: 1306-1315.
57. REBAÏ, A., P. BLANCHARD, D. PERRET and P. VINCOURT, 1997 Mapping quantitative trait loci controlling silking date in a diallel cross among four lines in maize. Theor. Appl. Genet. 95: 451-459.
58. REYMOND, M., B. MULLER, A. LEONARDI, A. CHARCOSSET and F. TARDIEU, 2003 Combining quantitative trait loci analysis and an ecophysiological model to analyze the genetic variability of the responses of maize leaf growth to temperature and water deficit. Plant Physiol. 131: 664-675.
59. RIBAUT, J.-M., D. HOISINGTON, J. A. DEUTSCH, C. JIANG and D. GONZALEZ-DE-LEON, 1996 Identification of quantitative trait loci under drought conditions in tropical maize. 1. Flowering parameters and the an thesis-silking interval. Theor. Appl. Genet. 92: 905-914.
60. SALVI, S., R. TUBEROSA, E. CHIAPPARINO, M. MACCAFERRI, S. VEILLET et al., 2002 Toward positional cloning of Vgt1, a QTL controlling the transition from the vegetative to the reproductive phase in maize. Plant Mol. Biol. 48: 601-613.
61. SIMON, R., M. I. IGENO and G. COUPLAND, 1996 Activation of floral meristem identity genes in Arabidopsis. Nature 384: 59-62.
62. STOREY, J. D., and R. TIBSHIRANI, 2003 Statistical significance for genomewide studies. Proc. Natl. Acad. Sci. USA 100: 9440-9445.
63. STUBER, C. W., S. E. LINCOLN, D. W. WOLFF, T. HELENTJARIS and E. S. LANDER, 1992 Identification of genetic factor contributing to heterosis in a hybrid from two elite maize indred lines vising molecular markers. Genetics 132: 823-839.
64. SUAREZ-LOPEZ, P., K. WHEATLEY, F. ROBSON, H. ONOUCHI, F. VALVERDE et al., 2001 CONSTANS mediates between the circadian clock and the control of flowering in Arabidopsis. Nature 410: 1116-1120.
65. TAKAHASHI, Y., A. SHOMURA, T. SASAKI and M. YANO, 2001 Hd6, a rice quantitative trait locus involved in photoperiod sensitivity, encodes the alpha subunit of protein kinase CK2. Proc. Natl. Acad. Sci. USA 98: 7922-7927.
66. TAKANO, M., H. KANEGAE, T. SHINOMURA, A. MIYAO, H. HIROCHIKA et al., 2001 Isolation and characterization of rice phytochrome A mutants. Plant Cell 13: 521-534.
67. THORNSBERRY, J. M., M. M. GOODMAN, J. F. DOEBLEY, S. KRESOVICH, D. NIELSEN et al., 2001 Dwarf8 polymorphisms associate with variation in flowering time. Nat. Genet. 28: 286-289.
68. VANDEPOELE, K., C. SIMILLION and Y. VAN DE PEER, 2003 Evidence that rice and other cereals are ancient aneuploids. Plant Cell 15: 2192-2202.
69. VAN NOCKE, S., M. MUSZYNSKI, K. BRIGGS and R. M. AMASINO, 2000 Characterization of a gene from Zea mays related to Arabidopsis flowering-time gene LUMINIDEPENDENS. Plant Mol. Biol. 44: 107-122.
70. VEGA, S. H., M. SAUER, J. A. J. ORKWISZEWSKI and R. S. POETHIG, 2002 The early phase change gene in maize. Plant Cell 14: 133-147.
71. VELDBOOM, L. R., and M. LEE, 1996 Genetic mapping of quantitative trait loci in maize in stress and nonstress environments: II. Plant height and flowering. Crop Sci. 36: 1320-1327.
72. VISSCHER, P. M., C. S. HALEY and R. D. THOMPSON, 1996 Marker-assisted introgression in backcross breeding programs. Genetics 144: 1923-1932.
73. VLADUTU, C., J. MCLAUGHLIN and R. L. PHILLIPS, 1999 Fine mapping and characterization of linked quantitative trait loci involved in the transition of the maize apical meristem from vegetative to generative structures. Genetics 153: 993-1007.
74. VOORRIPS, R. E., 2002 MapChart: software for the graphical presentation of linkage maps and QTLs. J. Hered. 93: 77-78.
75. WILSON, W. A., S. E. HARRINGTON, W. L. WOODMAN, M. LEE, M. E. SORRELLS et al., 1999 Inferences on the genome structure of progenitor maize through comparative analysis of rice, maize and the domesticated panicoids. Genetics 153: 453-473.
76. YANO, M., and T. SASAKI, 1997 Genetic and molecular dissection of quantitative traits in rice. Plant Mol. Biol. 35: 145-153.
77. YANO, M., Y. KATAYOSE, M. ASHIKARI, U. YAMANOUCHI, L. MONNA et al., 2000 Hd1, a major photoperiod sensitivity QTL in rice, is closely related to the Arabidopsis flowering time gene CONSTANS. Plant Cell 12: 2473-2483.
78. YANO, M., S. KOJIMA, Y. TAKAHASHI, H. LIN and T. SASAKI, 2001 Genetic control of flowering time in rice, a short-day plant. Plant Physiol. 127: 1425-1429.
79. YU, J., S. HU, J. WANG, G. K. WONG, S. LI et al., 2002 A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science 296: 79-92.