Recombination and linkage disequilibrium in Arabidopsis thaliana

Nature Genetics

Volumn 39, Issue 9, 2007, Pages 1151-1155

  Kim, Sung ^a   Plagnol, Vincent ^a,b   Hu, Tina T ^a   Toomajian, Christopher ^a   Clark, Richard M ^c   Ossowski, Stephan ^c   Ecker, Joseph R ^d   Weigel, Detlef ^c,d   Nordborg, Magnus ^a  

^a UNIVERSITY OF SOUTHERN CALIFORNIA   (United States)

^b UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^c MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY   (Germany)

^d SALK INSTITUTE FOR BIOLOGICAL STUDIES   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

SPACER DNA;

AFRICAN AMERICAN; ALGORITHM; ARABIDOPSIS; ARTICLE; GENE LINKAGE DISEQUILIBRIUM; GENE MAPPING; GENETIC RECOMBINATION; GENOME; GENOTYPE; NONHUMAN; PRIORITY JOURNAL; SAMPLE; SIMULATION; SINGLE NUCLEOTIDE POLYMORPHISM;

ARABIDOPSIS; CHROMOSOME MAPPING; CHROMOSOMES, PLANT; GENOME, PLANT; GENOTYPE; HAPLOTYPES; LINKAGE DISEQUILIBRIUM; MODELS, GENETIC; POLYMORPHISM, SINGLE NUCLEOTIDE; RECOMBINATION, GENETIC;

ARABIDOPSIS THALIANA;

EID: 34548016343     PISSN: 10614036     EISSN: 15461718     Source Type: Journal    
DOI: 10.1038/ng2115     Document Type: Article

References (27)

1. Clark, R.M. et al. Common sequence polymorphisms shaping genetic diversity in Arabidopsis thaliana. Science 317, 338-342 (2007).
2. Nordborg, M. et al. The pattern of polymorphism in Arabidopsis thaliana. PLoS Biol. 3, e196 (2005)(doi:10.1371/journal.pbio.0030196) .
3. Plagnol, V., Padhukasharam, B., Marjoram, P., Wall, J.D. & Nordborg, M. Relative influences of crossing-over and gene conversion on the pattern of linkage disequilibrium in Arabidopsis thaliana. Genetics 172, 2441-2448 (2006).
4. Nordborg, M. Linkage disequilibrium, gene trees, and selfing: An ancestral recombination graph with partial self-fertilization. Genetics 154, 923-929 (2000).
5. Hudson, R.R. Two-locus sample distributions and their applications. Genetics 159, 1805-1817 (2001).
6. Padhukasahasram, B., Wall, J.D., Marjoram, P. & Nordborg, M. Estimating recombination rates from single-nucleotide polymorphisms using summary statistics. Genetics 174, 1517-1528 (2006).
7. Haddrill, P.R., Thornton, K.R., Charlesworth, B. & Andolfatto, P. Multilocus patterns of nucleotide variability and the demographic and selection history of Drosophila melanogaster populations. Genome Res. 15, 790-799 (2005).
8. Przeworski, M. & Wall, J.D. Why is there so little intragenic linkage disequilibrium in humans? Genet. Res. 77, 143-151 (2001).
9. Frisse, L. et al. Gene conversion and different population histories may explain the contrast between polymorphism and linkage disequilibrium levels. Am. J. Hum. Genet. 69, 831-843 (2001).
10. Hagenblad, J. & Nordborg, M. Sequence variation and haplotype structure surrounding the flowering time locus FRI in Arabidopsis thaliana. Genetics 161, 289-298 (2002).
11. Haubold, B., Kroymann, J., Ratzka, A., Mitchell-Olds, T. & Wiehe, T. Recombination and gene conversion in a 170-kb genomic region of Arabidopsis thaliana. Genetics 161, 1269-1278 (2002).
12. Hinds, D.A. et al. Whole-genome patterns of common DNA variation in three human populations. Science 307, 1072-1079 (2005).
13. de Bakker, P.I.W. et al. Efficiency and power in genetic association studies. Nat. Genet. 37, 1217-1223 (2005).
14. Johnson, G.C. et al. Haplotype tagging for the identification of common disease genes. Nat. Genet. 29, 233-237 (2001).
15. Zondervan, K.T. & Cardon, L.R. The complex interplay among factors that influence allelic association. Nat. Rev. Genet. 5, 89-100 (2004).
16. International HapMap Consortium. A haplotype map of the human genome. Nature 437, 1299-1320 (2005).
17. Wall, J.D. & Pritchard, J.K. Haplotype blocks and linkage disequilibrium in the human genome. Nat. Rev. Genet. 4, 587-597 (2003).
18. Arnheim, N., Calabrese, P. & Nordborg, M. Hot and cold spots of recombination in the human genome: The reason we should find them and how this can be achieved. Am. J. Hum. Genet. 73, 5-16 (2003).
19. Drouaud, J. et al. Variation in crossing-over rates across chromosome4 of Arabidopsis thaliana reveals the presence of meiotic recombination hot spots. Genome Res. 16, 106-114 (2006).
20. Schmuths, H., Meister, A., Horres, R. & Bachmann, K. Genome size variation among accessions of Arabidopsis thaliana. Ann. Bot. (Lond.) 93, 317-321 (2004).
21. Nordborg, M. & Tavaré, S. Linkage disequilibrium: what history has to tell us. Trends Genet. 18, 83-90 (2002).
22. Hudson, R.R. & Kaplan, N.L. Statistical properties of the number of recombination events in the history of a sample of DNA sequences. Genetics 111, 147-164 (1985).
23. Andolfatto, P. Adaptive evolution of non-coding DNA in Drosophila. Nature 437, 1149-1152 (2005).
24. Li, N. & Stephens, M. Modeling linkage disequilibrium and identifying recombination hotspots using single-nucleotide polymorphism data. Genetics 165, 2213-2233 (2003).
25. Hudson, R.R. Generating samples under a Wright-Fisher neutral model. Bioinformatics 18, 337-338 (2002).
26. Andolfatto, P. & Nordborg, M. The effect of gene conversion on intralocus associations. Genetics 148, 1397-1399 (1998).
27. Barrett, J.C., Fry, B., Maller, J. & Daly, M.J. Haploview: analysis and visualization of LD and haplotype maps. Bioinformatics 21, 263-265 (2005).