Abstract
The utilization of heterosis make a great contribution to the productivity of many crops. The post-transcriptional splicing and polyadenylation are major forms of RNA processes to regulate gene expression. However, the molecular basis of heterosis is still elusive especially in transcription and RNA processes due to technical barriers. Here, we investigate the post-transcriptional splicing and polyadenylation of RNA by isolating the nucleus and cytoplasm sections in elite rice hybrid Shanyou 63 (SY63) and its parental lines Zhenshan 97 (ZS97) and Minghui 63 (MH63) using Nanopore-based Full-Length RNA sequencing. We found that some introns showed differential splicing status for polyadenylated RNA between the parents or its corresponding alleles of the hybrid. Unexpectedly, we found that the poly(A) tail length of both alleles showed directed global changes in the hybrid, resulting in the global increase of poly(A) tails of both alleles in the hybrid with respect to the parents. Further inspection of gene expression of candidate genes involved of poly(A) pathways unveiled that some genes showed differential expression levels between the hybrid and its parents. Of the high coverage genes, we found that some heterosis-associated genes showed differential poly(A) tail length in the hybrid compared to that of the parents, such as GW2 and GS5. The globally increased poly(A) tail length uniquely existed in the hybrid and may be related to more precise transcriptional regulation, which contribute to mRNA stability and further increase the expression abundance of the heterosis-associated genes. These results revealed a specific regulatory pattern of poly(A) tails in the hybrid and will further expand the molecular basis of heterosis in a new layer.
