Using mating designs to uncover QTL and the genetic architecture of complex traits

Heredity

Volumn 96, Issue 2, 2006, Pages 139-149

  Verhoeven, K J F ^a   Jannink, J L ^b   McIntyre, L M ^a  

^a PURDUE UNIVERSITY   (United States)

^b IOWA STATE UNIVERSITY   (United States)

Author keywords

Diallel; GCA; Power; QTL; SCA; Simulations

Indexed keywords

GENETIC STRUCTURE;

ANIMAL; ARTICLE; BIOLOGICAL MODEL; BREEDING; COMPUTER SIMULATION; FEMALE; GENETIC VARIABILITY; INBREEDING; MALE; PEDIGREE; QUANTITATIVE TRAIT; QUANTITATIVE TRAIT LOCUS;

ANIMALS; BREEDING; COMPUTER SIMULATION; FEMALE; INBREEDING; MALE; MODELS, GENETIC; PEDIGREE; QUANTITATIVE TRAIT LOCI; QUANTITATIVE TRAIT, HERITABLE; VARIATION (GENETICS);

EID: 31544436036     PISSN: 0018067X     EISSN: 13652540     Source Type: Journal    
DOI: 10.1038/sj.hdy.6800763     Document Type: Article

References (61)

1. Arcade A, Labourdette A, Falque M, Mangin B, Chardon F, Charcosset A et al (2004). BioMercator: integrating genetic maps and QTL towards discovery of candidate genes. Bioinformatics 20: 2324-2326.
2. Carlborg O, Andersson L, Kinghorn B (2000). The use of a genetic algorithm for simultaneous mapping of multiple interacting quantitative trait loci. Genetics 155: 2003-2010.
3. Chardon F, Virlon B, Moreau L, Falque M, Joets J, Decousset L et al (2004). Genetic architecture of flowering time in maize as inferred from quantitative trait loci meta-analysis and synteny conservation with the rice genome. Genetics 168: 2169-2185.
4. Clancy JA, Han F, Ullrich SE (2003). Comparative mapping of beta-amylase activity QTLs among three barley crosses. Crop Sci 43: 1043-1052.
5. Cockerham CC (1983). Covariances of relatives from self-fertilization. Crop Sci 23: 1177-1180.
6. Coffman CJ, Doerge RW, Simonsen KL, Nichols KD C, Wolfinger R, McIntyre LM (2005). Model selection in binary trait locus mapping. Genetics 170: 1281-1297.
7. Corander J, Sillanpää MJ (2002). A unified approach to joint modeling of multiple quantitative and qualitative traits in gene mapping. J Theor Biol 218: 435-446.
8. Dhillon BS, Singh J (1978). Evaluation of circulant partial diallel crosses in maize. Theor Appl Genet 52: 29-37.
9. Edwards JW, Lamkey KR (2002). Quantitative genetics of inbreeding in a synthetic maize population. Crop Sci 42: 1094-1104.
10. Flint-Garcia SA, Jampatong C, Darrah LL, McMullen MD (2003). Quantitative trait locus analysis of stalk strength in four maize populations. Crop Sci 43: 13-22.
11. Fyfe JL, Gilbert N (1963). Partial diallel crosses. Biometrics 19: 278-286.
12. Gardner CO, Eberhart SA (1966). Analysis and interpretation of the variety cross diallel and related populations. Biometrics 22: 439-452.
13. Gilbert DG (1985a). Estimating single gene effects on quantitative traits. 1. A diallel method applied to Est 6 in D. melanogaster. Theor Appl Genet 69: 625-629.
14. Gilbert DG (1985b). Estimating single gene effects on quantitative traits. 2. Statistical properties of five experimental methods. Theor Appl Genet 69: 631-636.
15. Goffinet B, Gerber S (2000). Quantitative trait loci: a meta-analysis. Genetics 155: 463-473.
16. Griffing B (1956). Concept of general and specific combining ability in relation to diallel crossing systems. Aust J Biol Sci 9: 463-493.
17. Haley CS, Knott SA (1992). A simple regression method for mapping quantitative trait loci in line crosses using flanking markers. Heredity 69: 315-324.
18. Hallauer AR, Miranda JB (1988). Quantitative Genetics in Maize Breeding, 2nd edn. Iowa State University Press: Ames, IA.
19. Hayman BI (1954a). The analysis of variance of diallel tables. Biometrics 10: 235-244.
20. Hayman BI (1954b). The theory and analysis of diallel crosses. I. Genetics 39: 789-809.
21. 2 diallel cross in wheat. Theor Appl Genet 102: 1076-1081.
22. Jannink JL, Jansen R (2001). Mapping epistatic quantitative trait loci with one-dimensional genome searches. Genetics 157: 445-454.
23. Jannink JL, Wu XL (2003). Estimating allelic number and identity in state of QTLs in interconnected families. Genet Res 81: 133-144.
24. Jansen RC (1993). Interval mapping of multiple quantitative trait loci. Genetics 135: 205-211.
25. Jansen RC, Jannink JL, Beavis WD (2003). Mapping quantitative trait loci in plant breeding populations: use of parental haplotype sharing. Crop Sci 43: 829-834.
26. Jansen RC, Stam P (1994). High-resolution of quantitative traits into multiple loci via interval mapping. Genetics 136: 1447-1455.
27. 2 and backcross generations from a set of diallel crosses. Heredity 10: 1-30.
28. Johnson GR, King JN (1998). Analysis of half diallel mating designs. Silvae Genet 47: 74-79.
