Skip to main content
NCBI home page
Genetics logoLink to Genetics
. 2002 May;161(1):289–298. doi: 10.1093/genetics/161.1.289

Sequence variation and haplotype structure surrounding the flowering time locus FRI in Arabidopsis thaliana.

Jenny Hagenblad 1, Magnus Nordborg 1
PMCID: PMC1462079  PMID: 12019242

Abstract

Linkage disequilibrium in highly selfing organisms is expected to extend well beyond the scale of individual genes. The pattern of polymorphism in such species must thus be studied over a larger scale. We sequenced 14 short (0.5-1 kb) fragments from a 400-kb region surrounding the flowering time locus FRI in a sample of 20 accessions of Arabidopsis thaliana. The distribution of allele frequencies, as quantified by Tajima's D, varies considerably over the region and is incompatible with a standard neutral model. The region is characterized by extensive haplotype structure, with linkage disequilibrium decaying over 250 kb. In particular, recombination is evident within 35 kb of FRI in a haplotype associated with a functionally important allele. This suggests that A. thaliana may be highly suitable for linkage disequilibrium mapping.

Full Text

The Full Text of this article is available as a PDF (370.3 KB).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Altshuler D., Daly M., Kruglyak L. Guilt by association. Nat Genet. 2000 Oct;26(2):135–137. doi: 10.1038/79839. [DOI] [PubMed] [Google Scholar]
  2. Andolfatto P., Nordborg M. The effect of gene conversion on intralocus associations. Genetics. 1998 Mar;148(3):1397–1399. doi: 10.1093/genetics/148.3.1397. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Bergelson J., Stahl E., Dudek S., Kreitman M. Genetic variation within and among populations of Arabidopsis thaliana. Genetics. 1998 Mar;148(3):1311–1323. doi: 10.1093/genetics/148.3.1311. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Gillespie J. H. Genetic drift in an infinite population. The pseudohitchhiking model. Genetics. 2000 Jun;155(2):909–919. doi: 10.1093/genetics/155.2.909. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Hanfstingl U., Berry A., Kellogg E. A., Costa J. T., 3rd, Rüdiger W., Ausubel F. M. Haplotypic divergence coupled with lack of diversity at the Arabidopsis thaliana alcohol dehydrogenase locus: roles for both balancing and directional selection? Genetics. 1994 Nov;138(3):811–828. doi: 10.1093/genetics/138.3.811. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Hudson R. R., Kaplan N. L. Statistical properties of the number of recombination events in the history of a sample of DNA sequences. Genetics. 1985 Sep;111(1):147–164. doi: 10.1093/genetics/111.1.147. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Innan H., Tajima F., Terauchi R., Miyashita N. T. Intragenic recombination in the Adh locus of the wild plant Arabidopsis thaliana. Genetics. 1996 Aug;143(4):1761–1770. doi: 10.1093/genetics/143.4.1761. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Jakobsen I. B., Easteal S. A program for calculating and displaying compatibility matrices as an aid in determining reticulate evolution in molecular sequences. Comput Appl Biosci. 1996 Aug;12(4):291–295. doi: 10.1093/bioinformatics/12.4.291. [DOI] [PubMed] [Google Scholar]
  9. Johanson U., West J., Lister C., Michaels S., Amasino R., Dean C. Molecular analysis of FRIGIDA, a major determinant of natural variation in Arabidopsis flowering time. Science. 2000 Oct 13;290(5490):344–347. doi: 10.1126/science.290.5490.344. [DOI] [PubMed] [Google Scholar]
  10. Kawabe A., Miyashita N. T. DNA variation in the basic chitinase locus (ChiB) region of the wild plant Arabidopsis thaliana. Genetics. 1999 Nov;153(3):1445–1453. doi: 10.1093/genetics/153.3.1445. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Kreitman M. Methods to detect selection in populations with applications to the human. Annu Rev Genomics Hum Genet. 2000;1:539–559. doi: 10.1146/annurev.genom.1.1.539. [DOI] [PubMed] [Google Scholar]
  12. Kruglyak L. Prospects for whole-genome linkage disequilibrium mapping of common disease genes. Nat Genet. 1999 Jun;22(2):139–144. doi: 10.1038/9642. [DOI] [PubMed] [Google Scholar]
  13. Langley C. H., Lazzaro B. P., Phillips W., Heikkinen E., Braverman J. M. Linkage disequilibria and the site frequency spectra in the su(s) and su(w(a)) regions of the Drosophila melanogaster X chromosome. Genetics. 2000 Dec;156(4):1837–1852. doi: 10.1093/genetics/156.4.1837. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Long A. D., Langley C. H. The power of association studies to detect the contribution of candidate genetic loci to variation in complex traits. Genome Res. 1999 Aug;9(8):720–731. [PMC free article] [PubMed] [Google Scholar]
