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PMID: 18725934 Published · epublish English Comparative Study Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S. Validation Study

Identification and functional analysis of light-responsive unique genes and gene family members in rice.

PLoS genetics ·Vol. 4 ·No. 8 ·2008-08-22 ·Pages e1000164

Jung KH, Lee J, Dardick C, Seo YS, Cao P, Canlas P, Phetsom J, Xu X, Ouyang S, An K, Cho YJ, Lee GC, Lee Y, An G, Ronald PC

Abstract

Functional redundancy limits detailed analysis of genes in many organisms. Here, we report a method to efficiently overcome this obstacle by combining gene expression data with analysis of gene-indexed mutants. Using a rice NSF45K oligo-microarray to compare 2-week-old light- and dark-grown rice leaf tissue, we identified 365 genes that showed significant 8-fold or greater induction in the light relative to dark conditions. We then screened collections of rice T-DNA insertional mutants to identify rice lines with mutations in the strongly light-induced genes. From this analysis, we identified 74 different lines comprising two independent mutant lines for each of 37 light-induced genes. This list was further refined by mining gene expression data to exclude genes that had potential functional redundancy due to co-expressed family members (12 genes) and genes that had inconsistent light responses across other publicly available microarray datasets (five genes). We next characterized the phenotypes of rice lines carrying mutations in ten of the remaining candidate genes and then carried out co-expression analysis associated with these genes. This analysis effectively provided candidate functions for two genes of previously unknown function and for one gene not directly linked to the tested biochemical pathways. These data demonstrate the efficiency of combining gene family-based expression profiles with analyses of insertional mutants to identify novel genes and their functions, even among members of multi-gene families.

MeSH Terms
Arabidopsis/genetics,metabolism Gene Expression/radiation effects Gene Expression Profiling/methods Light Molecular Sequence Data Multigene Family Mutagenesis, Insertional Oligonucleotide Array Sequence Analysis Oryza/genetics,physiology,radiation effects Phenotype Plant Proteins/genetics,metabolism Signal Transduction Transcription, Genetic/radiation effects
Chemicals
Plant Proteins
Authors & Affiliations
15 authors, click to expand affiliations / ORCID
Jung Ki-Hong
Department of Plant Pathology, University of California Davis, Davis, California, United States of America.
Lee Jinwon
Dardick Chris
Seo Young-Su
Cao Peijian
Canlas Patrick
Phetsom Jirapa
Xu Xia
Ouyang Shu
An Kyungsook
Cho Yun-Ja
Lee Geun-Cheol
Lee Yoosook
An Gynheung
Ronald Pamela C
Conflict of Interest

The authors have declared that no competing interests exist.

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Article Info
Journal
PLoS genetics
Abbr.
PLoS Genet
ISSN
1553-7404
DOI
10.1371/journal.pgen.1000164
Published
2008-08-22
Epub
2008-00-22
Pages
e1000164
Language
English
Region
United States
NLM ID
101239074
PMCID
PMC2515340
Subset
IM
Grants
NIGMS NIH HHS · R01 GM055962 · United States
NIGMS NIH HHS · (#5R01GM055962-0 · United States
Databases
GEO
GSE8261
External Links
PubMed source DOI: 10.1371/journal.pgen.1000164 PMC Full Text View journal details
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