Genome-wide identification and analysis of rice genes preferentially expressed in pollen at an early developmental stage

Abstract

Microspore production using endogenous developmental programs has not been well studied. The main limitation is the difficulty in identifying genes preferentially expressed in pollen grains at early stages. To overcome this limitation, we collected transcriptome data from anthers and microspore/pollen and performed meta-expression analysis. Subsequently, we identified 410 genes showing preferential expression patterns in early developing pollen samples of both japonica and indica cultivars. The expression patterns of these genes are distinguishable from genes showing pollen mother cell or tapetum-preferred expression patterns. Gene Ontology enrichment and MapMan analyses indicated that microspores in rice are closely linked with protein degradation, nucleotide metabolism, and DNA biosynthesis and regulation, while the pollen mother cell or tapetum are strongly associated with cell wall metabolism, lipid metabolism, secondary metabolism, and RNA biosynthesis and regulation. We also generated transgenic lines under the control of the promoters of eight microspore-preferred genes and confirmed the preferred expression patterns in plants using the GUS reporting system. Furthermore, cis-regulatory element analysis revealed that pollen specific elements such as POLLEN1LELAT52, and 5659BOXLELAT5659 were commonly identified in the promoter regions of eight rice genes with more frequency than estimation. Our study will provide new sights on early pollen development in rice, a model crop plant.

Transcriptome and Gene Editing Analyses Reveal MOF1a Defect Alters the Expression of Genes Associated with Tapetum Development and Chromosome Behavior at Meiosis Stage Resulting in Low Pollen Fertility of Tetraploid Rice

“…In addition, these 793 DEGs in mof1a were further compared with 2987 meiosis-related genes ( Table S10 ), which are specifically or preferentially expressed in PMCs, or were identified from defective meiosis process [ 10 , 26 , 27 , 32 , 33 , 34 , 35 , 40 , 41 ]. A total of 335 DEGs were meiosis-related genes (mDEGs), including 23 down- and 312 up-regulated mDEGs ( Table S11 ).…”

“…A total of 335 DEGs were meiosis-related genes (mDEGs), including 23 down- and 312 up-regulated mDEGs ( Table S11 ). Among these 335 mDEGs, 29 mDEGs were differentially expressed in neo-tetraploid line H1 relative to low pollen fertility line LF, 50 mDEGs were differentially expressed in another neo-tetraploid line HF relative to LF, 146 mDEGs were specifically or preferentially expressed in PMCs [ 33 , 34 , 41 ], and 287 mDEGs were differentially expressed in meiotic anthers of autotetraploid lines with low fertility relative to corresponding diploid lines [ 4 , 10 ]. Moreover, nine mDEGs were up-regulated in low pollen fertility lines among three groups (HF/LF, H1/LF, and mof1a /H1), while all of them were differentially expressed in meiotic anthers between different ploidy lines (02428-4x/02428-2x or Taichung65-4x/Taichung65-2x) [ 4 , 10 ], including LOC_Os03g61150 , LOC_Os03g59880 , LOC_Os08g28820 (S-phase kinase association protein 1, Skp1, family member), LOC_Os01g04409 , LOC_Os08g27220 , LOC_Os02g50690 , LOC_Os07g35370 , LOC_Os01g13610 , and LOC_Os11g47809 ( OsMT1a , a type 1 metallothionein) ( Table S12 ).…”

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

“…As we have described for previous investigations, we identified meaningful biological processes and visualized significant metabolic pathways through GO enrichment and MapMan analyses 26 , 63 . Results from the former suggested that biological processes mainly related to carbohydrate metabolism are important in the crosstalk between the drought up-regulation and diurnal rhythm.…”

Identification and validation of organ-preferential genes and analysis of corresponding upstream tissue-specific promoters in wheat

“…To meet the need of efficient wheat genetic engineering and avoid various types of unpredictable expression driven by homologous promoters from other species, more tissuespecific native promoters should be isolated and studied in wheat. Tissue/organ-specific genes and promoters can be commonly screened by microarray and next-generation sequencing (NGS) technology with high efficiency (Endo et al 2004, Ye et al 2012, Nguyen et al 2016. For instance, the organ-specific genes and promoters in seven tissues were efficiently isolated in rice by using microarrays (Chae et al 2016).…”