Bayesian analyses of multiple epistatic QTL models for body weight and body composition in mice

Genetical Research

Volumn 87, Issue 1, 2006, Pages 45-60

  Yi, Nengjun ^a   Zinniel, Denise K ^b   Kim, Kyoungmi ^a   Eisen, Eugene J ^c   Bartolucci, Alfred ^a   Allison, David B ^a   Pomp, Daniel ^d  

^a UNIVERSITY OF ALABAMA AT BIRMINGHAM   (United States)

^b UNIVERSITY OF NEBRASKA LINCOLN   (United States)

^c NORTH CAROLINA STATE UNIVERSITY   (United States)

^d IL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANIMAL EXPERIMENT; ARTICLE; BAYES THEOREM; BODY COMPOSITION; BODY FAT; BODY GROWTH; BODY WEIGHT; CONTROLLED STUDY; FEMALE; GENETIC EPISTASIS; GENETIC MODEL; GENETIC SELECTION; GROUPS BY AGE; GROWTH RATE; LEAN BODY WEIGHT; MALE; MOUSE; MOUSE STRAIN; NONHUMAN; OBESITY; ORGAN WEIGHT; PLEIOTROPY; QUANTITATIVE TRAIT LOCUS MAPPING;

ANIMALS; BAYES THEOREM; BODY COMPOSITION; BODY WEIGHT; EPISTASIS, GENETIC; MICE; MICE, INBRED ICR; MICE, INBRED STRAINS; MODELS, GENETIC; QUANTITATIVE TRAIT LOCI;

ANIMALIA;

EID: 33644949714     PISSN: 00166723     EISSN: 14695073     Source Type: Journal    
DOI: 10.1017/S0016672306007944     Document Type: Article

References (59)

