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

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.