Haplotype structure and phenotypic associations in the chromosomal regions surrounding two Arabidopsis thaliana flowering time loci

Genetics

Volumn 168, Issue 3, 2004, Pages 1627-1638

  Hagenblad, Jenny ^a,d   Tang, Chunlao ^a   Molitor, John ^a   Werner, Jonathan ^b   Zhao, Keyan ^a   Zheng, Honggang ^a   Marjoram, Paul ^a   Weigel, Detlef ^b,c   Nordborg, Magnus ^a  

^a UNIVERSITY OF SOUTHERN CALIFORNIA   (United States)

^b SALK INSTITUTE FOR BIOLOGICAL STUDIES   (United States)

^c MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY   (Germany)

^d UNIVERSITY OF EDINBURGH   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ALLELE; ARABIDOPSIS; ARTICLE; BAYES THEOREM; FLOWERING; GENE LINKAGE DISEQUILIBRIUM; GENE LOCUS; GENE MAPPING; GENETIC ASSOCIATION; GENETIC VARIABILITY; GENOME; HAPLOTYPE; MARKER GENE; NONHUMAN; PHENOTYPE; PLANT CHROMOSOME; PLANT GENETICS; POLYMORPHIC LOCUS; POPULATION STRUCTURE; PRIORITY JOURNAL;

ARABIDOPSIS; CHROMOSOME MAPPING; CHROMOSOMES; FLOWERS; GENETIC MARKERS; HAPLOTYPES; LINKAGE (GENETICS); MOLECULAR SEQUENCE DATA; PHENOTYPE; POLYMORPHISM, GENETIC;

ARABIDOPSIS; ARABIDOPSIS THALIANA;

EID: 10844255772     PISSN: 00166731     EISSN: None     Source Type: Journal    
DOI: 10.1534/genetics.104.029470     Document Type: Article

References (36)