1. Allan, M. F., Eisen, E. J. & Pomp, D. (2004). The M16 mouse: An outbred animal model of early onset obesity and diabesity. Obesity Research 12, 1397-1407.
2. Allison, D. B., Pietrobelli, A., Faith, M. S., Fontaine, K. R., Gropp, E., et al. (2002). Genetic influences on obesity. In Obesity: Mechanisms and Clinical Management (ed. R. H. Eckel). New York: Lippincott Williams & Wilkins.
3. Atchley, W. R., Riska, B., Kohn, L., Plummet, A. & Rutledge, J. J. (1984). A quantitative genetic analysis of brain and body size associations, their origin and ontogeny: Data from mice. Evolution 38, 1165-1179.
4. Atchley, W. R., Cowley, D. E. & Xu, S. (1997). Restricted index selection for altering developmental trajectories. Genetics 146, 629-640.
5. Brockmann, G. A. & Bevova, M. R. (2002). Using mouse models to dissect the genetics of obesity. Trends in Genetics 18, 367-376.
6. Brockmann, G. A., Kratzsch, J., Haley, C. S., Renne, U., Schwerin, M. & Karle, S. (2000). Single QTL effects, epistasis, and pleiotropy account for two-thirds of the phenotypic F2 variance of growth and obesity in DU6iXDBA/2 mice. Genome Research 10, 1941-1957.
7. Brockmann, G. A., Karatayli, E., Haley, C. S., Renne, U., Rottmann, O. J. & Karle, S. (2004). QTLs for pre- and post-weaning body weight and body composition in selected mice. Mammalian Genome 15, 593-609.
8. Bunger, L. & Hill, W. G. (2005). Genetics of body composition and metabolic rate. In The Mouse in Animal Genetics and Breeding Research (ed. E. J. Eisen), pp. 131-160. London: Imperial College Press.
9. Carlborg, Ö. & Haley, C. S. (2004). Epistasis: Too often neglected in complex trait studies? Nature Reviews Genetics 5, 618-625.
10. Carlborg, Ö., Andersson, L. & Kinghorn, B. (2000). The use of a genetic algorithm for simultaneous mapping of multiple interacting quantitative trait loci. Genetics 155, 2003-2010.
11. Chesler, E. J., Lu, L., Shou, S., Qu, Y., Gu, J., Wang, J., Hsu, H. C., Mountz, J. D., Baldwin, N. E., Langston, M. A., Threadgill, D. W., Mauley, K. F. & Williams, R. W. (2005). Complex trait analysis of gene expression uncovers polygenic and pleiotropic networks that modulate nervous system function. Nature Genetics 37, 233-242.
12. Cheverud, J. M. (2005). Genetics of growth in the mouse. In The Mouse in Animal Genetics and Breeding Research (ed. E. J. Eisen), pp. 113-129. London: Imperial College Press.
13. Cheverud, J. M., Routman, E. J., Duarte, F. A. M., van Swindern, B., Cothran, K. & Perel, C. (1996). Quantitative trait loci for murine growth. Genetics 142, 1305-1319.
14. Cheverud, J. M., Vaughn, T. T., Pletscher, L. S., Peripate, A. C., Adams, E. S., Erikson, C. F. & King-Ellison, K. J. (2001). Genetic architecture of adiposity in the cross of LG/J and SM/J inbred mice. Mammalian Genome 12, 3-12.
15. Dong, C., Wang, S., Li, W. D., Li, D., Zhao, H. & Price, R. A. (2003) Interacting genetic loci on chromosomes 20 and 10 influence extreme human obesity. American Journal of Human Genetics 72, 115-124.
16. Dong, C., Li, W.-D., Li, D. & Price, R. A. (2005). Interaction between obesity-susceptibility loci in chromosome regions 2p25-p24 and 13q13-q21. European Journal of Human Genetics 13, 102-108.
17. Eisen, E. J. (1975). Population size and selection intensity effects on long-term selection response in mice. Genetics 79, 305-323.
18. Eisen, E. J. (1986). Maturing patterns of organ weights in mice selected for rapid postweaning gain. Theoretical and Applied Genetics 73, 148-157.
19. Eisen, E. J. (1987). Selection for components related to body composition in mice: Correlated responses. Theoretical and Applied Genetics 75, 177-188.
20. Eisen, E. J. & Leatherwood, J. M. (1978a). Adipose cellularity and body composition in polygenic obese mice as influenced by preweaning nutrition. Journal of Nutrition 108, 1652-1662.
21. Eisen, E. J. & Leatherwood, J. M. (1978b). Effect of postweaning feed restriction on adipose cellularity and body composition in polygenic obese mice. Journal of Nutrition 108, 1663-1672.
22. Eisen, E. J. & Prasetyo, H. (1988). Estimates of genetic parameters and predicted selection responses for growth, fat and lean traits in mice. Journal of Animal Science 66, 1153-1165.
23. Eisen, E. J., Hayes, J. F., Allen, C. E., Bakker, H. & Nagai, J. (1978). Cellular characteristics of gonadal fat pads, livers and kidneys in two strains of mice selected for rapid growth. Growth 42, 7-25.
24. Eisen, E. J., Benyon, L. S. & Douglas, J. A. (1995). Long-term restricted index selection designed to change fat content without changing body size. Theoretical and Applied Genetics 91, 340-345.
25. Haley, C. S. & Knott, S. A. (1992). A simple regression method for mapping quantitative trait loci in line crosses using flanking markers. Heredity 69, 315-324.
26. Hanrahan, J. P., Eisen, E. J. & Legates, J. E. (1973). Effects of population size and selection intensity on short-term response to selection for postweaning gain in mice. Genetics 73, 513-530.
27. Hoeschele, I. (2001). Mapping quantitative trait loci in outbred pedigrees, In Handbook of Statistical Genetics (ed. D. J. Balding, M. Bishop & C. Cannings), pp. 599-644. New York: Wiley.
