Nested association mapping for identification of functional markers

Genetics

Volumn 186, Issue 1, 2010, Pages 373-383

  Guo, Baohong ^a   Sleper, David A ^b   Beavis, William D ^a  

^a IOWA STATE UNIVERSITY   (United States)

^b UNIVERSITY OF MISSOURI   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; AMPLICON; ARTICLE; CONTROLLED STUDY; FUNCTIONAL MARKER; GENE LINKAGE DISEQUILIBRIUM; GENE LOCUS; GENE MAPPING; GENE SEQUENCE; GENE STRUCTURE; GENETIC ASSOCIATION; GENETIC MARKER; GENOMICS; HEREDITY; NESTED ASSOCIATION MAPPING; PHENOTYPIC VARIATION; PRIORITY JOURNAL; PROGENY; SIMULATION; SINGLE NUCLEOTIDE POLYMORPHISM;

BREEDING; CHROMOSOME MAPPING; GENE FREQUENCY; GENETIC LOCI; GENETIC MARKERS; GENOMICS; LINKAGE DISEQUILIBRIUM; PLANTS; POLYMORPHISM, SINGLE NUCLEOTIDE;

EID: 78650758776     PISSN: 00166731     EISSN: 00166731     Source Type: Journal    
DOI: 10.1534/genetics.110.115782     Document Type: Article

References (36)

