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Integrated Multi-Omics Reveals Significant Roles of Non-Additively Expressed Small RNAs in Heterosis for Maize Plant
Jie Zhang1,2,3, Yuxin Xie2, Hongwei Zhang2
1Center of Seed Science and Technology, Beijing Innovation Center for Seed Technology (MOA), Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China.
International Journal of Molecular Sciences
|June 10, 2023
Summary
Small RNAs (sRNAs) play a key role in maize plant height heterosis. Non-additive expression of microRNAs (miRNAs) and small interfering RNAs (siRNAs) impacts growth and stress pathways, revealing novel epigenetic regulation mechanisms.
Area of Science:
- Plant biology
- Epigenetics
- Genomics
Background:
- Heterosis, or hybrid vigor, is crucial for crop improvement but its epigenetic underpinnings are not fully understood.
- Small RNAs (sRNAs), including microRNAs (miRNAs) and small interfering RNAs (siRNAs), are key epigenetic regulators.
- The specific roles of sRNAs in mediating heterosis, particularly in plant height, require further investigation.
Purpose of the Study:
- To investigate the role of small RNAs (sRNAs) in maize plant height (PH) heterosis.
- To analyze the non-additive expression patterns of miRNAs and siRNAs in maize hybrids compared to their parental lines.
- To elucidate the regulatory mechanisms of sRNAs in PH heterosis through multi-omics integration.
Main Methods:
- Integrative analysis of multi-omics sequencing data (sRNAome, transcriptome, methylome) from maize hybrids and parental lines.
- Identification and quantification of non-additively expressed miRNAs and 24-nt siRNAs.
- Correlation analysis between sRNA expression, gene expression, and DNA methylation patterns.
Main Results:
- A significant proportion of miRNAs (18.61%) and 24-nt siRNAs (54.00%) exhibited non-additive expression in hybrids.
- Non-additively expressed miRNAs influenced PH heterosis by modulating vegetative growth, reproductive, and stress response pathways.
- Non-additive methylation events were linked to non-additively expressed siRNAs, with distinct siRNA expression patterns (LPE vs. HPE) associated with specific biological processes.
Conclusions:
- Small RNAs, particularly non-additively expressed miRNAs and siRNAs, are critical regulators of maize plant height heterosis.
- sRNAs influence heterosis by coordinating gene expression and epigenetic modifications across growth, metabolism, and stress response pathways.
- This study provides novel insights into the epigenetic mechanisms of sRNA-mediated heterosis in plants.
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