Transcriptomic and methylomic analyses provide insights into the molecular mechanism and prediction of heterosis in rice
Chongyun Fu†, Ce Ma, Manshan Zhu, Wuge Liu, Xiaozhi Ma, Jinhua Li, Yilong Liao, Dilin Liu, Xiaofeng Gu*, Haiyang Wang*, Feng Wang*
The Plant Journal
Abstract
Heterosis has been widely used in multiple crops. However, the molecular
mechanism and prediction of heterosis remains elusive. We generated
five F1 hybrids [four showing better-parent heterosis (BPH)
and one showing mid-parent heterosis], and performed the transcriptomic
and methylomic analyses to identify the candidate genes for BPH and
explore the molecular mechanism of heterosis and the potential
predictors for heterosis. Transcriptomic results showed that most of the
differentially expressed genes shared in the four better-parent hybrids
were significantly enriched into the terms of molecular function, and
the additive and dominant effects played crucial roles for BPH. DNA
methylation level, especially in CG context, significantly and
positively correlated with grain yield per plant. The ratios of
differentially methylated regions in CG context in exons to
transcription start sites between the parents exhibited significantly
negative correlation with the heterosis levels of their hybrids, as was
further confirmed in 24 pairwise comparisons of other rice lines,
implying that this ratio could be a feasible predictor for heterosis
level, and this ratio of less than 5 between parents in early growth
stages might be a critical index for judging that their F1 hybrids would show BPH. Additionally, we identified some important genes
showing differential expression and methylation, such as OsDCL2, Pi5, DTH2, DTH8, Hd1 and GLW7 in the four better-parent hybrids as the candidate genes for BPH. Our
findings helped shed more light on the molecular mechanism and heterosis
prediction.
Keywords indica rice, heterosis, prediction, transcriptome, methylome.
附件：https://onlinelibrary.wiley.com/doi/10.1111/tpj.16217
