Genome-wide transcriptome analysis of female-sterile rice ovule shed light on its abortive mechanism

Abstract

The comprehensive transcriptome analysis of rice female-sterile line and wild-type line ovule provides an important clue for exploring the regulatory network of the formation of rice fertile female gametophyte. Ovules are the female reproductive tissues of rice (Oryza sativa L.) and play a major role in sexual reproduction. To investigate the potential mechanism of rice female gametophyte fertility, we used RNA sequencing, combined with genetic subtraction, to compare the transcriptome of the ovules of a high-frequency female-sterile line (fsv1) and a rice wild-type line (Gui 99) during ovule development. Ovules were harvested at three developmental stages: ovule containing megaspore mother cell in meiosis process (stage 1), ovule containing functional megaspore in mitosis process (stage 2), and ovule containing mature female gametophyte (stage 3). Six cDNA libraries generated a total of 42.2 million high-quality clean reads that aligned with 30,204 genes. The comparison between the fsv1 and Gui 99 ovules identified a large number of differentially expressed genes (DEGs), i.e., 45, 495, and 932 DEGs at the three ovule developmental stages, respectively. From the comparison of the two rice lines, Gene Ontology, Kyoto Encyclopedia of Genes and Genomes, and MapMan analyses indicated that a large number of DEGs associated with starch and sucrose metabolism, plant hormone signal transduction, protein modification and degradation, oxidative phosphorylation, and receptor kinase. These DEGs might play roles in ovule development and fertile female gametophyte formation. Many transcription factor genes and epigenetic-related genes also exhibit different expression patterns and significantly different expression levels in two rice lines during ovule development, which might provide important information regarding the abortive mechanism of the female gametophyte in rice.

Genetic Subtraction Profiling Identifies Candidate miRNAs Involved in Rice Female Gametophyte Abortion

“…Using psRobot and TargetFinder software, we predicted the potential target genes of all differentially expressed known miRNAs in all comparisons. Comparing the expression profiles of detected known miRNAs with the transcriptome profiles of their corresponding predicted targets, which we obtained from the same experimental system in Yang et al (2016), we found that some miRNAs exhibited the same expression trends as their corresponding predicted targets in the same comparison, while some miRNAs exhibited opposite expression trends as their corresponding predicted targets in the same comparison. As miRNAs usually negatively regulate the expression of their target genes, the predicted targets that exhibited the opposite expression trends as the miRNAs in the same comparison were defined as coherent target genes.…”

Single molecular real-time sequencing revealing the ovule abortion regulatory mechanisms in the female-sterile line of Pinus tabuliformis Carr.

“…1). Previous studies about female sterile are mainly using NGS [36,37], however, NGS was limited for the short length of reads, the sequencing products were incomplete and required assembly. SMRT sequencing can overcome the disadvantage of NGS because of its long reads [18].…”

RNA-seq Analysis Reveals Gene Expression Profiling of Female Fertile and Sterile Ovules of Pinus Tabulaeformis Carr. during Free Nuclear Mitosis of the Female Gametophyte

“…Recently, Yang et al revealed extensive changes in the transcriptome of Arabidopsis ovules during the course of ovule development [5] but little attention has been paid to gene expression of FG development in the woody gymnosperm P. tabulaeformis during the FNM process. In the present study, using RNA-Seq to examine global gene expression profiles over a time course of FNM in P. tabulaeformis ovules, we found the preferential expression of DEGs (|log 2 (ratio)| > 2) between the FL and SL ovules at three developmental stages, indicating considerable difference in the gene expression of ovules.…”

“…Accumulating evidence shows that the FNM is ensured by proper mitosis, cellular metabolism and developmental regulation [1]. Genetic studies [5,6] have revealed some functional genes that regulate FNMM, such as genes involved in the cell cycle and phytohormone response. For example, many FG mutations, which were identified through a distorted Mendelian segregation screen, display mitotic arrest of the FNM [7], indicating that the progression of the mitotic cycle is crucial for the formation of a functional gametophyte.…”