VOLUME 7 NUMBER 1 (January to June 2014)

PSL%202014 vol07-no01-p245-274%20Yap

Philipp. 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


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

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

¹Department of Computer Science, University of the Philippines Diliman Quezon City
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.

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