Whole-transcriptome sequencing reveals the global molecular responses and ceRNA regulatory network involved in programmed cell death of rice cultivars zyk639 and zyk-lm.

Background: Programmed cell death (PCD) can be triggered by biotic stress or abiotic stress in rice, which is a crucial factor throughout the lifecycle. Long non-coding RNAs (lncRNAs) have important roles in a variety of biological processes. However, the regulatory relationship between lncRNAs and rice PCD occurrence is unclear.

Methods: In this study, messenger RNAs (mRNAs) and lncRNAs associated with PCD regulation were identified in two rice cultivars: japonica rice (Oryza sativa) cultivar zheyoukang639 (zyk639) and its mutant zyk639-lesion mimic (zyk-lm). Besides, these data were used for weighted gene co-expression analysis (WGCNA) and construction of competitive endogenous RNAs (ceRNAs).

Results: As a result, 5,289 lncRNAs and 39,475 mRNAs were identified, of which 1,873 lncRNAs and 11,930 mRNAs were differentially expressed. In addition, WGCNA showed that the blue module was critical for the development of PCD in rice. The construction of the ceRNA regulatory network associated with the occurrence of PCD in rice identified 101 pairs of relationships, including 9 lncRNAs, 11 miRNAs and 76 mRNAs. Importantly, three major lncRNAs in zyk-lm, including MSTRG.24301.2, MSTRG.17476.1 and MSTRG.24898.1, may be involved in leaf PCD, with MSTRG.24898.1 binding to osa-miR580 to regulate transcription factors. Furthermore, the lncRNAs co-expression mRNAs rpl27-1 and OsRPS27, which were associated with ribosomal genesis, and Os11g0490900, a WRKY family transcription factor, may also regulate PCD genesis.

Conclusions: Models of protein synthesis regulation associated with zyk-lm PCD were discussed, lncRNAs may serve as key factors in regulating PCD and provide ideas for understanding PCD and genetic messaging.