The Studies On Gene Expression And Regulation In Developing Ovule Of Rice

Rice is an important kind of model monocot plant and food crop.Ovules have a very important role in sexual reproduction.However,the research on the molecular mechanism of rice ovule development is still limited.Although a series of genes related to ovule development has been identified,it is still not clear to systemtically illuminate gene expression regulation mechanism underly the ovule developmental process.To gain more understanding of the molecular events associated with the ovule development,we used RNA sequencing approach to perform transcriptome-profiling analysis of the leaf and ovules at four developmental stages(meiosis stage(OVR1),mitosis stage(OVR2),mature embryo sac stage(OVR3)and 2-days-after-fertilization stage(OVR4)).In total,25,401,23,343,23,647 and 23,806 genes were identified from the four developmental stages of the ovule,respectively.We identified a number of differently expressed genes(DEGs)from three adjacent stage comparisons,which may play crucial roles in ovule development.The DEGs were then conducted functional annotations and Kyoto encyclopedia of genes and genomes(KEGG)pathway analyses.Genes related to cellular component biogenesis,membrane-bounded organelles and reproductive regulation were identified to be highly expressed during the ovule development.Different expression levels of auxin-related and cytokinin-related genes were also identified at various stages(including the genes in OsPIN,OsYUCCA,OsIPT,OsARR,OsPUP gene families),providing evidence for the role of sporophytic ovule tissue in female gametophyte development from the aspect of gene expression.Generally,an overall transcriptome analysis for rice ovule development has been conducted.These results increased our knowledge of the complex molecular and cellular events that occur during the development of rice ovule and provided foundation for further studies on rice ovule developmentMicroRNAs are 20-24 nt small RNAs that play key roles in the regulation of many growth and developmental processes in plants.The development of rice ovule contains a series of biological events with complex molecular regulation mechanism.To gain more insight into the miRNA-mediated regulations in rice ovule development,Illumina sequencing was employed to examine the expression profiles of miRNAs from the megaspore mother cell meiosis stage to the fertilized ovule stage.Based on the sequencing data,a total of 486 known miRNAs and 204 novel miRNAs were identified,and a number of differentially expressed miRNAs from three adjacent stage comparisons may play key regulatory roles during ovule development(such as:osa-miR393,osa-miR396,osa-miR169,osa-miR159,osa-miR164).Integrated analysis with the transcriptome data of the rice developing ovule and the degradome data,we identified that the target genes of some miRNAs were related to plant hormone signal transduction pathways.The potential regulation role of miRNA between the ovule sporophytic tissue and female gametophyte has been raised.We also revealed the possible involvement of miRNAs in the programmed cell death(PCD)process after fertilization,indicating that miRNAs may play important roles in this process.Finally,this work constructed miRNA-mediated regulatory networks during rice ovule development,contributing to our understanding of miRNAs during this process.DNA methylation is an important epigenetic phenomenon that regulates gene expression without altering the DNA sequence.In this study,we use the whole genome bisulfite sequencing to analysis the methylation level of four developmental stages rice ovule.Our study revealed that the DNA methylation level showed the down regulated trend before fertilization.After fertilization,the methylation level reincreased.We aligned the differential methylation region to the reference genome.The genes included in these regions were statistically analyzed.In three comparisons,a total of 464,428 and 256 DMR-related genes have been identified,respectively.We made the GO analysis on these genes,and found that the genes were enriched with the terms of cell(GO:0005623),cell part(GO:0044464),organelle(GO:0043226),binding(GO:0005488),catalytic activity(GO:0003 824),cytology process(GO:0009987)and metabolic process(GO:0008152).By detecting the significant change on methylation level of the promoter region of genes(such as genes in bHLH family),it can be suggested that DNA methylation level may regulation the cross-talk communication between ovule sporophytic and the female gametophyte during ovule development,so as the PCD process of the ovule sporophytic tissue after fertilization.In summary,we have studied the gene expression,miRNA expression and the DNA methylation level during the rice ovule development by high-throughput sequencing technique,and constructed the gene expression regulation network during the rice ovule developmental stages,laiding the foundations for revealing the mechanism of gene expression regulation in this process.