Plant Meiosis pp 267-280 | Cite as

Rice Female Meiosis: Genome-Wide mRNA, Small RNA, and DNA Methylation Analysis During Ovule Development

  • Helian Liu
  • Aqin Cao
  • Liyu Yang
  • Jianbo WangEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 2061)


Meiosis is an essential process in sexual life cycle, not only for the genomic stability maintenance but also for the genetic diversity creation through recombination. In rice ovule, megaspore mother cells undergo meiosis to form megaspores; then the functional megaspore performs three rounds of mitoses to form female gametophyte. However, the mechanism of gene expression and regulation in female meiosis process is still poorly understood. As important gene regulatory factors, miRNAs and DNA methylation are widely involved in plant meiosis and ovule development. In order to systematically study the potential mechanism of gene expression and regulation in female meiosis, ovules at megaspore mother cell meiosis stage, functional megaspore mitosis stage, and mature female gametophytes are collected to perform genome-wide RNA sequencing, small RNA sequencing, and bisulfite sequencing. Through bioinformatics analysis, we obtained many differentially expressed genes, miRNAs, and differentially methylated genes related to female meiosis. These data may provide important clues for further revealing the mechanism of female meiosis in rice.

Key words

Rice Female meiosis Ovule development RNA sequencing Small RNA sequencing Bisulfite sequencing 



This work was supported by the State Key Basic Research and Development Plan of China (2013CB126900).


  1. 1.
    Yang WC, Shi DQ, Chen YH (2010) Female gametophyte development in flowering plants. Annu Rev Plant Biol 61:89–108CrossRefGoogle Scholar
  2. 2.
    Siddiqi I, Ganesh G, Grossniklaus U, Subbiah V (2000) The dyad gene is required for progression through female meiosis in Arabidopsis. Development 127:197–207PubMedGoogle Scholar
  3. 3.
    Barrell PJ, Grossniklaus U (2005) Confocal microscopy of whole ovules for analysis of reproductive development: the elongate1 mutant affects meiosis II. Plant J 43:309–320CrossRefGoogle Scholar
  4. 4.
    Panoli AP, Ravi M, Sebastian J, Nishal B, Reddy TV, Marimuthu MPA et al (2006) AtMND1 is required for hoMogous pairing during meiosis in Arabidopsis. BMC Mol Biol 7:24CrossRefGoogle Scholar
  5. 5.
    Schmidt A, Wuest SE, Vijverberg K, Baroux C, Kleen D, Grossniklaus U (2011) Transcriptome analysis of the Arabidopsis megaspore mother cell uncovers the importance of RNA helicases for plant germline development. PLoS Biol 9:e1001155CrossRefGoogle Scholar
  6. 6.
    Bencivenga S, Colombo L, Masiero S (2011) Cross talk between the sporophyte and the megagametophyte during ovule development. Sex Plant Reprod 24:113–121CrossRefGoogle Scholar
  7. 7.
    Millar AA, Gubler F (2005) The Arabidopsis GAMYB-like genes, MYB33 and MYB65, are microRNA-regulated genes that redundantly facilitate anther development. Plant Cell 17:705–721CrossRefGoogle Scholar
  8. 8.
    Wei LQ, Yan LF, Wang T (2011) Deep sequencing on genome-wide scale reveals the unique composition and expression patterns of microRNAs in developing pollen of Oryza sativa. Genome Biol 12:R53CrossRefGoogle Scholar
  9. 9.
    Fei Q, Yang L, Liang W, Zhang D, Meyers BC (2016) Dynamic changes of small RNAs in rice spikelet development reveal specialized reproductive phasiRNA pathways. J Exp Bot 67:6037–6049CrossRefGoogle Scholar
  10. 10.
    Chen ZX, Li FL, Yang SN, Dong YB, Yuan QH, Wang F et al (2013) Identification and functional analysis of flowering related microRNAs in common wild rice (Oryza rufipogon Griff.). PLoS One 8:e82844CrossRefGoogle Scholar
  11. 11.
    Kim MY, Zilberman D (2014) DNA methylation as a system of plant genomic immunity. Trends Plant Sci 19:320–326CrossRefGoogle Scholar
  12. 12.
    Niederhuth CE, Schmitz RJ (2017) Putting DNA methylation in context: from genomes to gene expression in plants. Biochim Biophys Acta 1860:149–156CrossRefGoogle Scholar
  13. 13.
    Omidvar V, Mohorianu I, Dalmay T, Zheng Y, Fei Z, Pucci A et al (2017) Transcriptional regulation of male-sterility in 7B-1 male-sterile tomato mutant. PLoS One 12:e0170715CrossRefGoogle Scholar
  14. 14.
    Yang X, Zhao Y, Xie D, Sun Y, Zhu X, Esmaeili N et al (2016) Identification and functional analysis of microRNAs involved in the anther development in cotton genic male sterile line Yu98-8A. Int J Mol Sci 17:1677CrossRefGoogle Scholar
  15. 15.
    Walker J, Gao H, Zhang J, Aldridge B, Vickers M, Higgins JD et al (2018) Sexual-lineage-specific DNA methylation regulates meiosis in Arabidopsis. Nat Genet 50:130–137CrossRefGoogle Scholar
  16. 16.
    Li B, Dewey CN (2011) RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics 12:323CrossRefGoogle Scholar
  17. 17.
    Wang L, Feng Z, Wang X, Wang X, Zhang X (2010) DEGseq: an R package for identifying differentially expressed genes from RNA-seq data. Bioinformatics 26:136–138CrossRefGoogle Scholar
  18. 18.
    Allen E, Xie Z, Gustafson AM, Carrington JC (2005) MicroRNA-directed phasing during trans-acting siRNA biogenesis in plants. Cell 121:207–221CrossRefGoogle Scholar
  19. 19.
    Schwab R, Palatnik JF, Riester M, Schommer C, Schmid M, Weigel D (2005) Specific effects of microRNAs on the plant transcriptome. Dev Cell 8:517–527CrossRefGoogle Scholar
  20. 20.
    Li M, Wu H, Luo Z, Xia Y, Guan J, Wang T et al (2012) An atlas of DNA methylomes in porcine adipose and muscle tissues. Nat Commun 3:850CrossRefGoogle Scholar

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© Springer Science+Business Media, LLC, part of Springer Nature 2020

Authors and Affiliations

  1. 1.College of Life SciencesWuhan UniversityWuhanChina

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