Identification and functional analysis of light-responsive unique or paralogous gene family members in rice using a near genomic gene microarray

Authors: JUNG, KI-HONG - UNIV OF CALIFORNIA; Dardick, Christopher - Chris; LEE, JINWON - UNIV OF SCI & TECH, KOREA; PHETSOM, JIRAPA - UNIV OF CALIFORNIA; XU, XIA - UNIV OF CALIFORNIA; SEO, YOUNG-SU - UNIV OF CALIFORNIA; OUYANG, SHU - J. CRAIG VENTER INST; LY, EUGENE - J. CRAIG VENTER INST; AN, KYUNGSOOK - UNIV OF SCI & TECH, KOREA; CHO, YUN-JA - UNIV OF SCI & TECH, KOREA; LEE, GEUN CHEOL - KONKUK UNIV, KOREA; BUELL, C. ROBIN - J. CRAIG VENTER INST; AN, GYNHEUNG - UNIV OF SCI & TECH, KOREA; RONALD, PAMELA - UNIV OF CALIFORNIA

Submitted to: PLoS Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/15/2008
Publication Date: 8/22/2008
Citation: Jung, K., Dardick, C.D., Lee, J., Phetsom, J., Xu, X., Seo, Y., Ouyang, S., Ly, E., An, K., Cho, Y., Lee, G., Buell, C., An, G., Ronald, P. 2008. Identification and functional analysis of light-responsive unique or paralogous gene family members in rice using a near genomic gene microarray. PLoS Genetics. 4(8):e1000164.

Interpretive Summary: Functional genomics involves large scale data collection for many genes at the same time and has the promise of providing methods to rapidly describe the functions of every gene within a living organism. The analysis and interpretation of functional genomic data is currently a major bottleneck in this endeavor. This is in part due to the current compartmentalization of data within each field of study. In this manuscript, we report the creation of a rice microarray platform capable of capturing gene expression data from over 40,000 genes at the same time. It was designed with several unique features that provide new capabilities for this technology including the ability to differentiate between very closely related genes and the detection of different gene splicing variants. This new rice microarray was validated by comparing gene expression profiles of plants maintained in light or dark conditions. The data was then coupled with other functional genomic data from different sources and with biological observations of plants containing mutations within targeted genes. Taken together, the results reveal how integration of functional genomic data can elucidate gene function. Also, the functions of several new rice genes that control light responses are described.

Technical Abstract: Using a NSF45K-gene-microarray, we performed expression-profiling experiments on 2-week-old light- and dark-grown rice leaf tissue to identify mutants of light-responsive genes. We identified 356 genes that were at least 8-fold light induced genes at FDR of 1.00E-06. Then, we screened rice T-DNA insertional mutants for 37 genes that were at least two mutant alleles. Mutants identified in rice chlorophyll biosynthesis pathway indicated that unique genes without paralogs or paralogous family gene members showing significant light induction could be good targets to study light-response. After excluding 12 not predominantly expressed genes, which can be compensated by other family genes, and 5 genes showing inconsistent results with referring to publicly available other light versus dark microarray data, we observed phenotypic changes. They associated with light perception or transduction in 7 out of 11 unique sequences without paralogs tested and 4 out of 9 genes belonging to multi-gene families, which were the predominantly expressed family member in the light. Of the 11 mutants, the functions of 5 have not yet been characterized in Arabidopsis. These data demonstrate the efficiency of combining rice gene expression profiles with rice insertional mutant analyses to identify novel genes and their functions, even among members of multi-gene families.