The development of ovule in rice (Oryza sativa) is vital during its life cycle. 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. 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, 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 development.

Inter-specific hybridization and backcrossing commonly occur in plants. The use of progeny generated from inter-specific hybridization and backcrossing has been developed as a novel model system to explore gene expression divergence. The present study investigated the analysis of gene expression and miRNA regulation in backcrossed introgression lines constructed from cultivated and wild rice. High-throughput sequencing was used to compare gene and miRNA expression profiles in three progeny lines (L1710, L1817 and L1730), with different plant heights resulting from the backcrossing of introgression lines (BC2F12) and their parents (O. sativa and O. longistaminata). A total of 25,387 to 26,139 mRNAs and 379 to 419 miRNAs were obtained in these rice lines. More differentially expressed genes and miRNAs were detected in progeny/O. longistaminata comparison groups than in progeny/O. sativa comparison groups. Approximately 80% of the genes and miRNAs showed expression level dominance to O. sativa, indicating that three progeny lines were closer to the recurrent parent, which might be influenced by their parental genome dosage. Approximately 16% to 64% of the differentially expressed miRNAs possessing coherent target genes were predicted, and many of these miRNAs regulated multiple target genes. Most genes were up-regulated in progeny lines compared with their parents, but down-regulated in the higher plant height line in the comparison groups among the three progeny lines. Moreover, certain genes related to cell walls and plant hormones might play crucial roles in the plant height variations of the three progeny lines. Taken together, these results provided valuable information on the molecular mechanisms of hybrid backcrossing and plant height variations based on the gene and miRNA expression levels in the three progeny lines.

The regulation of female fertility is an important field of rice sexual reproduction research. DNA methylation is an essential epigenetic modification that dynamically regulates gene expression during development processes. However, few reports have described the methylation profiles of female-sterile rice during ovule development. In this study, ovules were continuously acquired from the beginning of megaspore mother cell meiosis until the mature female gametophyte formation period, and global DNA methylation patterns were compared in the ovules of a high-frequency female-sterile line (fsv1) and a wildtype rice line (Gui99) using whole-genome bisulfite sequencing (WGBS). Profiling of the global DNA methylation revealed hypo-methylation, and 3471 significantly differentially methylated regions (DMRs) were observed in fsv1 ovules compared with Gui99. Based on functional annotation and Kyoto encyclopedia of genes and genomes (KEGG) pathway analysis of differentially methylated genes (DMGs), we observed more DMGs enriched in cellular component, reproduction regulation, metabolic pathway, and other pathways. In particular, many ovule development genes and plant hormone-related genes showed significantly different methylation patterns in the two rice lines, and these differences may provide important clues for revealing the mechanism of female gametophyte abortion. Rice (Oryza sativa L.) not only feeds half of the global population, but it is also useful for basic molecular and genetic studies because of its relatively small genome size and complete genome information (Goff 1999;Delseny et al. 2001). As an important participant in the sexual reproduction of rice, the fertility of male and female gametes is directly related to rice yield. In recent years, attention has been focused on the mechanism of male fertility regulation, while few studies have been conducted to elucidate the mechanism of female fertility in rice. The rice ovule is an important sexual reproductive organ, and previous studies have demonstrated the inseparability of ovule development and female gametophyte formation (Reiser and Fischer 1993). Generally, the process of female gametophyte formation is mainly divided into three stages: meiotic division of the megaspore mother cell (MMC), mitotic stage of functional megaspore cells, and mature stage of embryo sac. In detail, the MMC originating from a sporogenous cell derives from below the epidermis of the nucellus and divides into the linear tetrad type after meiosis. Subsequently, the megaspore near the chalaza becomes the functional megaspore, and the remaining three megaspores die during ovule development. The functional megaspore undergoes three rounds of mitotic division and finally forms the female gametophyte with eight nuclei (Yadegari and Drews 2004;Pagnussat et al. 2005). The ovule sporophyte tissue provides the necessary nutritional and mechanical support for the formation of the female gametophyte, and communication between the ovule sporophyte and the female gametophyte has bee...

Background: Distant hybridization is an important way to create interspecific genetic variation and breed new varieties in rice. A lot of backcross introgression lines (BILs) had been constructed for the scientific issues in rice. However, studies on the critical regulatory factor lncRNA in cultivated rice, wild rice and their BIL progenies were poorly reported. Results: Here, high-throughput RNA sequencing technology was used to explore the functional characteristics and differences of lncRNAs in O. sativa, O. longistaminata and their three BC 2 F 12 progenies. A total of 1254 lncRNAs were screened out, and the number of differentially expressed lncRNAs between progenies and O. sativa were significantly less than that between progenies and O. longistaminata. Some lncRNAs regulated more than one mRNA, and 89.5% of lncRNAs regulated the expression of target genes through cis-acting. A total of 78 lncRNAs and 271 mRNAs were targeted by 280 miRNAs, and 22 lncRNAs were predicted to be the precursor of 20 microRNAs. Some miRNAs were found to target their own potential precursor lncRNAs. Over 50% of lncRNAs showed parental expression level dominance (ELD) in all three progenies, and most lncRNAs showed ELD-O. sativa rather than ELD-O. longistaminata. Further analysis showed that lncRNAs might regulate the expression of plant hormone-related genes and the adaptability of O. sativa, O. longistaminata and their progenies. Conclusions: Taken together, the above results provided valuable clues for elucidating the functional features and expression differences of lncRNAs between O. sativa, O. longistaminata and their BIL progenies, and expanded our understanding about the biological functions of lncRNAs in rice.

High-throughput sequencing was used to distinguish the gene and miRNA expression profiles in the leaves of three progenies from a rice backcross introgression line (BC2F12) and their parents (Oryza sativa and wild rice, O. longistaminata). A total of 33,419 genes and 513 miRNAs were identified in two parents and three lines, and the majority of the genes and miRNAs were commonly expressed. The results show that 10.23% to 17.94% of the genes were differentially expressed genes (DEGs) in the progenies compared with those of the two parents, and the majority of them were up-regulated. Of the miRNAs, 12.56% to15.43% were differentially expressed in the progeny/O. sativa comparisons and the majority of which were up-regulated, while 42.02% to 45.21% of miRNAs were differentially expressed in the progeny/O. longistaminata comparisons, of which nearly half were down-regulated. Most of the DEGs and differentially expressed miRNAs showed expression levels close to that of O. sativa, indicating that the expression of genes and miRNAs in progenies was closely related to their chromosome complements and that the miRNAs were more susceptible than the genes to the effects of genomic composition. Furthermore, a larger number of target genes were predicted in the progeny/O. longistaminata comparisons. Finally, we found that the expression of some genes and miRNAs might increase the possibility for abiotic stress responses and adaptation in progenies. Together, our findings increase the understanding of the molecular mechanisms of hybridization and backcrossing on the expression levels of genes and miRNAs in rice leaves.