Low genetic diversity and functional constraint of miRNA genes participating pollen–pistil interaction in rice
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.
KeywordsMicroRNA 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.
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.
- Bartel DP (2007) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 131:11–29. (Reprinted from Cell, vol 116, pg 281–297, 2004) Google Scholar
- Huang XH, Kurata N, Wei XH, Wang ZX, Wang A, Zhao Q, Zhao Y, Liu KY, Lu HY, Li WJ, Guo YL, Lu YQ, Zhou CC, Fan DL, Weng QJ, Zhu CR, Huang T, Zhang L, Wang YC, Feng L, Furuumi H, Kubo T, Miyabayashi T, Yuan XP, Xu Q, Dong GJ, Zhan QL, Li CY, Fujiyama A, Toyoda A, Lu TT, Feng Q, Qian Q, Li JY, Han B (2012) A map of rice genome variation reveals the origin of cultivated rice. Nature 490:497–501CrossRefPubMedGoogle Scholar
- Huang J, Li ZY, Zhao DZ (2016) Deregulation of the OsmiR160 target gene osarf18 causes growth and developmental defects with an alteration of auxin signaling in rice. Scientific Reports 6.Google Scholar