MiR2118-dependent U-rich phasiRNA production in rice anther wall development

Saori Araki,Masaki Endo,Koji Koizumi,Reina Komiya,Ken-Ichi Nonomura,Haruhiko Inoue,Alejandro Villar-Briones,Ngoc Tu Le,Hidetoshi Saze

doi:10.1038/s41467-020-16637-3

Abstract

Reproduction-specific small RNAs are vital regulators of germline development in animals and plants. MicroRNA2118 (miR2118) is conserved in plants and induces the production of phased small interfering RNAs (phasiRNAs). To reveal the biological functions of miR2118, we describe here rice mutants with large deletions of the miR2118 cluster. Our results demonstrate that the loss of miR2118 causes severe male and female sterility in rice, associated with marked morphological and developmental abnormalities in somatic anther wall cells. Small RNA profiling reveals that miR2118-dependent 21-nucleotide (nt) phasiRNAs in the anther wall are U-rich, distinct from the phasiRNAs in germ cells. Furthermore, the miR2118-dependent biogenesis of 21-nt phasiRNAs may involve the Argonaute proteins OsAGO1b/OsAGO1d, which are abundant in anther wall cell layers. Our study highlights the site-specific differences of phasiRNAs between somatic anther wall and germ cells, and demonstrates the significance of miR2118/U-phasiRNA functions in anther wall development and rice reproduction.

Highlights

Reproduction-specific small RNAs are vital regulators of germline development in animals and plants
We demonstrated in this study that the deletion of the miR2118 cluster in the rice genome induces severe defects in anther wall development and sterility via the reduction of 21-nt phasiRNA production
We identified novel U-rich 21-nt phasiRNAs as miR2118-dependent small RNAs in the anther wall (Figs. 1–5). It remains unclear whether the 21-nt anther wall phasiRNAs with specific nucleotides at the 5′ terminals are sorted to AGOs, which results in the enrichment of the nucleotides (Fig. 5)

Summary

Introduction

Reproduction-specific small RNAs are vital regulators of germline development in animals and plants. Small RNA profiling reveals that miR2118-dependent 21-nucleotide (nt) phasiRNAs in the anther wall are U-rich, distinct from the phasiRNAs in germ cells. Our study highlights the site-specific differences of phasiRNAs between somatic anther wall and germ cells, and demonstrates the significance of miR2118/U-phasiRNA functions in anther wall development and rice reproduction. Even though the phasiRNA biogenesis triggered by miR2118 cleavage is conserved in both monocots and dicots, miR2118 targets reproductive lincRNAs in monocots, while it generally targets protein-coding RNAs, especially derived from disease-resistant genes in dicots[14,15,16]. By integrating small RNA profiling, proteome analysis, and 3Dhistochemical analyses of miR2118 mutants, we demonstrate the functions of miR2118 in anther wall development, and propose a model for the biogenesis of miR2118-dependent UphasiRNA with AGO1 subfamilies during male reproduction in rice

Methods

Results

Conclusion