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Research paper | Open Access

Genome-wide alternative splicing variation and its potential contribution to maize immature-ear heterosis

Xiaojiao Hu, Hongwu Wang, Kun Li, Xiaogang Liu, Zhifang Liu, Yujin Wu, Shuqiang Li, Changling Huang( )
National Engineer Laboratory of Crop Molecular Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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Abstract

Heterosis is a well-known phenomenon widely applied in agriculture. Recent studies have suggested that differential gene and protein expression between hybrids and their parents play important roles in heterosis. Alternative splicing (AS) is an essential posttranscriptional mechanism that can greatly affect the transcriptome and proteome diversity in plants. However, genome-wide AS divergence in hybrids compared to their parents and its potential contribution to heterosis have not been comprehensively investigated. We report the direct profiling of the AS landscape using RNA sequencing data from immature ears of the maize hybrid ZD808 and its parents NG5 and CL11. Our results revealed a large number of significant differential AS (DAS) events in ZD808 relative to its parents, which can be further classified into parental-dominant and novel DAS patterns. Parental-dominant, especially NG5-dominant, events were prevalent in the hybrid, accounting for 42% of all analyzed DAS events. Functional enrichment analysis revealed that the NG5-dominant AS events were involved mainly in regulating the expression of genes associated with carbon/nitrogen metabolism and cell division processes and contributed greatly to maize ear heterosis. Among ZD808, CL11, and NG5, 32.5% of DAS contained or lacked binding sites of at least one annotated maize microRNA (miRNA) and may be involved in miRNA-mediated posttranscriptional regulation. Cis regulation was the predominant contributor to AS variation and participates in many important biological processes associated with immature ear development. This study provides a comprehensive view of genome-wide alternative splicing variation in a maize hybrid.

Keywords

HeterosisMaizeDominant alternative splicingCis-regulation

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The Crop Journal
Volume 9 Issue 2,
April 2021
Pages 476-486
DOI: 10.1016/j.cj.2020.09.003
Cite this article:
Hu X, Wang H, Li K, et al. Genome-wide alternative splicing variation and its potential contribution to maize immature-ear heterosis. The Crop Journal, 2021, 9(2): 476-486. https://doi.org/10.1016/j.cj.2020.09.003

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Received: 27 November 2019
Revised: 14 August 2020
Accepted: 23 October 2020
Published: 17 November 2020
© 2020 Crop Science Society of China and Institute of Crop Science, CAAS.

This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).
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