miRNA and Transcriptome Analysis Provides Insight into Heterosis Mechanism of Hybrid Radish (Raphanus sativus L.)

Heterosis has been widely used in the crop breeding, and plays a significant role in enhancing stress resistances, improving quality and yield. However, the molecular mechanism underlying heterosis remains largely unknown in root vegetable crops including radish (Raphanus sativus L.). In this study, the miRNA-seq and mRNA-seq analyses of roots at expanding stage in F₁ hybrid and its corresponding parental lines were performed to uncover the gene regulatory pathways involved in heterosis. A total of 75 conserved and 13 non-conserved miRNAs were detected, from which 10 and 15 miRNAs were differentially expressed from comparison of F₁ vs. maternal line and F₁ vs. paternal line, respectively. KEGG pathway enrichment analysis showed that these miRNAs were mainly involved in the processes of 'Starch and sucrose metabolism', 'Circadian rhythm-plant' and 'Biosynthesis of secondary metabolites'. In addition, a large number of non-additively expressed genes exhibiting parental expression level dominance and transgressive regulation were identified. The association analysis of heterosis-related miRNAs and genes were explored, and RsSUT1, RsSTP4, RsSWEET11, RsG4, RsCAB1 and RsLHCA3 were found to play crucial roles in promoting sugar transport, photosynthesis and carbon fixation in plants. Taken together, these results provided novel insights into the molecular mechanism of heterosis, and would facilitate further genetic improvement of radish and other root vegetable crops.