Genome-Wide Identification and Functional Analysis of Genes Expressed Ubiquitously in Rice

Abstract

Genes that are expressed ubiquitously throughout all developmental stages are thought to be necessary for basic biological or cellular functions. Therefore, determining their biological roles is a great challenge. We identified 4034 of these genes in rice after studying the results of Agilent 44K and Affymetrix meta-anatomical expression profiles. Among 105 genes that were characterized by loss-of-function analysis, 79 were classified as members of gene families, the majority of which were predominantly expressed. Using T-DNA insertional mutants, we examined 43 genes and found that loss of expression of six genes caused developing seed- or seedling-defective phenotypes. Of these, three are singletons without similar family members and defective phenotypes are expected from mutations. Phylogenomic analyses integrating genome-wide transcriptome data revealed the functional dominance of three ubiquitously expressed family genes. Among them, we investigated the function of Os03g19890, which is involved in ATP generation within the mitochondria during endosperm development. We also created and evaluated functional networks associated with this gene to understand the molecular mechanism. Our study provides a useful strategy for pheonome analysis of ubiquitously expressed genes in rice.

OsPhyB-Mediating Novel Regulatory Pathway for Drought Tolerance in Rice Root Identified by a Global RNA-Seq Transcriptome Analysis of Rice Genes in Response to Water Deficiencies

“…Promoter traps employing the GUS reporter gene system have been used to identify promoters involved in regulating tissue-specific and stress-responsive expression patterns (Jung et al, 2005, 2006, 2015). Our RNA-Seq data analysis revealed 98 genes showing >3 (log 2 scale)-fold upregulation by stress when compared with the control (Table S3).…”

Genome-Wide Identification and Analysis of Genes, Conserved between japonica and indica Rice Cultivars, that Respond to Low-Temperature Stress at the Vegetative Growth Stage

“…These lines were obtained from a mixed pool of PFG T-DNA tagging lines from POSTECH in Korea (Lee et al, 2004; Jung et al, 2005, 2006, 2015; Hong et al, 2017; Wei et al, 2017). The resultant plantlets were then exposed to cold stress (4°C) for 0 or 24 h. Afterward, whole seedlings from all treatment groups were soaked for 8 h in a GUS -staining solution before their roots were photographed with a camera (Canon EOS 550D; Cannon, Tokyo, Japan).…”

Crosstalk between diurnal rhythm and water stress reveals an altered primary carbon flux into soluble sugars in drought-treated rice leaves

“…To confirm the expression patterns of candidate genes up-regulated by drought, we used two strategies: screening of promoter trap lines (as we have described previously) and generation of transgenic plants carrying the β-glucuronidase (GUS) reporter gene vector under the control of the target gene promoter (Fig. 2 ) 37 , 38 . For the former approach, we analyzed promoter trap lines for 70 candidate genes and found that only one had positive GUS expression that matched the activity of its co-segregating genotypes.…”

“…Screening of the promoter trap lines and GUS staining were performed as described previously 37 , 38 , 86 . We used a T-DNA-specific primer in the pGA2715 vector as well as gene-specific primer sequences to confirm, via PCR, the co-segregation of GUS expression and T-DNA insertion in rice Line PFG_3A-02918 (Table S8 ).…”

“…PFG 4A-04197 is a promoter trap line of LOC_Os03g08010 and PFG 5A-00191 is a promoter trap line of LOC_Os03g01910 . Both genes showed ubiquitous expression and are not in our candidate gene list (Figure S3 ) 38 .…”