TITLE

Multitrait analysis of quantitative trait loci using Bayesian composite space approach

AUTHOR(S)
Ming Fang; Dan Jiang; Li Jun Pu; Hui Jiang Gao; Peng Ji; Hong Yi Wang; Run Qing Yang
PUB. DATE
January 2008
SOURCE
BMC Genetics;2008, Vol. 9, Special section p1
SOURCE TYPE
Academic Journal
DOC. TYPE
Article
ABSTRACT
Background: Multitrait analysis of quantitative trait loci can capture the maximum information of experiment. The maximum-likelihood approach and the least-square approach have been developed to jointly analyze multiple traits, but it is difficult for them to include multiple QTL simultaneously into one model. Results: In this article, we have successfully extended Bayesian composite space approach, which is an efficient model selection method that can easily handle multiple QTL, to multitrait mapping of QTL. There are many statistical innovations of the proposed method compared with Bayesian single trait analysis. The first is that the parameters for all traits are updated jointly by vector or matrix; secondly, for QTL in the same interval that control different traits, the correlation between QTL genotypes is taken into account; thirdly, the information about the relationship of residual error between the traits is also made good use of. The superiority of the new method over separate analysis was demonstrated by both simulated and real data. The computing program was written in FORTRAN and it can be available for request. Conclusion: The results suggest that the developed new method is more powerful than separate analysis.
ACCESSION #
36086245

 

Related Articles

  • Bayesian Mapping of Genomewide Interacting Quantitative Trait Loci for Ordinal Traits. Nengjun Yi; Banerjee, Samprit; Pomp, Daniel; Yandeilt, Brian S. // Genetics;Jul2007, Vol. 176 Issue 3, p1855 

    Development of statistical methods and software for mapping interacting QTL has been the focus of much recent research. We previously developed a Bayesian model selection framework, based on the composite model space approach, for mapping multiple epistatic QTL affecting continuous traits. In...

  • Bayesian shrinkage mapping for multiple QTL in half-sib families. Gao, H.; Fang, M.; Liu, J.; Zhang, Q. // Heredity;Nov2009, Vol. 103 Issue 5, p368 

    Recently, an effective Bayesian shrinkage estimation method has been proposed for mapping QTL in inbred line crosses. However, with regard to outbred populations, such as half-sib populations with maternal information unavailable, it is not straightforward to utilize such a shrinkage estimation...

  • Hierarchical likelihood opens a new way of estimating genetic values using genome-wide dense marker maps. Xia Shen; Rönnegård, Lars; Carlborg, Örjan // BMC Proceedings;2011 Supplement 3, Vol. 5 Issue Suppl 3, p1 

    Background: Genome-wide dense markers have been used to detect genes and estimate relative genetic values. Among many methods, Bayesian techniques have been widely used and shown to be powerful in genome-wide breeding value estimation and association studies. However, computation is known to be...

  • Gene Mapping via Bulked Segregant RNA-Seq (BSR-Seq). Sanzhen Liu; Cheng-Ting Yeh; Ho Man Tang; Nettleton, Dan; Schnable, Patrick S. // PLoS ONE;May2012, Vol. 7 Issue 5, p1 

    Bulked segregant analysis (BSA) is an efficient method to rapidly and efficiently map genes responsible for mutant phenotypes. BSA requires access to quantitative genetic markers that are polymorphic in the mapping population. We have developed a modification of BSA (BSR-Seq) that makes use of...

  • Another Look at Bayesian Analysis of AMMI Models for Genotype-Environment Data. Josse, Julie; Eeuwijk, Fred; Piepho, Hans-Peter; Denis, Jean-Baptiste // Journal of Agricultural, Biological & Environmental Statistics (;Jun2014, Vol. 19 Issue 2, p240 

    Linear-bilinear models are frequently used to analyze two-way data such as genotype-by-environment data. A well-known example of this class of models is the additive main effects and multiplicative interaction effects model (AMMI). We propose a new Bayesian treatment of such models offering a...

  • R/qtlDesign: inbred line cross experimental design. Sen, Śaunak; Satagopan, Jaya; Broman, Karl; Churchill, Gary // Mammalian Genome;Feb2007, Vol. 18 Issue 2, p87 

    An investigator planning a QTL (quantitative trait locus) experiment has to choose which strains to cross, the type of cross, genotyping strategies, and the number of progeny to raise and phenotype. To help make such choices, we have developed an interactive program for power and sample size...

  • Genetic Mapping in the Presence of Genotyping Errors. Cartwright, Dustin A.; Troggio, Michela; Velasco, Riccardo; Gutin, Alexander // Genetics;Aug2007, Vol. 176 Issue 4, p2521 

    Genetic maps are built using the genotypes of many related individuals. Genotyping errors in these data sets can distort genetic maps, especially by inflating the distances. We have extended the traditional likelihood model used for genetic mapping to include the possibility of genotyping...

  • Geographic and Genetic Population Differentiation of the Amazonian Chocolate Tree (Theobroma cacao L). Motamayor, Juan C.; Lachenaud, Philippe; e Mota, Jay Wallace da Silva; Loor, Rey; Kuhn, David N.; Brown, J. Steven; Schnell, Raymond J. // PLoS ONE;2008, Vol. 3 Issue 10, p1 

    Numerous collecting expeditions of Theobroma cacao L. germplasm have been undertaken in Latin-America. However, most of this germplasm has not contributed to cacao improvement because its relationship to cultivated selections was poorly understood. Germplasm labeling errors have impeded breeding...

  • BM-Map: an efficient software package for accurately allocating multireads of RNA-sequencing data. Norris, Clift; Yuan Yuan; Kam-Wah Tsui; Yanxun Xu; Han Liang; Yuan Ji // BMC Genomics;2012, Vol. 13 Issue Suppl 8, p1 

    Background: RNA sequencing (RNA-seq) has become a major tool for biomedical research. A key step in analyzing RNA-seq data is to infer the origin of short reads in the source genome, and for this purpose, many read alignment/mapping software programs have been developed. Usually, the majority of...

Share

Read the Article

Courtesy of THE LIBRARY OF VIRGINIA

Sorry, but this item is not currently available from your library.

Try another library?
Sign out of this library

Other Topics