Methods for linkage disequilibrium mapping in crops

Trends in Plant Science

Volumn 12, Issue 2, 2007, Pages 57-63

  Mackay, Ian ^a   Powell, Wayne ^a  

^a NATIONAL INSTITUTE OF AGRICULTURAL BOTANY   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

CHROMOSOME MAP; CROP; GENE LINKAGE DISEQUILIBRIUM; GENETIC MARKER; GENETICS; GENOME; HAPLOTYPE; METHODOLOGY; QUANTITATIVE TRAIT LOCUS; REVIEW; STATISTICAL MODEL;

CHROMOSOME MAPPING; CROPS, AGRICULTURAL; GENETIC MARKERS; GENOME, PLANT; HAPLOTYPES; LINKAGE DISEQUILIBRIUM; LOGISTIC MODELS; QUANTITATIVE TRAIT LOCI;

EID: 33846933954     PISSN: 13601385     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.tplants.2006.12.001     Document Type: Review

References (44)

1. Bodmer W.F. Human genetics: the molecular challenge. Cold Spring Harb. Symp. Quant. Biol. 51 (1986) 1-13
2. Duggan D., et al. Recent developments in genomewide association scans: a workshop summary and review. Am. J. Hum. Genet. 77 (2005) 337-345
3. Gupta P.K., et al. Linkage disequilibrium and association studies in higher plants: present status and future prospects. Plant Mol. Biol. 57 (2005) 461-485
4. Winkler C.R., et al. On the determination of recombination rates in intermated recombinant inbred populations. Genetics 164 (2003) 741-745
5. Darvasi A., and Soller M. Advanced intercross lines, an experimental population for fine genetic mapping. Genetics 141 (1995) 1199-1207
6. Mott R., et al. A method for fine mapping quantitative trait loci in outbred animal stocks. Proc. Natl. Acad. Sci. U. S. A. 97 (2000) 12649-12654
7. Mott R., and Flint J. Simultaneous detection and fine mapping of quantitative trait loci in mice using heterogeneous stocks. Genetics 160 (2002) 1609-1618
8. Yalcin B., et al. Using progenitor strain information to identify quantitative trait nucleotides in outbred mice. Genetics 171 (2005) 673-681
9. Valdar W., et al. Simulating the collaborative cross: power of quantitative trait loci detection and mapping resolution in large sets of recombinant inbred strains of mice. Genetics 172 (2006) 1783-1797
10. Valdar W., et al. Genome-wide genetic association of complex traits in heterogeneous stock mice. Nat. Genet. 38 (2006) 879-887
11. Metzker M.L. Emerging technologies in DNA sequencing. Genome Res. 15 (2005) 1767-1776
12. Syvänen A.-C. Toward genome-wide SNP genotyping. Nat. Genet. 57 (2005) S5-S10
13. Macdonald S.J., et al. A low-cost open-source SNP genotyping platform for association mapping applications. Genome Biol. 6 (2005) R105
14. Spielman R.S., et al. Transmission test for linkage disequilibrium: the insulin gene region and insulin-dependent diabetes mellitus (IDDM). Am. J. Hum. Genet. 52 (1993) 506-516
15. Mitchell A.A., and Chakravarti A. Undetected genotyping errors cause apparent overtransmission of common alleles in the transmission/disequilibrium test. Am. J. Hum. Genet. 72 (2003) 598-610
16. Gordon D., et al. A transmission/disequilibrium test that allows for genotyping errors in the analysis of single-nucleotide polymorphism data. Am. J. Hum. Genet. 69 (2001) 371-380
17. Gordon D., et al. A transmission disequilibrium test for general pedigrees that is robust to the presence of random genotyping errors and any number of untyped parents. Eur. J. Hum. Genet. 12 (2004) 752-761
18. Allen A.S., et al. Informative missingness in genetic association studies: case-parent designs. Am. J. Hum. Genet. 72 (2003) 671-680
19. Laird N.M., and Lange C. Family-based designs in the age of large-scale gene-association studies. Nat. Rev. Genet. 7 (2006) 385-394
