ISSN 2094-2818

Editors: Eduardo A. Padlan and
Gisela P. Padilla-Concepcion
VOLUME 7 NUMBER 1 (January to June 2014)
 

Phil. Sci. Lett. 2014 7 (1) 245-274
available online: June 25, 2014

*Corresponding author
Email Address: jcyap@dcs.upd.edu.ph
Received: October 21, 2013
Revised: March 8, 2014
Accepted: March 20, 2014
Published: June 25, 2014
Editor-in-charge: Eduardo A. Padlan

Keywords: partial regression coefficient analysis, recombinant inbred lines, genetic markers, gene expression, quantitative trait loci, candidate causal genes

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  ARTICLE
A partial regression coefficient analysis framework to infer candidate genes potentially causal to traits in recombinant inbred lines

by Jan Michael Yap1*, Ramil Mauleon2, Eduardo Mendoza1,3, and Henry Adorna1

1Department of Computer Science, University of the Philippines Diliman Quezon City Philippines
2T.T. Chang Genetic Resources Center, International Rice Research Institute, Los Baños, Laguna, Philippines
3Department of Membrane Biochemistry, Max Planck Institute of Biochemistry, Martinsried, Germany

An important task in genetics research is to be able to generate a set of candidate genes causal towards expression of a particular trait. In this paper, a partial regression coefficient analysis framework to infer candidate genes causal to a trait, particularly for recombinant inbred lines, is proposed. The framework integrates marker data, quantitative trait loci data, phenotypic data, and gene expression and location data to generate set of candidate genes. The framework was applied to infer candidate causal genes to salt tolerance in rice. Results suggest 91 genes to be potentially causal to salt tolerance in rice. Review of the literature substantiated the results in mentioning the role of genes related to cell wall and membrane-related function, signal transduction, and gene expression-related functions to salt tolerance in rice.