Integration of transcriptome and DNA methylome analysis reveals the molecular mechanism of taproot yield heterosis in radish.

Heterosis, a crucial biological phenomenon, plays a vital role in determining the yield and quality of plants. Radish, an important root vegetable crop, exhibits notable heterosis in terms of root yield and quality. Nevertheless, the molecular mechanism underlying the formation of heterosis in radish remains unclear. Herein, both the transcriptome and DNA methylome analyses were performed on the F1 hybrids and parental lines. Expression level dominance (ELD) genes and allele-specific expression (ASE) genes together significantly contribute to heterosis, primarily through energy metabolism and plant hormone signal transduction pathway. An increase in average methylation level in the F1 hybrids was observed compared to the parental lines. Interestingly, a negative correlation was found between the methylation level of differentially expressed genes (DEGs) in gene body regions and their expression levels in NAU-LB and the F1 hybrids. Moreover, the hybrids were more sensitive to the 5-azacytidine than their parents, and the root weight and total sugar content in the F1 hybrids were dramatically decreased compared to the control. Immunolocalization results indicated that the auxin content of the F1 hybrids were reduced under 5- azacytidine treatment. Proliferating cell nuclear antigen immunolocalization revealed significant inhibition of vascular cambium activity in both the hybrids and parental lines. Notably, the expression profiles of a few differentially methylated DEGs including RsSUS1, RsSUC2a, RsIAA7, and RsIAA18, were significantly increased in the root of hybrids compared to their parents, suggesting a potential role of DNA methylation in yield heterosis. Collectively, these findings would provide valuable insight into the molecular mechanism underlying taproot yield heterosis and facilitate the genetic improvement of taproot yield and quality in radish breeding programs. [ABSTRACT FROM AUTHOR]

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