Gene Expression and miRNA Regulation Changes in Leaves of Rice Backcross Introgression Lines

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

La Vigie marocaine

24 juillet 19391939/07/24 (A31,N11200)-1939/07/24

Genome-Wide Analysis of DNA Methylation During Ovule Development of Female-Sterile Rice fsv1

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 wild-type 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

GO classification of all 30,858 genes in leaf and four developmental stages of ovule.

<p>The results are summarized in three main GO categories (cellular component, molecular function and biological process. The x-axis represents the name of GO sub-categories. The left y-axis represents the percent of a specific category of genes in that main category. The right y-axis represents the number of genes expressed in the given sub-category.</p

Morphological phenotypes characterizations of the three progeny lines and their parents.

<p>(A) The rice height of five lines. (B) The third internode length of five lines. (C) The cell length of third internode in five lines. (D) The cell number of third internode in five lines. Asterisks indicate a significant difference (P< 0.01) between progeny line and their parents through t-test.</p

Pathway of plant hormone signal transduction analysis in the three progeny lines.

<p>The up/down regulation of plant hormone signal transduction pathway in the progeny/<i>O</i>. <i>sativa</i> comparison groups (A) and the progeny/<i>O</i>. <i>longistaminata</i> comparison groups (B). Red standing for up-regulated and blue standing for down-regulated.</p

Hierarchical cluster analysis of gene expression based on log ratio RPKM data.

<p>The color key represented RPKM normalized log₂transformed counts. The green color represented lower expression, and the red color represented higher expression. Each column represented an experimental condition, each row represented a gene.</p

An overview of eight types of expression patterns of the genes from different pathways.

<p>An overview of eight types of expression patterns of the genes from different pathways.</p

MapMan overview of cellular metabolism (a) and regulation (b)in OVR1-vs-OVR4.Each square represented a gene, and the color key represented the value of RPKM normalized log₂.

<p>Red meant down-regulation of the gene and the blue color meant up-regulation.</p