Mapping genome-wide QTL of ratio traits with Bayesian shrinkage analysis for its component traits

Genetica

Volumn 138, Issue 8, 2010, Pages 853-860

  Yang, Runqing ^a,b   Jin, Tianbo ^c   Li, Wenbin ^d  

^a HEILONGJIANG BAYI AGRICULTURAL UNIVERSITY   (China)

^b SHANGHAI JIAO TONG UNIVERSITY   (China)

^c NORTHWEST UNIVERSITY   (China)

^d NORTHEAST AGRICULTURAL UNIVERSITY   (China)

Author keywords

Bayesian shrinkage; QTL; Ratio trait; Relative growth rate

Indexed keywords

ARTICLE; BAYES THEOREM; CHROMOSOME MAP; GENETICS; METHODOLOGY; QUANTITATIVE TRAIT LOCUS; STATISTICAL MODEL;

BAYES THEOREM; CHROMOSOME MAPPING; LIKELIHOOD FUNCTIONS; QUANTITATIVE TRAIT LOCI;

GLYCINE MAX;

EID: 77956274084     PISSN: 00166707     EISSN: None     Source Type: Journal    
DOI: 10.1007/s10709-010-9468-6     Document Type: Article

References (45)

1. Banerjee S, Yandell BS, Yi N (2008) Bayesian quantitative trait loci mapping for multiple traits. Genetics 179: 2275-2289.
2. Casas E, Shackelford SD, Keele JW, Koohmaraie M, Smith TPL, Stone RT (2003) Detection of quantitative trait loci for growth and carcass composition in cattle. J Anim Sci 81: 2976-2983.
3. Chib S, Greenberg E (1998) Analysis of multivariate probit models. Biometrika 2: 347-361.
4. Coppieters W, Kvasz A, Arranz JJ, Grisart B, Farnir F, Mackinnon M, Georges M (1998) A rank-based non parametric method to map QTL in outbred half-sib pedigrees: application to milk production in a grand-daughter design. Genetics 149: 1547-1555.
5. Corander J, Sillanpää MJ (2002) An unified approach to joint modeling of multiple quantitative and qualitative traits in gene mapping. J Theor Biol 218: 435-446.
6. Gunsett FC (1984) Linear index selection to improve traits defined as ratios. J Anim Sci 59: 1185-1193.
7. Gunsett FC (1987) Merit of utilizing the heritability of a ratio to predict genetic change of a ratio. J Anim Sci 65: 936-942.
8. Gunsett FC, Andriano KN, Rutledge JJ (1982) Estimating the precision of estimates of genetic parameters realized from multiple-trait selection experiments. Biometrics 4: 981-989.
9. Hackett CA (1997) Model diagnostics for fitting QTL models to trait and marker data by interval mapping. Heredity 79: 319-328.
10. Hastings WK (1970) Monte Carlo sampling methods using Markov chains and their applications. Biometrika 57: 97-109.
11. Hinkley DV (1969) On the ratio of two correlated normal random variables. Biometrika 56: 635-639.
12. Jansen RC (1992) A general mixture model for mapping quantitative trait loci by using molecular markers. Theor Appl Genet 85: 252-260.
13. Jin C, Fine JP, Yandell BS (2007) A unified semiparametric framework for quantitative trait loci analyses, with application to Spike phenotypes. JASA 477: 56-67.
14. Kao CH (2000) On the differences between maximum likelihood and regression interval mapping in the analysis of quantitative trait loci. Genetics 156: 855-865.
15. Kendall M, Stuart A (1979) The advanced theory of statistics, 4th edn. Griffin, London.
16. Kruglyak L, Lander ES (1995) A nonparametric approach for mapping quantitative trait loci. Genetics 139: 1421-1428.
17. Mao Y, Xu S (2004) Mapping QTLs for traits measured as percentages. Genet Res 83: 159-168.
18. Metropolis N, Rosenbluth AW, Rosenbluth MN, Teller AH, Teller E (1953) Equations of state calculations by fast computing machines. J Chem Phys 21: 1087-1091.
19. Rebaï A (1997) Comparison of methods for regression interval mapping in QTL analysis with non-normal traits. Genet Res 69: 69-74.
20. Rohr PV, Hoeschele I (2002) Bayesian QTL mapping using skewed Student-t distributions. Genet Sel Evol 34: 1-2.
