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

Ki Hong Jung, Jinwon Lee, Chris Dardick, Young Su Seo, Peijian Cao, Patrick Canlas, Jirapa Phetsom, Xia Xu, Shu Ouyang, Kyungsook An, Yun Ja Cho, Geun Cheol Lee, Yoosook Lee, Gynheung An, Pamela C. Ronald

Research output: Contribution to journalArticle

47 Scopus citations

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.

Original languageEnglish (US)
Article numbere1000164
JournalPLoS Genetics
Volume4
Issue number8
DOIs
StatePublished - Aug 1 2008

ASJC Scopus subject areas

  • Genetics
  • Molecular Biology
  • Ecology, Evolution, Behavior and Systematics
  • Cancer Research
  • Genetics(clinical)

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    Jung, K. H., Lee, J., Dardick, C., Seo, Y. S., Cao, P., Canlas, P., Phetsom, J., Xu, X., Ouyang, S., An, K., Cho, Y. J., Lee, G. C., Lee, Y., An, G., & Ronald, P. C. (2008). Identification and functional analysis of light- responsive unique genes and gene family members in rice. PLoS Genetics, 4(8), [e1000164]. https://doi.org/10.1371/journal.pgen.1000164