20. Stich B. A new test for family-based association mapping with inbred lines from plant breeding programs. Theor. Appl. Genet. 113 (2006) 1121-1130
21. Devlin B., and Roeder K. Genomic control for association studies. Biometrics 55 (1999) 997-1004
22. Reich D.E., and Goldstein D.B. Detecting association in a case-control study while correcting for population stratification. Genet. Epidemiol. 20 (2001) 4-16
23. Bacanu S.-A., et al. Association studies for quantitative traits in structured populations. Genet. Epidemiol. 22 (2002) 78-93
24. Devlin B., et al. Genomic control in the extreme. Nat. Genet. 36 (2004) 1129-1130
25. Clayton D.G., et al. Population structure, differential bias and genomic control in a large-scale, case-control association study. Nat. Genet. 37 (2005) 1243-1246
26. Zheng G., et al. Robust genomic control for association studies. Am. J. Hum. Genet. 78 (2006) 350-356
27. Setakis E., et al. Logistic regression protects against population structure in genetic association studies. Genome Res. 16 (2006) 290-296
28. Price A.L. Principal components analysis corrects for stratification in genome-wide association studies. Nat. Genet. 38 (2006) 904-909
29. Pritchard J.K., et al. Inference of population structure using multilocus genotype data. Genetics 155 (2000) 945-959
30. Pritchard J.K., et al. Association mapping in structured populations. Am. J. Hum. Genet. 67 (2000) 170-181
31. Falush D., et al. Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics 164 (2003) 1567-1587
32. Aranzana M.J., et al. Genome-wide association mapping in Arabidopsis identifies previously known flowering time and pathogen resistance genes. PLoS Genet 1 (2005) e60
33. Yu J., et al. A unified mixed-model method for association mapping that accounts for multiple levels of relatedness. Nat. Genet. 38 (2006) 203-208
34. Kraakman A.T., et al. Linkage disequilibrium mapping of yield and yield stability in modern spring barley cultivars. Genetics 168 (2004) 435-446
35. Buntjer J.B., et al. Haplotype diversity: the link between statistical and biological association. Trends Plant Sci. 10 (2005) 466-471
36. Caldwell K.S., et al. Extreme population-dependent linkage disequilibrium detected in an inbreeding plant species, Hordeum vulgare. Genetics 172 (2006) 557-567
37. Maynard Smith J., and Haig J. The hitchhiking effect of a favourable gene. Genet. Res. 23 (1974) 23-35
38. Barton N. Genetic hitchhiking. Philos. Trans. R. Soc. Lond. B Biol. Sci. 355 (2000) 1553-1562
39. Palaisa K., et al. Long-range patterns of diversity and linkage disequilibrium surrounding the maize Y1 gene are indicative of an asymmetric selective sweep. Proc. Natl. Acad. Sci. U. S. A. 101 (2004) 9885-9890
40. Tian D., et al. Signature of balancing selection in Arabidopsis. Proc. Natl. Acad. Sci. U. S. A. 99 (2002) 11525-11530
41. Darvasi A., and Shifman S. The beauty of admixture. Nat. Genet. 37 (2005) 118-119
42. Smith M.W., and O'Brien S.J. Mapping by admixture linkage disequilibrium: advances, limitations and guidelines. Nat. Rev. Genet. 6 (2005) 623-632
43. Hu Z.-M. Detection of linkage disequilibrium QTLs controlling low-temperature growth and metabolite accumulations in an admixed breeding population of Leymus wildryes. Euphytica 141 (2005) 263-280
44. Lexer C., et al. Admixture in European Populus hybrid zones makes feasible the mapping of loci that contribute to reproductive isolation and trait differences. Heredity 98 (2007) 74-84