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Planta. 2016 Nov;244(5):1011-1028. Epub 2016 Jun 29.

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

Author information

1
State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China.
2
State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, 410125, China.
3
State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, 410125, China. brzhao652@hhrrc.ac.cn.
4
State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China. jbwang@whu.edu.cn.

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.

KEYWORDS:

Female gametophyte; Ovule development; RNA-Seq; Rice; Transcriptome

PMID:
27357232
DOI:
10.1007/s00425-016-2563-x
[Indexed for MEDLINE]

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