21. Satagopan JM, Yandell BS (1996) Estimating the number of quantitative trait loci via Bayesian model determination. Special contributed paper session on genetic analysis of quantitative traits and complex diseases, biometrics section, joint Statistical meetings. Chicago, IL.
22. Sen S, Churchill GA (2001) A statistical framework for quantitative trait mapping. Genetics 159: 371-387.
23. Sillanpää MJ, Arjas E (1999) Bayesian mapping of multiple quantitative trait loci from incomplete outbred offspring data. Genetics 151: 1605-1619.
24. Stephens DA, Fisch RD (1998) Bayesian analysis of quantitative trait locus data using reversible jump Markov chain Monte Carlo. Biometrics 54: 1334-1347.
25. Sun D, Li W, Zhang Z, Cheng Q, Yang Q (2006) Analysis of QTL for plant height at different developmental stages in soybean. Acta Agronomica Sinica 4: 509-514.
26. Sutherland TM (1965) The correlation between feed efficiency and rate of gain, a ratio and its denominator. Biometrics 21: 739-749.
27. Tsarouhas V, Gullberg U, Lagercrantz U (2002) An AFLP and RFLP linkage map and quantitative trait locus (QTL) analysis of growth traits in Salix. Theor Appl Genet 2-3: 277-288.
28. Uimari P, Sillanpää MJ (2001) Bayesian oligogenic analysis of quantitative and qualitative traits in general pedigrees. Genet Epidemiol 21: 224-242.
29. van Kaam JB, Bink MC, Bovenhuis H, Quaas RL (2002) Scaling to account for heterogeneous variances in a Bayesian analysis of broiler quantitative trait loci. J Anim Sci 80: 45-56.
30. Viitala SM, Schulman NF, De Koning DJ, Elo K, Kinos R, Virta A, Virta J, Mäki-Tanila A, Vilkki JH (2003) Quantitative trait loci affecting milk production traits in Finnish Ayrshire dairy cattle. J Dairy Sci 86: 1828-1836.
31. Wang H, Zhang YM, Li X, Masinde GL, Mohan S, Baylink DJ, Xu S (2005) Bayesian shrinkage estimation of quantitative trait loci parameters. Genetics 170: 465-480.
32. Weller JI, Golik M, Seroussi E, Ezra E, Ron M (2003) Population-wide analysis of a QTL affecting milk-fat production in the Israeli Holstein population. J Dairy Sci 86: 2219-2227.
33. Xu S (2003) Estimating polygenic effects using markers of the entire genome. Genetics 163: 789-801.
34. Xu C, Wang X, Li Z, Xu S (2009) Mapping QTL for multiple traits using Bayesian statistics. Genet Res 91: 23-37.
35. Yang R, Xu S (2007) Bayesian shrinkage analysis of quantitative trait loci for dynamic traits. Genetics 176: 1169-1185.
36. Yang R, Yi N, Xu S (2006) Box-Cox transformation for QTL mapping. Genetica 128: 133-143.
37. Yang R, Li J, Xu S (2008) Mapping quantitative trait loci for traits defined as ratios. Genetica 132: 323-329.
38. Yi N, Xu S (2000) Bayesian mapping of quantitative trait loci under the identity-by-descent-based variance component model. Genetics 156: 411-422.
39. Yi N, Xu S (2002) Mapping quantitative trait loci with epistatic effects. Genet Res 79: 185-198.
40. Yi N, Allison DB, Xu S (2003a) Bayesian model choice and search strategies for mapping multiple epistatic quantitative trait loci. Genetics 165: 867-883.
41. Yi N, George V, Allison DB (2003b) Stochastic search variable selection for identifying multiple quantitative trait loci. Genetics 164: 1129-1138.
42. Yi N, Yandell BS, Churchill GA, Allison DB, Eisen EJ, Pomp D (2005) Bayesian model selection for genome-wide epistatic quantitative trait loci analysis. Genetics 170: 1333-1344.
43. Zellner A (1962) An efficient method of estimating seemingly unrelated regressions and tests for aggregation bias. J Am Stat Assoc 57: 348-368.
44. Zhang YM, Xu S (2005) Advanced statistical methods for detecting multiple quantitative trait loci. Recent Res Devel Genet Breed 2: 1-23.
45. Zou F, Fine JP, Yandell BS (2002) On empirical likelihood for a semiparametric mixture model. Biometrika 89: 61-75.