Mapping Quantitative Trait Loci Using the MCMC Procedure in SAS

Overview

Journal Heredity (Edinb)

Specialty Genetics

Date 2010 Jun 17

PMID 20551982

Authors

S Xu

Z Hu

Affiliations

Soon will be listed here.

Abstract

The MCMC procedure in SAS (called PROC MCMC) is particularly designed for Bayesian analysis using the Markov chain Monte Carlo (MCMC) algorithm. The program is sufficiently general to handle very complicated statistical models and arbitrary prior distributions. This study introduces the SAS/MCMC procedure and demonstrates the application of the program to quantitative trait locus (QTL) mapping. A real life QTL mapping experiment in wheat female fertility trait was used as an example for the demonstration. The fertility trait phenotypes were described under three different models: (1) the Poisson model, (2) the Bernoulli model and (3) the zero-truncated Poisson model. One QTL was identified on the second chromosome. This QTL appears to control the switch of seed-producing ability of female plants but does not affect the number of seeds produced once the switch is turned on.

References

Yandell B, Mehta T, Banerjee S, Shriner D, Venkataraman R, Moon J . R/qtlbim: QTL with Bayesian Interval Mapping in experimental crosses. Bioinformatics. 2007; 23(5):641-3. PMC: 4995770. DOI: 10.1093/bioinformatics/btm011. View

Jiang C, Zeng Z . Mapping quantitative trait loci with dominant and missing markers in various crosses from two inbred lines. Genetica. 1997; 101(1):47-58. DOI: 10.1023/a:1018394410659. View

Dou B, Hou B, Xu H, Lou X, Chi X, Yang J . Efficient mapping of a female sterile gene in wheat (Triticum aestivum L.). Genet Res (Camb). 2009; 91(5):337-43. DOI: 10.1017/S0016672309990218. View

Lander E, Botstein D . Mapping mendelian factors underlying quantitative traits using RFLP linkage maps. Genetics. 1989; 121(1):185-99. PMC: 1203601. DOI: 10.1093/genetics/121.1.185. View

Sillanpaa M, Arjas E . Bayesian mapping of multiple quantitative trait loci from incomplete inbred line cross data. Genetics. 1998; 148(3):1373-88. PMC: 1460044. DOI: 10.1093/genetics/148.3.1373. View

Balmain A . Cancer as a complex genetic trait: tumor susceptibility in humans and mouse models. Cell. 2002; 108(2):145-52. DOI: 10.1016/s0092-8674(02)00622-0. View

Yi N, Xu S . Bayesian LASSO for quantitative trait loci mapping. Genetics. 2008; 179(2):1045-55. PMC: 2429858. DOI: 10.1534/genetics.107.085589. View

Churchill G, Doerge R . Empirical threshold values for quantitative trait mapping. Genetics. 1994; 138(3):963-71. PMC: 1206241. DOI: 10.1093/genetics/138.3.963. View

Hu Z, Xu S . PROC QTL-A SAS Procedure for Mapping Quantitative Trait Loci. Int J Plant Genomics. 2009; 2009:141234. PMC: 2796467. DOI: 10.1155/2009/141234. View

10.

Rankinen T, Zuberi A, Chagnon Y, Weisnagel S, Argyropoulos G, Walts B . The human obesity gene map: the 2005 update. Obesity (Silver Spring). 2006; 14(4):529-644. DOI: 10.1038/oby.2006.71. View

11.

Haley C, Knott S . A simple regression method for mapping quantitative trait loci in line crosses using flanking markers. Heredity (Edinb). 1992; 69(4):315-24. DOI: 10.1038/hdy.1992.131. View

12.

Wang H, Zhang Y, Li X, Masinde G, Mohan S, Baylink D . Bayesian shrinkage estimation of quantitative trait loci parameters. Genetics. 2005; 170(1):465-80. PMC: 1449727. DOI: 10.1534/genetics.104.039354. View

13.

Xu S, Atchley W . Mapping quantitative trait loci for complex binary diseases using line crosses. Genetics. 1996; 143(3):1417-24. PMC: 1207409. DOI: 10.1093/genetics/143.3.1417. View

14.

Xu S . Estimating polygenic effects using markers of the entire genome. Genetics. 2003; 163(2):789-801. PMC: 1462468. DOI: 10.1093/genetics/163.2.789. View

15.

Yi N, Xu S . Bayesian mapping of quantitative trait loci for complex binary traits. Genetics. 2000; 155(3):1391-403. PMC: 1461151. DOI: 10.1093/genetics/155.3.1391. View

16.

Xu C, Wang X, Li Z, Xu S . Mapping QTL for multiple traits using Bayesian statistics. Genet Res (Camb). 2009; 91(1):23-37. DOI: 10.1017/S0016672308009956. View

17.

Geman S, Geman D . Stochastic relaxation, gibbs distributions, and the bayesian restoration of images. IEEE Trans Pattern Anal Mach Intell. 2012; 6(6):721-41. DOI: 10.1109/tpami.1984.4767596. View

18.

Baima J, Nicolaou M, Schwartz F, DeStefano A, Manolis A, Gavras I . Evidence for linkage between essential hypertension and a putative locus on human chromosome 17. Hypertension. 1999; 34(1):4-7. DOI: 10.1161/01.hyp.34.1.4. View

19.

Satagopan J, Yandell B, Newton M, Osborn T . A bayesian approach to detect quantitative trait loci using Markov chain Monte Carlo. Genetics. 1996; 144(2):805-16. PMC: 1207571. DOI: 10.1093/genetics/144.2.805. View

20.

Cui Y, Yang W . Zero-inflated generalized Poisson regression mixture model for mapping quantitative trait loci underlying count trait with many zeros. J Theor Biol. 2008; 256(2):276-85. DOI: 10.1016/j.jtbi.2008.10.003. View