Plant Molecular Biology

, Volume 95, Issue 1–2, pp 89–98 | Cite as

Low genetic diversity and functional constraint of miRNA genes participating pollen–pistil interaction in rice



Key message

In this study, we sequenced and analyzed the expression and evolution of rice miRNA genes participating pollen-pistil interaction that is crucial to rice yield.


Pollen–pistil interaction is an essential reproductive process for all flowering plants. While microRNAs (miRNAs) are important noncoding small RNAs that regulate mRNA levels in eukaryotic cells, there is little knowledge about which miRNAs involved in the early stages of pollen–pistil interaction in rice and how they evolve under this conserved process. In this study, we sequenced the small RNAs in rice from unpollinated pistil (R0), pistil from 5 min and 15 min after pollination, respectively, to identify known and novel miRNAs that are involved in this process. By comparing the corresponding mRNA-seq dataset, we identified a group of miRNAs with strong negative expression pattern with their target genes. Further investigation of all miRNA loci (MIRNAs) across 1083 public rice accessions revealed significantly reduced genetic diversity in MIRNAs with strong negative expression of their targets when comparing to those with little or no impact on targets during pollen–pistil interaction. Annotation of targets suggested that those MIRNAs with strong impact on targets were pronounced in cell wall related processes such as xylan metabolism. Additionally, plant conserved miRNAs, such as those with functions in gibberellic acid, auxin and nitrate signaling, were also with strong negative expression of their targets. Overall, our analyses identified key miRNAs participating pollen–pistil interaction and their evolutionary patterns in rice, which can facilitate the understanding of molecular mechanisms associated with seed setting.


MicroRNA Oryza sativa Evolution Pistil–pollination interaction 



This work was supported by the National Natural Science Foundation of China (No. 31671775 and No. 31100230), the National Key Research and Development Program of China (2016YFD0100904) and the Open Research Fund of State Key Laboratory of Hybrid Rice, Wuhan University (No. KF201306). We thank Rebecca Njeri from Wuhan Botanical Garden, Chinese Academy of Sciences for revising the manuscript.

Author contributions

The experiment was designed by K. W. and P. Y. The experiment was performed by K. W. M. L. and X. W. performed some of the experiment. T. S. performed the analysis and wrote the manuscript.

Supplementary material

11103_2017_638_MOESM1_ESM.jpg (322 kb)
Supplementary Fig. 1—Length distribution of small RNA sequences in R0 (A), R5 (B) and R15 (C) (JPG 322 KB)
11103_2017_638_MOESM2_ESM.jpg (99 kb)
Supplementary Fig. 2—Pollen-specific miRNAs are absent in pollinated pistil samples (R5 and R15) (JPG 99 KB)
11103_2017_638_MOESM3_ESM.jpg (263 kb)
Supplementary Fig. 3—Scatter plot of differential expression of miRNAs between samples (JPG 263 KB)
11103_2017_638_MOESM4_ESM.jpg (397 kb)
Supplementary Fig. 4—Stem-loop real-time PCR validation of the expression of 25 miRNAs during the three stages of pollen-pistil interaction. (A) Expression in sRNA-seq. (B) Expression in qRT-PCR experiment. Expression values in (A) and (B) for a selected miRNA across three samples were standardized to have mean 0.3333 and standard deviation 1. (C) Correlation coefficient of expression of each miRNAs between sRNA-seq and qRT-PCR (JPG 396 KB)
11103_2017_638_MOESM5_ESM.xlsx (1.2 mb)
Supplementary Tables S1–S6 (XLSX 1198 KB)


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Copyright information

© Springer Science+Business Media B.V. 2017

Authors and Affiliations

  1. 1.Key Laboratory of Plant Germplasm Enhancement and Specialty AgricultureWuhan Botanical Garden, Chinese Academy of SciencesWuhanChina
  2. 2.College of Life SciencesWuhan UniversityWuhanChina
  3. 3.Sino-African Joint Research CenterChinese Academy of SciencesWuhanChina

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