Time-Series Analysis of RNA Profiles During Rice Endosperm Development

Endosperm development is crucial in seed germination and seedling growth for propagation. A high-throughput of transcriptome using RNA-Seq was used to comprehend gene regulation during various stages of endosperm development. Oryza sativa, ssp. japonica, cv Taikeng 8 (TK8) and its derived mutant line, WY14, were used to harvest caryopses at three time-points of days after pollination (DAP), DAP 4, DAP 7, and DAP 15. A total of six cDNA libraries were subjected for high throughput RNA-seq by using HiSeq, Illumina. After trimming of last 16 bases for obtaining high quality reads, more than 95% reads were mapped to the rice reference sequences from RAP-DB using Tophat. To estimate gene expression, mapped reads were transformed into read count for each gene using HTSeq. In TK8, 28,503, 28,191 and 26,881 genes were expressed at DAP 4, 7 and 15, respectively. In WY14, 28,818, 26,459 and 27,265 genes were expressed at day 4, 7 and 15, respectively. Five house-keeping genes were used as a standard to normalize gene expressions across different libraries. As the results, expression profiling at early developmental stage was more similar than other stages, implying that endosperm development could be a gradual process. Nevertheless, there were 419 and 193 genes differentially expressed (DE) for TK8 and WY14, respectively, during endosperm development in rice. Differentially expressed genes involved in nutrient reservoir activity were enriched in TK8, suggests that the storages of protein of fatty acid could be signatures in endosperm development between these two accessions.