English

Abstract

Rice seed development involves an intricate regulatory network that directly determines seed size and weight. Long noncoding RNAs (lncRNAs) have been defined as key regulators of gene expression involved in diverse biological processes. However, the function of lncRNAs in rice seed development is still poorly understood. We performed paired-end RNA sequencing of Nipponbare rice at 5, 10 and 15 DPA (days post anthesis) in two different environments (early and middle-season rice). A total of 382 lncRNAs were detected as differentially expressed among these stages, including 344 and 307 lncRNAs in early and middle-season rice, respectively, and 70.42% (269 of 382) of the lncRNAs were found in both environments. The results showed that environment had little effect on the expression of lncRNAs. Furthermore, there were 127, 172, and 31 DElncs (differentially expressed lncRNAs) and 154, 140, and 59 DElncs in early and middle-season rice, respectively, in comparisons of 10_DPA vs 5_DPA, 15_DPA vs 5_DPA and 15_DPA vs 10_DPA. This result indicated that the number and expression level of lncRNAs at 5 DAP were significantly different from those at 10 DAP and 15 DAP. Furthermore, GO pathway analysis of cis target genes of DElncs in 10_DPA vs 5_DPA and 15_DPA vs 5_DPA revealed that the significant GO pathways were extracellular region, nutrient reservoir activity and cell wall macromolecule catabolic process. Our study revealed dynamic expression of lncRNAs in three stages and systematically explored the differences in lncRNAs between early and middle-season rice, which could provide a valuable resource for future high-yield breeding. © 2021 Friends Science Publishers© 2021 Friends Science Publishers© 2021 Friends Science Publishers© 2021 Friends Science Publishers© 2021 Friends Science Publishers© 2021 Friends Science Publishers© 2021 Friends Science Publishers© 2021 Friends Science Publishers© 2021 Friends Science Publishers© 2021 Friends Science Publishers© 2021 Friends Science Publishers© 2021 Friends Science Publishers© 2021 Friends Science Publishers© 2021 Friends Science Publishers© 2021 Friends Science Publishers© 2021 Friends Science Publishers© 2021 Friends Science Publishers© 2021 Friends Science Publishers© 2021 Friends Science Publishers© 2021 Friends Science Publishers© 2021 Friends Science Publishers© 2021 Friends Science Publishers© 2021 Friends Science Publishers© 2021 Friends Science Publishers © 2021 Friends Science Publishers© 2021 Friends Science Publishers© 2021 Friends Science Publishers© 2021 Friends Science Publishers© 2021 Friends Science Publishers© 2021 Friends Science Publishers© 2021 Friends Science Publishers©