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Genetics. 1998 Mar; 148(3): 1311–1323.
PMCID: PMC1460032

Genetic variation within and among populations of Arabidopsis thaliana.

Abstract

We investigated levels of nucleotide polymorphism within and among populations of the highly self-fertilizing Brassicaceous species, Arabidopsis thaliana. Four-cutter RFLP data were collected at one mitochondrial and three nuclear loci from 115 isolines representing 11 worldwide population collections, as well as from seven commonly used ecotypes. The collections include multiple populations from North America and Eurasia, as well as two pairs of collections from locally proximate sites, and thus allow a hierarchical geographic analysis of polymorphism. We found no variation at the mitochondrial locus Nad5 and very low levels of intrapopulation nucleotide diversity at Adh, Dhs1, and Gpa1. Interpopulation nucleotide diversity was also consistently low among the loci, averaging 0.0014. gst, a measure of population differentiation, was estimated to be 0.643. Interestingly, we found no association between geographical distance between populations and genetic distance. Most haplotypes have a worldwide distribution, suggesting a recent expansion of the species or long-distance gene flow. The low level of polymorphism found in this study is consistent with theoretical models of neutral mutations and background selection in highly self-fertilizing species.

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Selected References

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  • Hardtke CS, Müller J, Berleth T. Genetic similarity among Arabidopsis thaliana ecotypes estimated by DNA sequence comparison. Plant Mol Biol. 1996 Dec;32(5):915–922. [PubMed]
  • Holsinger KE, Mason-Gamer RJ. Hierarchical analysis of nucleotide diversity in geographically structured populations. Genetics. 1996 Feb;142(2):629–639. [PMC free article] [PubMed]
  • Hudson RR. Estimating genetic variability with restriction endonucleases. Genetics. 1982 Apr;100(4):711–719. [PMC free article] [PubMed]
  • Hudson RR, Kaplan NL. The coalescent process in models with selection and recombination. Genetics. 1988 Nov;120(3):831–840. [PMC free article] [PubMed]
  • Innan H, Tajima F, Terauchi R, Miyashita NT. Intragenic recombination in the Adh locus of the wild plant Arabidopsis thaliana. Genetics. 1996 Aug;143(4):1761–1770. [PMC free article] [PubMed]
  • Kimura M. The rate of molecular evolution considered from the standpoint of population genetics. Proc Natl Acad Sci U S A. 1969 Aug;63(4):1181–1188. [PMC free article] [PubMed]
  • Konieczny A, Ausubel FM. A procedure for mapping Arabidopsis mutations using co-dominant ecotype-specific PCR-based markers. Plant J. 1993 Aug;4(2):403–410. [PubMed]
  • Kreitman M, Aguadé M. Genetic uniformity in two populations of Drosophila melanogaster as revealed by filter hybridization of four-nucleotide-recognizing restriction enzyme digests. Proc Natl Acad Sci U S A. 1986 May;83(10):3562–3566. [PMC free article] [PubMed]
  • Kreitman ME, Aguadé M. Excess polymorphism at the Adh locus in Drosophila melanogaster. Genetics. 1986 Sep;114(1):93–110. [PMC free article] [PubMed]
  • Kreitman M, Hudson RR. Inferring the evolutionary histories of the Adh and Adh-dup loci in Drosophila melanogaster from patterns of polymorphism and divergence. Genetics. 1991 Mar;127(3):565–582. [PMC free article] [PubMed]
  • Langley CH, MacDonald J, Miyashita N, Aguadé M. Lack of correlation between interspecific divergence and intraspecific polymorphism at the suppressor of forked region in Drosophila melanogaster and Drosophila simulans. Proc Natl Acad Sci U S A. 1993 Mar 1;90(5):1800–1803. [PMC free article] [PubMed]
  • Smith JM, Haigh J. The hitch-hiking effect of a favourable gene. Genet Res. 1974 Feb;23(1):23–35. [PubMed]
  • Berry AJ, Ajioka JW, Kreitman M. Lack of polymorphism on the Drosophila fourth chromosome resulting from selection. Genetics. 1991 Dec;129(4):1111–1117. [PMC free article] [PubMed]
  • Nei M, Takahata N. Effective population size, genetic diversity, and coalescence time in subdivided populations. J Mol Evol. 1993 Sep;37(3):240–244. [PubMed]
  • Chang C, Bowman JL, DeJohn AW, Lander ES, Meyerowitz EM. Restriction fragment length polymorphism linkage map for Arabidopsis thaliana. Proc Natl Acad Sci U S A. 1988 Sep;85(18):6856–6860. [PMC free article] [PubMed]
  • Nordborg M. Structured coalescent processes on different time scales. Genetics. 1997 Aug;146(4):1501–1514. [PMC free article] [PubMed]
  • Chang C, Bowman JL, DeJohn AW, Lander ES, Meyerowitz EM. Restriction fragment length polymorphism linkage map for Arabidopsis thaliana. Proc Natl Acad Sci U S A. 1988 Sep;85(18):6856–6860. [PMC free article] [PubMed]
  • Charlesworth B, Morgan MT, Charlesworth D. The effect of deleterious mutations on neutral molecular variation. Genetics. 1993 Aug;134(4):1289–1303. [PMC free article] [PubMed]
  • Nordborg M, Donnelly P. The coalescent process with selfing. Genetics. 1997 Jul;146(3):1185–1195. [PMC free article] [PubMed]
  • Ohta T. Linkage disequilibrium due to random genetic drift in finite subdivided populations. Proc Natl Acad Sci U S A. 1982 Mar;79(6):1940–1944. [PMC free article] [PubMed]
  • Church GM, Gilbert W. Genomic sequencing. Proc Natl Acad Sci U S A. 1984 Apr;81(7):1991–1995. [PMC free article] [PubMed]
  • Cocciolone SM, Cone KC. Pl-Bh, an anthocyanin regulatory gene of maize that leads to variegated pigmentation. Genetics. 1993 Oct;135(2):575–588. [PMC free article] [PubMed]
  • Rédei GP. Arabidopsis as a genetic tool. Annu Rev Genet. 1975;9:111–127. [PubMed]
  • Colosi JC, Schaal BA. Tissue grinding with ball bearings and vortex mixer for DNA extraction. Nucleic Acids Res. 1993 Feb 25;21(4):1051–1052. [PMC free article] [PubMed]
  • Golding GB, Strobeck C. Linkage disequilibrium in a finite population that is partially selfing. Genetics. 1980 Mar;94(3):777–789. [PMC free article] [PubMed]
  • Rose AB, Li J, Last RL. An allelic series of blue fluorescent trp1 mutants of Arabidopsis thaliana. Genetics. 1997 Jan;145(1):197–205. [PMC free article] [PubMed]
  • Wakeley J. Distinguishing migration from isolation using the variance of pairwise differences. Theor Popul Biol. 1996 Jun;49(3):369–386. [PubMed]
  • Wayne ML, Kreitman M. Reduced variation at concertina, a heterochromatic locus in Drosophila. Genet Res. 1996 Oct;68(2):101–108. [PubMed]
  • Wolfe KH, Li WH, Sharp PM. Rates of nucleotide substitution vary greatly among plant mitochondrial, chloroplast, and nuclear DNAs. Proc Natl Acad Sci U S A. 1987 Dec;84(24):9054–9058. [PMC free article] [PubMed]
  • Vos P, Hogers R, Bleeker M, Reijans M, van de Lee T, Hornes M, Frijters A, Pot J, Peleman J, Kuiper M, et al. AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res. 1995 Nov 11;23(21):4407–4414. [PMC free article] [PubMed]

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