Identification and functional analysis of light-responsive unique genes and gene family members in rice.
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.
Jung
Ki-Hong
KH
Department of Plant Pathology, University of California Davis, Davis, California, United States of America.
Lee
Jinwon
J
Dardick
Chris
C
Seo
Young-Su
YS
Cao
Peijian
P
Canlas
Patrick
P
Phetsom
Jirapa
J
Xu
Xia
X
Ouyang
Shu
S
An
Kyungsook
K
Cho
Yun-Ja
YJ
Lee
Geun-Cheol
GC
Lee
Yoosook
Y
An
Gynheung
G
Ronald
Pamela C
PC
D017360:Arabidopsis / Q000235:genetics / Q000378:metabolism; D015870:Gene Expression / Q000528:radiation effects*; D020869:Gene Expression Profiling / Q000379:methods*; D008027:Light; D008969:Molecular Sequence Data; D005810:Multigene Family; D016254:Mutagenesis, Insertional; D020411:Oligonucleotide Array Sequence Analysis; D012275:Oryza / Q000235:genetics* / Q000502:physiology / Q000528:radiation effects*; D010641:Phenotype; D010940:Plant Proteins / Q000235:genetics* / Q000378:metabolism; D015398:Signal Transduction; D014158:Transcription, Genetic / Q000528:radiation effects
D010940:Plant Proteins