Skip to main content
PMC home page
Genetics logoLink to Genetics
. 2000 Jun;155(2):863–872. doi: 10.1093/genetics/155.2.863

Nucleotide variation at the CHALCONE ISOMERASE locus in Arabidopsis thaliana.

H Kuittinen 1, M Aguadé 1
PMCID: PMC1461127  PMID: 10835405

Abstract

An approximately 1.9-kb region encompassing the CHI gene, which encodes chalcone isomerase, was sequenced in 24 worldwide ecotypes of Arabidopsis thaliana (L.) Heynh. and in 1 ecotype of A. lyrata ssp. petraea. There was no evidence for dimorphism at the CHI region. A minimum of three recombination events was inferred in the history of the sampled ecotypes of the highly selfing A. thaliana. The estimated nucleotide diversity theta(TOTAL) = 0.004, theta(SIL) = 0. 005 was on the lower part of the range of the corresponding estimates for other gene regions. The skewness of the frequency spectrum toward an excess of low-frequency polymorphisms, together with the bell-shaped distribution of pairwise nucleotide differences at CHI, suggests that A. thaliana has recently experienced a rapid population growth. Although this pattern could also be explained by a recent selective sweep at the studied region, results from the other studied loci and from an AFLP survey seem to support the expansion hypothesis. Comparison of silent polymorphism and divergence at the CHI region and at the Adh1 and ChiA revealed in some cases a significant deviation of the direct relationship predicted by the neutral theory, which would be compatible with balancing selection acting at the latter regions.

Full Text

The Full Text of this article is available as a PDF (174.0 KB).

Selected References

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

  1. Charlesworth B., Morgan M. T., Charlesworth D. The effect of deleterious mutations on neutral molecular variation. Genetics. 1993 Aug;134(4):1289–1303. doi: 10.1093/genetics/134.4.1289. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Cummings M. P., Clegg M. T. Nucleotide sequence diversity at the alcohol dehydrogenase 1 locus in wild barley (Hordeum vulgare ssp. spontaneum): an evaluation of the background selection hypothesis. Proc Natl Acad Sci U S A. 1998 May 12;95(10):5637–5642. doi: 10.1073/pnas.95.10.5637. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Fu Y. X., Li W. H. Statistical tests of neutrality of mutations. Genetics. 1993 Mar;133(3):693–709. doi: 10.1093/genetics/133.3.693. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Griffing B. Genetic analysis of plant mixtures. Genetics. 1989 Aug;122(4):943–956. doi: 10.1093/genetics/122.4.943. [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. Harpending H. C. Signature of ancient population growth in a low-resolution mitochondrial DNA mismatch distribution. Hum Biol. 1994 Aug;66(4):591–600. [PubMed] [Google Scholar]
  7. Hedrick P. W. Hitchhiking: a comparison of linkage and partial selfing. Genetics. 1980 Mar;94(3):791–808. doi: 10.1093/genetics/94.3.791. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Hudson R. R., Bailey K., Skarecky D., Kwiatowski J., Ayala F. J. Evidence for positive selection in the superoxide dismutase (Sod) region of Drosophila melanogaster. Genetics. 1994 Apr;136(4):1329–1340. doi: 10.1093/genetics/136.4.1329. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Hudson R. R. Estimating the recombination parameter of a finite population model without selection. Genet Res. 1987 Dec;50(3):245–250. doi: 10.1017/s0016672300023776. [DOI] [PubMed] [Google Scholar]
  10. 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]
  11. Hudson R. R., Kreitman M., Aguadé M. A test of neutral molecular evolution based on nucleotide data. Genetics. 1987 May;116(1):153–159. doi: 10.1093/genetics/116.1.153. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. 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]
  13. Kawabe A., Innan H., Terauchi R., Miyashita N. T. Nucleotide polymorphism in the acidic chitinase locus (ChiA) region of the wild plant Arabidopsis thaliana. Mol Biol Evol. 1997 Dec;14(12):1303–1315. doi: 10.1093/oxfordjournals.molbev.a025740. [DOI] [PubMed] [Google Scholar]
  14. 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]
  15. Kuittinen H., Mattila A., Savolainen O. Genetic variation at marker loci and in quantitative traits in natural populations of Arabidopsis thaliana. Heredity (Edinb) 1997 Aug;79(Pt 2):144–152. doi: 10.1038/hdy.1997.137. [DOI] [PubMed] [Google Scholar]
  16. Li J., Ou-Lee T. M., Raba R., Amundson R. G., Last R. L. Arabidopsis Flavonoid Mutants Are Hypersensitive to UV-B Irradiation. Plant Cell. 1993 Feb;5(2):171–179. doi: 10.1105/tpc.5.2.171. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. McDonald J. H., Kreitman M. Adaptive protein evolution at the Adh locus in Drosophila. Nature. 1991 Jun 20;351(6328):652–654. doi: 10.1038/351652a0. [DOI] [PubMed] [Google Scholar]
  18. Miyashita N. T., Kawabe A., Innan H. DNA variation in the wild plant Arabidopsis thaliana revealed by amplified fragment length polymorphism analysis. Genetics. 1999 Aug;152(4):1723–1731. doi: 10.1093/genetics/152.4.1723. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Moriyama E. N., Powell J. R. Intraspecific nuclear DNA variation in Drosophila. Mol Biol Evol. 1996 Jan;13(1):261–277. doi: 10.1093/oxfordjournals.molbev.a025563. [DOI] [PubMed] [Google Scholar]
  20. Pollak E. On the theory of partially inbreeding finite populations. I. Partial selfing. Genetics. 1987 Oct;117(2):353–360. doi: 10.1093/genetics/117.2.353. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Purugganan M. D., Suddith J. I. Molecular population genetics of floral homeotic loci. Departures from the equilibrium-neutral model at the APETALA3 and PISTILLATA genes of Arabidopsis thaliana. Genetics. 1999 Feb;151(2):839–848. doi: 10.1093/genetics/151.2.839. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Purugganan M. D., Suddith J. I. Molecular population genetics of the Arabidopsis CAULIFLOWER regulatory gene: nonneutral evolution and naturally occurring variation in floral homeotic function. Proc Natl Acad Sci U S A. 1998 Jul 7;95(14):8130–8134. doi: 10.1073/pnas.95.14.8130. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Rogers A. R., Harpending H. Population growth makes waves in the distribution of pairwise genetic differences. Mol Biol Evol. 1992 May;9(3):552–569. doi: 10.1093/oxfordjournals.molbev.a040727. [DOI] [PubMed] [Google Scholar]
  24. Rozas J., Rozas R. DnaSP version 2.0: a novel software package for extensive molecular population genetics analysis. Comput Appl Biosci. 1997 Jun;13(3):307–311. [PubMed] [Google Scholar]
  25. Savolainen O., Langley C. H., Lazzaro B. P., Fr H. Contrasting patterns of nucleotide polymorphism at the alcohol dehydrogenase locus in the outcrossing Arabidopsis lyrata and the selfing Arabidopsis thaliana. Mol Biol Evol. 2000 Apr;17(4):645–655. doi: 10.1093/oxfordjournals.molbev.a026343. [DOI] [PubMed] [Google Scholar]
  26. 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]
  27. Ullrich H., Lättig K., Brennicke A., Knoop V. Mitochondrial DNA variations and nuclear RFLPs reflect different genetic similarities among 23 Arabidopsis thaliana ecotypes. Plant Mol Biol. 1997 Jan;33(1):37–45. doi: 10.1023/a:1005720910028. [DOI] [PubMed] [Google Scholar]

Articles from Genetics are provided here courtesy of Oxford University Press

RESOURCES