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

PLoS Genetics
Ki-Hong JungPamela Ronald

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...Continue Reading

References

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Citations

Mar 25, 2014·Plant Physiology and Biochemistry : PPB·Peter D MabbittJulian J Eaton-Rye
Nov 6, 2012·Journal of Plant Physiology·Geun-Ho JinKi-Hong Jung
Dec 27, 2011·Progress in Lipid Research·Andréa HemmerlinThomas J Bach
Aug 1, 2015·Rice·Ki-Hong JungPamela C Ronald
Oct 23, 2012·Biochimica Et Biophysica Acta·Shinya SakataHajime Wada
May 26, 2009·Assistenza infermieristica e ricerca : AIR·John Berger
May 5, 2020·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Liu DuanElena Monte

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Datasets Mentioned

BETA
GSE8261

Methods Mentioned

BETA
PCR
genotyping
PCRs
phosphotransferase

Software Mentioned

R
BLASTP
GenomeNet browser
LMGene Package
TIGR MultiExperiment Viewer
LMGene
MeV
Cytoscape
RiceCyc

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