1. ABECASIS, G. R., L. R. CARDON and W. O. C. COOKSON, 2000 A general test of association for quantitative traits in nuclear families. Am. J. Hum. Genet. 66: 279-292.
2. ANDERSEN, J. R., and T. LUBBERSTEDT, 2003 Functional markers in plants. Trends Plant Sci. 8: 554-560.
3. ANDERSON, M. J., and C. J. F. TER BRAAK, 2003 Permutation tests for multi-factorial analysis of variance. J. Stat. Comput. Simul. 73: 85-113.
4. BUCKLER, E., and M. GORE, 2007 An Arabidopsis haplotype map takes root. Nat. Genet. 39: 1056-1057.
5. BURDICK, J. T., W. CHEN, G. R. ABECASIS and V. G. CHEUNG, 2006 In silico method for inferring genotypes in pedigrees. Nat. Genet. 38: 1002-1004.
6. CHRISTENSEN, R., 2002 Plane Answers to Complex Questions: The Theory of Linear Models, Ed. 3. Springer, New York.
7. CHURCHILL, G. A., and R. W. DOERGE, 1994 Empirical threshold values for quantitative trait mapping. Genetics 138: 963-971.
8. DARVASI, A., and M. SOLLER, 1997 A simple method to calculate resolving power and confidence interval of QTL map location. Behav. Genet. 27: 125-132.
9. FARNIR, F., B. GRISART, W. COPPIETERS, J. RIQUET, P. BERZI et al., 2002 Simultaneous mining of linkage and linkage disequilibrium to fine map quantitative trait loci in outbred half-sib pedigrees: revisiting the location of a quantitative trait locus with major effect on milk production on bovine chromosome 14. Genetics 161: 275-287.
10. GUO, B., D. A. SLEPER, J. SUN, H. T. NGUYEN, P. R. ARELLI et al., 2006 Pooled analysis of data from multiple quantitative trait locus mapping populations. Theor. Appl. Genet. 113: 39-48.
11. HALEY, C. S., and S. A. KNOTT, 1992 A simple regression method for mapping quantitative trait loci in line crosses using flanking markers. Heredity 69: 315-324.
12. HILLIER, F. S., 2005 Introduction to Operations Research, Ed. 8. McGraw-Hill, New York.
13. KATHIRESAN, S., K. MUSUNURU and M. ORHO-MELANDER 2008 Defining the spectrum of alleles that contribute to blood lipid concentrations in humans. Curr. Opin. Lipidol. 19: 122-127.
14. JANNINK, J., and R. JANSEN, 2000 The diallel mating design for mapping interacting QTLs, pp. 81-88 in Quantitative Genetics and Breeding Methods: The Way Ahead, edited by A. GALLAIS, C. DILLMANN and I. GOLDRINGER. Institut National de la Recherche Agronomique, Paris.
15. JANNINK, J., and X. L. WU, 2003 Estimating allelic number and identity in state of QTLs in interconnected families. Genet. Res. 81: 133-144.
16. JANSEN, R. C., J. L. JANNINK and W. D. BEAVIS, 2003 Mapping quantitative trait loci in plant breeding populations: use of parental haplotype sharing. Crop Sci. 43: 829-834.
17. JIANG, C., and Z.-B. ZENG, 1995 Multiple trait analysis of genetic mapping for quantitative trait loci. Genetics 140: 1111-1127.
18. JUNG, J., R. FAN and L. JIN, 2005 Combined linkage and association mapping of quantitative trait loci by multiple markers. Genetics 170: 881-898. (Pubitemid 40980688)
19. LEBRETON, C. M., and P. M. VISSCHER, 1998 Empirical nonparametric bootstrap strategies in quantitative trait loci mapping: conditioning on the genetic model. Genetics 148: 525-535.
20. LIU, K., M. GOODMAN, S. MUSE, J. S. SMITH and E. BUCKLER, 2003 Genetic structure and diversity among maize inbred lines as inferred from DNA microsatellites. Genetics 165: 2117-2128.
21. MYLES, S., J. PEIFFER, P. J. BROWN, E. S. ERSOZ, Z. ZHANG et al., 2009 Association mapping: critical considerations shift from genotyping to experimental design. Plant Cell 21: 2194-2202.
22. NAIR, R. P., K. C. DUFFIN, C. HELMS, J. DING, P. E. STUARTR et al., 2009 Genome-wide scan reveals association of psoriasis with IL-23 and NF-κB pathways. Nat. Genet. 41: 199-204.
23. NORDBORG, M., and D. WEIGEL, 2008 Next-generation genetics in plants. Nature 456: 720-723.
24. PEREZ-ENCISO, M., 2003 Fine mapping of complex trait genes combining pedigree and linkage disequilibrium information: a Bayesian unified framework. Genetics 163: 1497-1510.
25. SABATTI, C., S. K. SERVICE, A. L. HARTIKAINEN, A. POUTA, S. RIPATTI et al., 2009 Genome-wide association analysis of metabolic traits in a birth cohort from a founder population. Nat. Genet. 41: 35-46.
26. SEN, S., and G. A. CHURCHILL, 2001 A statistical framework for quantitative trait mapping. Genetics 159: 371-387.
27. VISSCHER, P. M., R. THOMPSON and C. S. HALEY, 1996 Confidence intervals in QTL mapping by bootstrapping. Genetics 143: 1013-1020.
28. WALLING, G. A., P. M. VISSCHER, L. ANDERSSON, M. F. ROTHSCHILD, L. WANG et al., 2000 Combined analysis of data from quantitative trait loci mapping studies: chromosome 4 effects on porcine growth and fatness. Genetics 155: 1369-1378.
29. WU, R., C. MA and G. CASELLA, 2002 Joint linkage and linkage disequilibrium mapping of quantitative trait loci in natural populations. Genetics 160: 779-792. (Pubitemid 34194546)
30. XIONG, M., and L. JIN, 2000 Combined linkage and linkage disequilibrium mapping for genome screens. Genet. Epidemiol. 19: 211-234.
31. XU, S., 1998a Mapping quantitative trait loci using multiple families of line crosses. Genetics 148: 517-524.
32. XU, S., 1998b Iteratively reweighted least squares mapping of quantitative trait loci. Behav. Genet. 28: 341-355.
33. XU, S., 2003 Estimating polygenic effects using markers of the entire genome. Genetics 163: 789-801.
34. YI, N., and D. SHRINER, 2008 Advances in Bayesian multiple QTL mapping in experimental 11 designs. Heredity 100: 240-252.
35. YU, J., J. B. HOLLAND, M. D. MCMULLEN and E. S. BUCKLER, 2008 Genetic design and statistical power of nested association mapping in maize. Genetics 178: 539-551.
36. ZENG, Z. B., 1994 Precision mapping of quantitative trait loci. Genetics 136: 1457-1468.