Profiling rice seed transcriptome and small RNAome during seed maturation

This study aimed to profile transcriptome and small RNAome from embryo and endosperm of rice seeds, and to seek associated molecular factors/pathways affecting changes in seed dormancy level during their maturation in panicle before their harvest. Each 10 seeds at 30, 45 and 60 days after heading (DAH) were sampled from a single individual of Oryza sativa (cv. Nipponbare), and their embryo and endosperm was seperately sampled. Each biological replicate consists of embryo or endosperm sampled from 12 individual plants (i.e., 120 embryos/endosperms per biological replicate). Total RNAs were extracted from each of biological replicates and were subjected to the construction of strand-specific RNA-Seq libraries and small RNA-Seq libraries.The global transcriptome dynamics observed from embryo was consistent with the changes of PHS rate, which differed from the dynamics observed from endosperm transcriptome. In-depth investigation on embryo transcriptome revealed that the dynamics occurring in embryo during 45-to-60 DAH maturation are largely associated with the changes of key regulatory genes involved in various phytohormone signaling pathways, including GA, ABA, auxin, ethylene and BR, which suggests complexed cross-talk between phytohormones in the modulation of seed germination and dormancy during the period between 45-60 DAH. In addition, profiling of miRNAome and the prediction of DEmiRs in embryo suggested potential miRNA-target modules, which may be linked to the regulation of ethylene biosynthesis and ABA transport in rice seeds. Results from this study will expand our knowledge in the transcriptome/small RNAome dynamics and their effects on the regulation of seed dormancy level after the end of endosperm filling.