29. Kamoshita A, Wade LJ, Ali ML, Pathan MS, Zhang J, Sarkarung S et al (2002). Mapping QTLs for root morphology of a rice population adapted to rainfed lowland conditions. Theor Appl Genet 104: 880-893.
30. Kao CH, Zeng ZB, Teasdale RD (1999). Multiple interval mapping for quantitative trait loci. Genetics 152: 1203-1216.
31. Kempthorne O, Curnow RN (1961). The partial diallel cross. Biometrics 17: 229-250.
32. Khatkar MS, Thomson PC, Tammen I, Raadsma HW (2004). Quantitative trait loci mapping in dairy cattle: review and meta-analysis. Genet Sel Evol 36: 163-190.
33. Kolb FL, Bai GH, Muehlbauer GJ, Anderson JA, Smith KP, Fedak G (2001). Host plant resistance genes for fusarium head blight: mapping and manipulation with molecular markers. Crop Sci 41: 611-619.
34. Liu YF, Zeng ZB (2000). A general mixture model approach for mapping quantitative trait loci from diverse cross designs involving multiple inbred lines. Genet Res 75: 345-355.
35. Lynch M, Walsh B (1998). Genetics and Analysis of Quantitative Traits. Sinauer: Sunderland.
36. Mather K (1941). Variation and selection of polygenic characters. J Genet 41: 159-193.
37. McIntyre LM, Coffman CJ, Doerge RW (2001). Detection and localization of a single binary trait locus in experimental populations. Genet Res 78: 79-92.
38. Muranty H (1996). Power of tests for quantitative trait loci detection using full-sib families in different schemes. Heredity 76: 156-165.
39. Rao SQ, Li X (2000). Strategies for genetic mapping of categorical traits. Genetica 109: 183-197.
40. Rebaï A, Goffinet B (1993). Power of tests for QTL detection using replicated progenies derived from a diallel cross. Theor Appl Genet 86: 1014-1022.
41. Rebaï A, Goffinet B (2000). More about quantitative trait locus mapping with diallel designs. Genet Res 75: 243-247.
42. Satagopan JM, Yandell YS, Newton MA, Osborn TC (1996). A Bayesian approach to detect quantitative trait loci using Markov chain Monte Carlo. Genetics 144: 805-816.
43. Sawkins MC, Farmer AD, Hoisington D, Sullivan J, Tolopko A, Jiang Z et al (2004). Comparative Map and Trait Viewer (CMTV): an integrated bioinformatic tool to construct consensus maps and compare QTL and functional genomics data across genomes and experiments. Plant Mol Biol 56: 465-480.
44. Searle SR, Casella G, McCulloch CE (1992). Variance Components. John Wiley & Sons: New York.
45. Simko I (2002). Comparative analysis of quantitative trait loci for foliage resistance to Phytophthora infestans in tuber-bearing Solanum species. Am J Potato Res 79: 125-132.
46. Soller M, Genizi A (1978). The efficiency of experimental designs for the detection of linkage between a marker locus and a locus affecting a quantitative trait in segregating populations. Biometrics 34: 47-55.
47. Sprague GF, Tatum LA (1942). General versus specific combining ability in crosses of corn. J Am Soc Agron 34: 923-932.
48. Toojinda T, Siangliw M, Tragoonrung S, Vanavichit A (2003). Molecular genetics of submergence tolerance in rice: QTL analysis of key traits. Ann Bot 91: 243-253.
49. Tuberosa R, Salvi S, Sanguineti MC, Maccaferri M, Giuliani S, Landi P (2003). Searching for quantitative trait loci controlling root traits in maize: a critical appraisal. Plant Soil 255: 35-54.
50. Viana JMS, Cruz CD, Cardoso AA (1999). Theory and analysis of partial diallel crosses. Genet Mol Biol 22: 591-599.
51. Welz HG, Geiger HH (2000). Genes for resistance to northern corn leaf blight in diverse maize populations. Plant Breed 119: 1-14.
52. Wu XL, Jannink JL (2004). Optimal sampling of a population to determine QTL location, variance, and allelic number. Theor Appl Genet 108: 1434-1442.
53. Xie CQ, Gessler DDG, Xu SZ (1998). Combining different line crosses for mapping quantitative trait loci using the identical by descent-based variance component method. Genetics 149: 1139-1146.
54. Xu S (1996). Mapping quantitative trait loci using four-way crosses. Genet Res 68: 175-181.
55. Xu S (1998). Mapping quantitative trait loci using multiple families of line crosses. Genetics 148: 517-524.
56. Yi NJ, Xu SZ (2000). Bayesian mapping of quantitative trait loci for complex binary traits. Genetics 155: 1391-1403.
57. Yi NJ, Xu SZ (2002a). Linkage analysis of quantitative trait loci in multiple line crosses. Genetica 114: 217-230.
58. Yi NJ, Xu SZ (2002b). Mapping quantitative trait loci with epistatic effects. Genet Res 79: 185-198.
59. Yi NJ, Xu SZ, George V, Allison DB (2004). Mapping multiple quantitative trait loci for ordinal traits. Behav Genet 34: 3-15.
60. Zeng ZB (1994). Precision mapping of quantitative trait loci. Genetics 136: 1457-1468.
61. Zhu J, Weir BS (1996). Mixed model approaches for diallel analysis based on a bio-model. Genet Res 68: 233-240.