Small RNA and PARE sequencing in rice (photoperiod sensitive male sterility lines and wild type) panicles under long-day and short-day conditions

Purpose: The goals of this study are to detect the small RNAs generated from the PMS1T gene and the cleavage sites mediated by small RNAs (microRNAs or phasiRNAs). Methods: The rice panicles were collected in liquid nitrogen and their total RNA were extracted for library construction and subsequent sequencing on an Illumina HiSeq 2000. Results: Using an optimized data analysis workflow, we mapped a series of small RNAs generated from the PMS1T region of the rice genome; most of these small RNAs were 21-nt phasiRNAs. The results from PARE sequencing validated the cleavage site on the PMS1T transcript, with the cleavage mediated by miR2118. Conclusions: Our results show that the 21-nt phasiRNA generated from the PMS1T transcript are associated with photoperiod-sensitive male sterility in rice. Overall design: The young panicles were collected for the sequencing from different sizes of genotypes Nongken 58S and NIL(MH), plus transgenic plants, all grown under long-day (daylength>14 h) and short-day (daylength<13.5 h) conditions.