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OsDCL3b affects grain yield and quality in rice

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We reported that knockdown of OsDCL3b decreased grain yield but increased grain quality in rice, which is helpful for molecular breeding in crops.

Abstract

Multiple DICER-LIKE (DCL) genes usually exist and show diverse biochemical and phenotypic functions in land plants. In rice, the biochemical function of OsDCL3b is known to process 24-nucleotide panicle phased small RNAs, however, its phenotypic functions are unclear. Here we reported that knockdown of OsDCL3b led to reduced pollen fertility, seed setting rate, and decreased grain yield but increased grain quality in rice. To reveal the molecular mechanism of the above phenomena, extracted RNAs from rice panicles of the wild type (WT) and OsDCL3b-RNAi line S6-1 were analyzed by deep sequencing. It showed that knockdown of OsDCL3b affected the biogenesis of both 21- and 24-nucleotide small RNAs including miRNAs and phased small RNAs. Using RNA-seq, 644 up- and 530 down-regulated mRNA genes were identified in panicles of line S6-1, and 550 and 273 differentially spliced genes with various alternative splicing (AS) events were observed in panicles of line S6-1 and WT, respectively, suggesting that OsDCL3b involved in influencing the transcript levels of mRNA genes and the AS events in rice panicles. Thus, our results show that knockdown of OsDCL3b will affect the biogenesis of small RNAs, which is involved in regulating the transcription of mRNA genes, and consequently influence the grain yield and quality in rice.

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Acknowledgements

We thank Professor Yaoguang Liu (College of Life Sciences, South China Agricultural University) for providing the RNAi vector and Dr. Zuyu Chen (School of Environmental Engineering, Wuhan Textlie University) for advice on doing RNA verification experiment. This work was mainly supported by grants from the National Natural Science Foundation of China (31260313, 31471426 and 31560383).

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  1. Peng-Fei Liao and Jie-Xiu Ouyang have contributed equally to this work

Authors and Affiliations

  1. Key Laboratory of Molecular Biology and Gene Engineering in Jiangxi Province, School of Life Sciences, Nanchang University, Nanchang, 330031, China

    Peng-Fei Liao, Jie-Xiu Ouyang, Lan Yang, Xin Wang, Xiao-Jue Peng, Dong Wang, You-Lin Zhu & Shao-Bo Li

  2. College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China

    Jian-Jun Zhang

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  1. Peng-Fei Liao
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Contributions

Experiments were designed by SL, YZ and PL. SL, PL, JO, JZ and XP conducted experiments. DW, LY and SL analyzed the data. SL, DW and XW wrote the manuscript and all authors edited the manuscript. All authors read and approved the final manuscript.

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Correspondence to You-Lin Zhu or Shao-Bo Li.

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11103_2018_806_MOESM1_ESM.tif

Fig. S1 Transcript levels of OsDCL family genes in rice young panicle by qRT-PCR. Data are mean ± SE for three replicates. ** indicates significant difference at the 1% level. (TIF 4831 KB)

11103_2018_806_MOESM2_ESM.jpg

Fig. S2 Expression patterns of pri-miRNAs in rice young panicles by qRT-PCR. Data are mean ± SE for three replicates. * and ** represent significant difference at the 5% and 1% levels, respectively.

Fig. S3 Original gel images for Fig. 5d. (TIFF 3347 KB)

11103_2018_806_MOESM4_ESM.tif

Fig. S4 Visualization of exon skipping event of Os01g04190 in S6-1 by Integrative Genomic Viewer (IGV). Gene structures are annotated at the bottom, thick and thin lines represent exons and introns, respectively. (TIF 57525 KB)

Table S1 Primers used this study. (DOC 82 KB)

Table S2 Summary of small RNA profiling. (DOCX 12 KB)

Table S3 Summary of phased small RNA clusters. (DOC 30 KB)

Table S4 Data statistics of mRNA transcription. (DOC 32 KB)

Table S5 DEGs in OsDCL3b-RNAi line S6-1. (XLS 252 KB)

Table S6 Go function enrichments for DEGs. (XLS 23 KB)

Table S7 AS events differentially happened in S6-1 or WT. (XLS 261 KB)

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Liao, PF., Ouyang, JX., Zhang, JJ. et al. OsDCL3b affects grain yield and quality in rice. Plant Mol Biol 99, 193–204 (2019). https://doi.org/10.1007/s11103-018-0806-x

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