1. BOREVITZ, J. O., and M. NORDBORG, 2003 The impact of genomics on the study of natural variation in Arabidopsis. Plant Physiol. 132: 718-725.
2. CARDON, L. R., and G. R. ABECASIS, 2003 Using haplotype blocks to map human complex trait loci. Trends Genet. 19: 135-140.
3. DE LUCA, M., N. V. ROSHINA, G. L. GEIGER-THORNSBERRY, R. F. LYMAN, E. G. PASYUKOVA et al., 2003 Dopa decarboxylase (Ddc) affects variation in Drosophila longevity. Nat. Genet. 34: 429-433.
4. DEVLIN, B., and K. ROEDER, 1999 Genomic control for association studies. Biometrics 55: 997-1004.
5. EWENS, W. J., and R. S. SPIELMAN, 1995 The transmission/disequilibrium test: history, subdivision, and admixture. Am. J. Hum. Genet. 57: 455-464.
6. GAZZANI, S., A. R. GENDALL, C. LISTER and C. DEAN, 2003 Analysis of the molecular basis of flowering time variation in Arabidopsis accessions. Plant Physiol. 132: 1107-1114.
7. HAGENBLAD, J., and M. NORDBORG, 2002 Sequence variation and haplotype structure surrounding the flowering time locus FRI in Arabidopsis thaliana. Genetics 161: 289-298.
8. INTERNATIONAL HAPMAP CONSORTIUM, 2003 The international hapmap project. Nature 426: 789-796.
9. JOHANSON, U., J. WEST, C. LISTER, S. MICHAELS, R. AMASINO et al., 2000 Molecular analysis of FRIGIDA, a major determinant of natural variation in Arabidopsis flowering time. Science 290: 344-347.
10. LAM, J. C., K. ROEDER and B. DEVLIN, 2000 Haplotype fine mapping by evolutionary trees. Am. J. Hum. Genet. 66: 659-673.
11. LE CORRE, V., F. ROUX and X. REBOUD, 2002 DNA polymorphism at the FRIGIDA gene in Arabidopsis thaliana: extensive nonsynonymous variation is consistent with local selection for flowering time. Mol. Biol. Evol. 19: 1261-1271.
12. LIU, J. S., C. SABATTI, J. TENG, B. J. B. KEATS and N. RISCH, 2001 Bayesian analysis of haplotypes for linkage disequilibrium mapping. Genome Res. 11: 1716-1724.
13. LONG, A. D., and C. H. LANGLEY, 1999 The power of association studies to detect the contribution of candidate genetic loci to variation in complex traits. Genome Res. 9: 720-731.
14. LONG, A. D., R. F. LYMAN, C. H. LANGLEY and T. F. C. MACKAY, 1998 Two sites in the Delta gene region contribute to naturally occurring variation in bristle number in Drosophila melanogaster. Genetics 149: 999-1017.
15. LU, X., T. NIU and J. S. LIU, 2003 Haplotype information and linkage disequilibrium mapping for single nucleotide polymorphisms. Genome Res. 13: 2112-2117.
16. MCPEEK, M. S., and A. STRAHS, 1999 Assessment of linkage disequilibrium by the decay of haplotype sharing, with application to fine-scale genetic mapping. Am. J. Hum. Genet. 65: 858-875.
17. MICHAELS, S. D., and R. M. AMASINO, 1999 FLOWERING LOCUS C encodes a novel MADS domain protein that acts as a repressor of flowering. Plant Cell 11: 949-956.
18. MICHAELS, S. D., Y. HE, K. C. SCORTECCI and R. M. AMASINO, 2003 Attenuation of FLOWERING LOCUS C activity as a mechanism for the evolution of summer-annual flowering behavior in Arabidopsis. Proc. Natl. Acad. Sci. USA 100: 10102-10107.
19. MOLITOR, J., P. MARJORAM and D. THOMAS, 2003a Application of Bayesian spatial statistics methods to analysis of haplotypes effects and gene mapping. Genet. Epidemiol. 25: 95-105.
20. MOLITOR, J., P. MARJORAM and D. THOMAS, 2003b Fine-scale mapping of disease genes with multiple mutations via spatial clustering techniques. Am. J. Hum. Genet. 73: 1368-1384.
21. MORRIS, A. P., J. C. WHITTAKER, C.-F. XU, L. K. HOSKING and D. J. BALDING, 2003 Multipoint linkage-disequilibrium mapping narrows location interval and identifies mutation heterogeneity. Proc. Natl. Acad. Sci. USA 100: 13442-13446.
22. NORDBORG, M., 2000 Linkage disequilibrium, gene trees, and selfing: an ancestral recombination graph with partial self-fertilization. Genetics 154: 923-929.
23. NORDBORG, M., and S. TAVARÉ, 2002 Linkage disequilibrium: what history has to tell us. Trends Genet. 18: 83-90.
24. NORDBORG, M., J. O. BOREVITZ, J. BERGELSON, C. C. BERRY, J. CHORY et al., 2002 The extent of linkage disequilibrium in Arabidopsis thaliana. Nat. Genet. 30: 190-193.
25. PATIL, N., A. J. BERNO, D. A. HINDS, W. A. BARRETT, J. M. DOSHI et al., 2001 Blocks of limited haplotype diversity revealed by high-resolution scanning of human chromosome 21. Science 294: 1719-1723.
26. PRITCHARD, J. K., and N. A. ROSENBERG, 1999 Use of unlinked genetic markers to detect population stratification in association studies. Am. J. Hum. Genet. 65: 220-228.
27. PRITCHARD, J. K., M. STEPHENS, N. A. ROSENBERG and P. DONNELLY, 2000 Association mapping in structured populations. Am. J. Hum. Genet. 67: 170-181.
28. PTAK, S. E., and M. PRZEWORSKI, 2002 Evidence for population growth in humans is confounded by fine-scale population structure. Trends Genet 18: 559-563.
29. RANNALA, B., and J. P. REEVE, 2001 High-resolution multipoint linkage-disequilibrium mapping in the context of the human genome sequence. Am. J. Hum. Genet. 69: 159-178.
30. SANDA, S. L., M. JOHN and R. M. AMASINO, 1997 Analysis of flowering time in ecotypes of Arabidopsis thaliana. J. Hered. 88: 69-72.
31. SERVICE, S. K., D. W. TEMPLE LANG, N. B. FREIMER and L. A. SANDKUIJL, 1999 Linkage-disequilibrium mapping of disease genes by reconstruction of ancestral haplotypes in founder populations. Am. J. Hum. Genet. 64: 1728-1738.
32. SHELDON, C. C., J. E. BURN, P. P. PEREZ, J. METZGER, J. A. EDWARDS et al., 1999 The FLF MADS box gene: a repressor of flowering in Arabidopsis regulated by vernalization and methylation. Plant Cell 11: 445-458.
33. SIEGEL, S., and N. J. CASTELLAN, JR., 1988 Nonparametric Statistics for the Behavioral Sciences, Vol. 2. McGraw-Hill, New York.
34. TOIVONEN, H. T. T., P. ONKAMO, K. VASKO, V. OLLIKAINEN, P. SEVON et al., 2000 Data mining applied to linkage disequilibrium mapping. Am. J. Hum. Genet. 67: 133-145.
35. WEISS, K. M., and A. G. CLARK, 2002 Linkage disequilibrium and the mapping of complex human traits. Trends Genet. 18: 19-24.
36. ZONDERVAN, K. T., and L. R. CARDON, 2004 The complex interplay among factors that influence allelic association. Nat. Rev. Genet. 5: 89-100.