The lowdown on linkage disequilibrium

Plant Cell

Volumn 15, Issue 7, 2003, Pages 1502-1506

  Gaut, Brandon S ^a   Long, Anthony D ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARABIDOPSIS; ZEA MAYS;

EID: 0037705665     PISSN: 10404651     EISSN: None     Source Type: Journal    
DOI: 10.1105/tpc.150730     Document Type: Editorial

References (27)

1. Charlesworth, B., and Charlesworth, D. (1979). The evolutionary genetics of sexual systems in flowering plants. Proc. R. Soc. Lond. Ser. B Biol. Sci. 205, 513-530.
2. Ching, A., Caldwell, K.S., Jung, M., Dolan, M., Smith, O.S., Tingey, S., Morgante, M., and Rafalski, A.J. (2002). SNP frequency, haplotype structure and linkage disequilibrium in elite maize inbred lines. BMC Genet. 8, 19-33.
3. El-Assal, S.E., Alonso-Blanco, C., Peeters, A.J.M., Raz, V., and Koornneef, M. (2001). A QTL for flowering time in Arabidopsis reveals a novel allele of CRY2. Nat. Genet. 29, 435-440.
4. Fearnhead, P., and Donnelly, P. (2001). Estimating recombination rates from population genetic data. Genetics 159, 1299-1318.
5. Fu, H.H., Zheng, Z.W., and Dooner, H.K. (2002). Recombination rates between adjacent genic and retrotransposon regions in maize vary by 2 orders of magnitude. Proc. Natl. Acad. Sci. USA 99, 1082-1087.
6. Hagenblad, J., and Nordborg, M. (2002). Sequence variation and haplotype structure surrounding the flowering time locus FRI in Arabidopsis thaliana. Genetics 61, 289-298.
7. Hill, W.G., and Robertson, A. (1968). Linkage disequilibrium in finite populations. Theor. Appl. Genet. 38, 226-231.
8. Hudson, R.R. (2001). Two-locus sampling distributions and their application. Genetics 159, 1805-1817.
9. Jeffreys, A.J., Kauppi, L., and Neumann, R. (2001). Intensely punctate meiotic recombination in the class II region of the major histocompatibility complex. Nat. Genet. 29, 217-222.
10. Lai, C.G., Lyman, R.F., Long, A.D., Langley, C.H., and Mackay, T.F.C. (1994). Naturally occurring variation in bristle number and DNA polymorphisms at the scabrous locus of Drosophila melanogaster. Science 266, 1697-1702.
11. Lander, E.S., and Schork, N.J. (1994). Genetic dissection of complex traits. Science 265, 2037-2048.
12. Lewontin, R.C. (1964). The interaction of selection and linkage. I. General considerations; heterotic models. Genetics 49, 49-67.
13. Long, A.D., and Langley, C.H. (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., Lyman, R.F., Langley, C.H., and Mackay, T.F.C. (1998). Two sites in the Delta gene region contribute to naturally occurring variation in bristle number in Drosophila melanogaster. Genetics 149, 999-1017.
15. Matsuoka, Y., Vigouroux, Y., Goodman, M.M., Sanchez, J., Buckler, E., and Doebley, J. (2002). A single domestication for maize shown by multilocus microsatellite genotyping. Proc. Natl. Acad. Sci. USA 99, 6080-6084.
16. Nordborg, M., Borevitz, J.O., Bergelson, J., Berry, C.C., Chory, J., Hagenblad, J., Kreitman, M., Maloof, J.N., Noyes, T., Oefner, P.J., Stahl, E.A., and Weigel, D. (2002). The extent of linkage disequilibrium in Arabidopsis thaliana. Nat. Genet. 30, 190-193.
17. Pritchard, J.K., and Przeworski, M. (2001). Linkage disequilibrium in humans: Models and data. Am. J. Hum. Genet. 69, 1-14.
18. Pritchard, J.K., Stephens, M., Rosenberg, N.A., and Donnelly, P. (2000). Association mapping in structured populations. Am. J. Hum. Genet. 67, 170-181.
19. Przeworski, M. (2002). The signature of positive selection at randomly chosen loci. Genetics 160, 1179-1189.
20. Remington, D.L., Thornsberry, J.M., Malsuoka, Y., Wilson, L.M., Whitt, S.R., Doebley, J., Kresovich, S., Goodman, M.M., and Buckler, E.S. (2001). Structure of linkage disequilibrium and phenotypic associations in the maize genome. Proc. Natl. Acad. Sci. USA 98, 11479-11484.
21. Shepard, K.A., and Purugganan, M.D. (2003). Molecular population genetics of the Arabidopsis CLAVATA2 region: The genomic scale of variation and selection in a selfing species. Genetics 263, 1083-1095.
22. Tenaillon, M., Sawkins, M.C., Long, A.D., Gaul, R.L., Doebley, J.F., and Gaul, B.S. (2001). Patterns of DNA sequence polymorphism along chromosome 1 of maize (Zea mays ssp. mays L.). Proc. Natl. Acad. Sci. USA 98, 9161-9166.
23. Tenaillon, M.I., Sawkins, M.C., Anderson, L.K., Stack, S.M., Doebley, J., and Gaut, B.S. (2002). Patterns of diversity and recombination along chromosome 1 of maize (Zea mays ssp. mays L.). Genetics 162, 1401-1413.
24. Thornsberry, J.M., Goodman, M.M., Doebley, J., Kresovich, S., Nielsen, D., and Buckler, E.S. (2001). Dwarf8 polymorphisms associate with variation in flowering time. Nat. Genet. 28, 286-289.
25. Tian, D., Araki, H., Stahl, E.A., Bergelson, J., and Kreitman, M. (2002). Signature of balancing selection in Arabidopsis. Proc. Natl. Acad. Sci. USA 99, 11525-11530.
26. Wall, J.D., Andolfatto, P., and Przeworski, M. (2002). Testing models of selection and demography in Drosophila simulans. Genetics 162, 203-216.
27. Whitt, S.R., Wilson, L.M., Tenaillon, M.I., Gaut, B.S., and Buckler, E.S. (2002). Genetic diversity and selection in the maize starch pathway. Proc. Natl. Acad. Sci. USA 99, 12959-12962.