Global transcriptional profiling between inbred parents and hybrids provides comprehensive insights into ear-length heterosis of maize (Zea mays)

BACKGROUND: Maize (Zea mays) ear length, which is an important yield component, exhibits strong heterosis. Understanding the potential molecular mechanisms of ear-length heterosis is critical for efficient yield-related breeding. RESULTS: Here, a joint netted pattern, including six parent-hybrid triplets, was designed on the basis of two maize lines harboring long (T121 line) and short (T126 line) ears. Global transcriptional profiling of young ears (containing meristem) was performed. Multiple comparative analyses revealed that 874 differentially expressed genes are mainly responsible for the ear-length variation between T121 and T126 lines. Among them, four key genes, Zm00001d049958, Zm00001d027359, Zm00001d048502 and Zm00001d052138, were identified as being related to meristem development, which corroborated their roles in the superior additive genetic effects on ear length in T121 line. Non-additive expression patterns were used to identify candidate genes related to ear-length heterosis. A non-additively expressed gene (Zm00001d050649) was associated with the timing of meristematic phase transition and was determined to be the homolog of tomato SELF PRUNING, which assists SINGLE FLOWER TRUSS in driving yield-related heterosis, indicating that Zm00001d050649 is a potential contributor to drive heterotic effect on ear length. CONCLUSION: Our results suggest that inbred parents provide genetic and heterotic effects on the ear lengths of their corresponding F(1) hybrids through two independent pathways. These findings provide comprehensive insights into the transcriptional regulation of ear length and improve the understanding of ear-length heterosis in maize. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12870-021-02890-1.