  15. Long A. D., Lyman R. F., Langley C. H., Mackay T. F. Two sites in the Delta gene region contribute to naturally occurring variation in bristle number in Drosophila melanogaster. Genetics. 1998 Jun;149(2):999–1017. doi: 10.1093/genetics/149.2.999. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Michaels S. D., Amasino R. M. FLOWERING LOCUS C encodes a novel MADS domain protein that acts as a repressor of flowering. Plant Cell. 1999 May;11(5):949–956. doi: 10.1105/tpc.11.5.949. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Morris A. P., Whittaker J. C., Balding D. J. Bayesian fine-scale mapping of disease loci, by hidden Markov models. Am J Hum Genet. 2000 Jun 1;67(1):155–169. doi: 10.1086/302956. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Nordborg M., Bergelson J. The effect of seed and rosette cold treatment on germination and flowering time in some Arabidopsis thaliana (Brassicaceae) ecotypes. Am J Bot. 1999 Apr;86(4):470–475. [PubMed] [Google Scholar]
  19. Nordborg M. Linkage disequilibrium, gene trees and selfing: an ancestral recombination graph with partial self-fertilization. Genetics. 2000 Feb;154(2):923–929. doi: 10.1093/genetics/154.2.923. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Nordborg Magnus, Borevitz Justin O., Bergelson Joy, Berry Charles C., Chory Joanne, Hagenblad Jenny, Kreitman Martin, Maloof Julin N., Noyes Tina, Oefner Peter J. The extent of linkage disequilibrium in Arabidopsis thaliana. Nat Genet. 2002 Jan 7;30(2):190–193. doi: 10.1038/ng813. [DOI] [PubMed] [Google Scholar]
  21. Nordborg Magnus, Tavaré Simon. Linkage disequilibrium: what history has to tell us. Trends Genet. 2002 Feb;18(2):83–90. doi: 10.1016/s0168-9525(02)02557-x. [DOI] [PubMed] [Google Scholar]
  22. Sanda S., John M., Amasino R. Analysis of flowering time in ecotypes of Arabidopsis thaliana. J Hered. 1997 Jan-Feb;88(1):69–72. doi: 10.1093/oxfordjournals.jhered.a023061. [DOI] [PubMed] [Google Scholar]
  23. Sharbel T. F., Haubold B., Mitchell-Olds T. Genetic isolation by distance in Arabidopsis thaliana: biogeography and postglacial colonization of Europe. Mol Ecol. 2000 Dec;9(12):2109–2118. doi: 10.1046/j.1365-294x.2000.01122.x. [DOI] [PubMed] [Google Scholar]
  24. Sheldon C. C., Burn J. E., Perez P. P., Metzger J., Edwards J. A., Peacock W. J., Dennis E. S. The FLF MADS box gene: a repressor of flowering in Arabidopsis regulated by vernalization and methylation. Plant Cell. 1999 Mar;11(3):445–458. doi: 10.1105/tpc.11.3.445. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Smith J. M. The detection and measurement of recombination from sequence data. Genetics. 1999 Oct;153(2):1021–1027. doi: 10.1093/genetics/153.2.1021. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Tajima F. Evolutionary relationship of DNA sequences in finite populations. Genetics. 1983 Oct;105(2):437–460. doi: 10.1093/genetics/105.2.437. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Tajima F. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics. 1989 Nov;123(3):585–595. doi: 10.1093/genetics/123.3.585. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Templeton A. R., Clark A. G., Weiss K. M., Nickerson D. A., Boerwinkle E., Sing C. F. Recombinational and mutational hotspots within the human lipoprotein lipase gene. Am J Hum Genet. 2000 Jan;66(1):69–83. doi: 10.1086/302699. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Thornsberry J. M., Goodman M. M., Doebley J., Kresovich S., Nielsen D., Buckler E. S., 4th Dwarf8 polymorphisms associate with variation in flowering time. Nat Genet. 2001 Jul;28(3):286–289. doi: 10.1038/90135. [DOI] [PubMed] [Google Scholar]
  30. Toivonen H. T., Onkamo P., Vasko K., Ollikainen V., Sevon P., Mannila H., Herr M., Kere J. Data mining applied to linkage disequilibrium mapping. Am J Hum Genet. 2000 Jun 9;67(1):133–145. doi: 10.1086/302954. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Weiss K. M., Terwilliger J. D. How many diseases does it take to map a gene with SNPs? Nat Genet. 2000 Oct;26(2):151–157. doi: 10.1038/79866. [DOI] [PubMed] [Google Scholar]

Articles from Genetics are provided here courtesy of Oxford University Press

RESOURCES