28. Ishikawa, A., Hatada, S., Nagamine, Y. & Namikawa, T. (2005). Further mapping of quantitative trait loci for postnatal growth in an intersubspecific backcross of wild Mus musculus castaneus and C57BL/6J mice. Genetical Research 85, 127-137.
29. Jerez-Timaure, N. C., Eisen, E. J. & Pomp, D. (2005). Fine mapping of a QTL region with large effects on growth and fatness on mouse chromosome 2. Physiological Genomics 21, 411-422.
30. Jiang, C. & Zeng, Z.-B. (1995). Multiple trait analysis of genetic mapping for quantitative trait loci. Genetics 140, 1111-1127.
31. Lander, E. S. & Botstein, E. (1989). Mapping Mendelian factors underlying quantitative traits using RFLP maps. Genetics 121, 185-199.
32. Lander, E. S. & Kruglyak, L. (1995). Genetics dissection of complex traits: Guidelines for interpreting and reporting linkage results. Nature Genetics 11, 241-247.
33. Leamy, L. J., Pomp, D., Eisen, E. J. & Cheverud, J. M. (2002). Pleiotropy of quantitative trait loci for organ weights and limb bone lengths in mice. Physiological Genomics 10, 21-29.
34. Lerner, I. M. (1954). Genetic Homeostasis. New York: Wiley.
35. Lincoln, S., Daly, M. & Lander, E. S. (1992). Constructing genetic maps with MAPMAKER/EXP 3.0. Technical report. Cambridge, MA: Whitehead Institute.
36. Moore, J. H. (2005). A global view of epistasis. Nature Genetics 37, 13-14.
37. Morris, K. H., Ishikawa, A. & Keightley, P. D. (1999). Quantitative trait loci for growth traits in C57BL/6J × DBA/2J mice. Mammalian Genome 10, 225-228.
38. Plummer, M., Best, N., Cowles, K. & Vines, K. (2005). Output analysis and diagnostics for MCMC, R package version 0.10-3, URL http://cran.r-project.org/
39. Pomp, D. (1997). Genetic dissection of obesity in polygenic animal models. Behavior Genetics 27, 285-306.
40. Pomp, D. (2005). Genomic dissection of complex trait predisposition. In The Mouse in Animal Genetics and Breeding Research (ed. E. J. Eisen), pp. 237-262. London: Imperial College Press.
41. Pomp, D., Allan, M. F. & Wesolowski, S. (2004). Quantitative genomics: Exploring the genetic architecture of complex trait predisposition. Journal of Animal Science 82, E300-E312.
42. Rocha, J., Eisen, E. J., Van Vleck, D. L. & Pomp, D. (2004a). A large sample QTL study in mice. I. Growth. Mammalian Genome 15, 83-99.
43. Rocha, J., Eisen, E. J., Van Vleck, D. L. & Pomp, D. (2004b). A large sample QTL study in mice. II. Body Composition. Mammalian Genome 15, 100-115.
44. Rutledge, J. J., Robison, O. W., Eisen, E. J. & Legates, J. E. (1972) Dynamics of genetic and maternal effects in mice. Journal of Animal Science 35, 1441-1444.
45. Schadt, E. E., Monks, S. A., Darke, T. A., Lusis, A. J., Che, N., et al. (2003). Genetics of gene expression surveyed in maize, mouse and man. Nature Genetics 422, 297-302.
46. Segrè, D., DeLuna, A., Church, G. M. & Kiskony, R. (2005). Modular epistasis in yeast metabolism. Nature Genetics 37, 77-83.
47. Sillanpää, M. J. & Arjas, E. (1998). Bayesian mapping of multiple quantitative trait loci from incomplete inbred line cross data. Genetics 148, 1373-1388.
48. Vaughn, T. T., Pletscher, L. S., Peripato, A., King-Ellison, K., Adams, E., Erikson, C. & Cheverud, J. M. (1999). Mapping quantitative trait loci for murine growth: A closer look at genetic architecture. Genetical Research 74, 313-322.
49. Warden, C. H., Yi, N. & Fisler, J. (2004). Epistasis among genes is a universal phenomenon in obesity: Evidence from rodent models. Nutrition 20, 74-77.
50. Wu, R., Chang-Xing Ma, C.-X., Hou, W., Corva, P. & Medrano, J. F. (2005). Functional mapping of quantitative trait loci that interact with the hg mutation to regulate growth trajectories in mice. Genetics 171, 239-249.
51. Yamada, T., Miyake, T., Sugiura, K., Narita, A., Wei, K., Wei, S., Moralejo, D. H., Ogino, T., Gaillard, C., Sasaki, Y. & Matsumoto, K. (2001). Identification of epistatic interactions involved in non-insulin dependent diabetes mellitus in the Otsuka Long-Evans Tokushima fatty rat. Experimental Animals 50, 115-123.
52. Yang, R. C. (2004). Epistasis of quantitative trait loci under different gene action models. Genetics 167, 1493-1505.
53. Yi, N. & Xu, S. (2002). Mapping quantitative trait loci with epistatic effects. Genetical Research 79, 185-198.
54. Yi, N., Xu, S. & Allison, D. B. (2003). Bayesian model choice and search strategies for mapping interacting quantitative trait loci. Genetics 165, 867-883.
55. Yi, N., Diamont, A., Chiu, S., Kim, K., Allison, D. B., Fisler, J. S. & Warden, H. (2004a). Characterization of epistasis influencing complex spontaneous obesity in the B5B model. Genetics 167, 399-409.
56. Yi, N., Chiu, S., Allison, D. B., Fisler, J. & Warden, C. H. (2004b). Epistatic interaction between two nonstructural loci on chromosomes 7 and 3 influences hepatic lipase activity in B5B mice. Journal of Lipid Research 45, 2063-2070.
57. Yi, N., Yandell, B., Churchill, G., Allison, D., Eisen, E. J. & Pomp, D. (2005). Bayesian model selection for genome-wide QTL analysis. Genetics 170, 1333-1344.
58. Zeng, Z.-B., Wang, T. & Zou, W. (2005). Modeling quantitative trait loci and interpretation of models. Genetics 169, 1711-1725.
59. Zhang, Y. M. & Xu, S. (2005). A penalized maximum likelihood method for estimating epistatic effects of QTL. Heredity 95, 96-104.