Identification and molecular characterization of tissue-preferred rice genes and their upstream regularly sequences on a genome-wide level

Abstract

BackgroundGene upstream regularly sequences (URSs) can be used as one of the tools to annotate the biological functions of corresponding genes. In addition, tissue-preferred URSs are frequently used to drive the transgene expression exclusively in targeted tissues during plant transgenesis. Although many rice URSs have been molecularly characterized, it is still necessary and valuable to identify URSs that will benefit plant transformation and aid in analyzing gene function.ResultsIn this study, we identified and characterized root-, seed-, leaf-, and panicle-preferred genes on a genome-wide level in rice. Subsequently, their expression patterns were confirmed through quantitative real-time RT-PCR (qRT-PCR) by randomly selecting 9candidate tissue-preferred genes. In addition, 5 tissue-preferred URSs were characterized by investigating the URS::GUS transgenic plants. Of these URS::GUS analyses, the transgenic plants harboring LOC_Os03g11350 URS::GUS construct showed the GUS activity only in young pollen. In contrast, when LOC_Os10g22450 URS was used to drive the reporter GUS gene, the GUS activity was detected only in mature pollen. Interestingly, the LOC_Os10g34360 URS was found to be vascular bundle preferred and its activities were restricted only to vascular bundles of leaves, roots and florets. In addition, we have also identified two URSs from genes LOC_Os02G15090 and LOC_Os06g31070 expressed in a seed-preferred manner showing the highest expression levels of GUS activities in mature seeds.ConclusionBy genome-wide analysis, we have identified tissue-preferred URSs, five of which were further characterized using transgenic plants harboring URS::GUS constructs. These data might provide some evidence for possible functions of the genes and be a valuable resource for tissue-preferred candidate URSs for plant transgenesis.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-014-0331-2) contains supplementary material, which is available to authorized users.

Genome‐wide analysis of polymorphisms identified domestication‐associated long low‐diversity region carrying important rice grain size/weight quantitative trait loci

“…It seems that the G/A SNP could cause variation in the grain size/weight trait more effectively in indica and tropical japonica rice genotypes. Intriguingly, this nucleotide variation (G/A) was found to be present just 4 bases away from the GTCAT element known as cis ‐regulatory Skn‐1_motif (Lescot et al ., 2002), which is required for the expression of genes in the endosperm (Takaiwa et al ., 1991; Wu et al ., 2000; Jiang et al ., 2014). In addition, an ubiquitin conjugating enzyme coding gene ( OsUBC43 , LOC_Os05g14300) having preferential expression during panicle and seed development was found at 6.4 kb downstream of the G/A SNP site (Kawahara et al ., 2013).…”

Identification and analysis of the stigma and embryo sac-preferential/specific genes in rice pistils

“…The methods of reverse transcription and RT-PCR were performed according to Zhao et al [ 98 ]. The threshold cycle (C T ) value was automatically calculated by the Bio-Rad CFX Manager 3.1 system software, and the delta-delta Ct method was used to calculate the relative expression levels [ 99 , 100 ]. The rice eEF-1α gene was used as an internal control for quantitative RT-PCR, while Actin gene for semi-quantitative RT-PCR [ 54 ].…”

Genome-wide analysis of polymorphisms identified domestication-associated polymorphism desert carrying important rice grain size/weight QTL

“…It seems that G/A SNP could cause variation in grain size/weight more effectively in indica and tropical japonica rice genotypes. This nucleotide variation (G/A) was found to be present just 4 bases away from GTCAT element known as cis-regulatory Skn-1_motif (Lescot et al, 2002), which is required for the expression of genes in the endosperm (Takaiwa et al, 1991;Wu et al, 2000;Jiang et al, 2014). In addition, an ubiquitin conjugating enzyme coding gene (OsUBC43, LOC_Os05g14300) having preferential expression during panicle and seed development was found at 6.4 kb downstream of G/A SNP site (Kawahara et al, 2013).…”