Article

Plant Molecular Biology

, Volume 81, Issue 4, pp 363-378

Transcriptomic analysis of rice (Oryza sativa) endosperm using the RNA-Seq technique

  • Yi GaoAffiliated withState Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University
  • , Hong XuAffiliated withState Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University
  • , Yanyue ShenAffiliated withState Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University
  • , Jianbo WangAffiliated withState Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University Email author 

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Abstract

The endosperm plays an important role in seed formation and germination, especially in rice (Oryza sativa). We used a high-throughput sequencing technique (RNA-Seq) to reveal the molecular mechanisms involved in rice endosperm development. Three cDNA libraries were taken from rice endosperm at 3, 6 and 10 days after pollination (DAP), which resulted in the detection of 21,596, 20,910 and 19,459 expressed gens, respectively. By ERANGE, we identified 10,371 differentially expressed genes (log2Ratio ≥1, FDR ≤0.001). The results were compared against three public databases (Gene Ontology, Kyoto Encyclopedia of Genes and Genomes and MapMan) in order to annotate the gene descriptions, associate them with gene ontology terms and to assign each to pathways. A large number of genes related to ribosomes, the spliceosome and oxidative phosphorylation were found to be expressed in the early and middle stages. Plant hormone, galactose metabolism and carbon fixation related genes showed a significant increase in expression at the middle stage, whereas genes for defense against disease or response to stress as well as genes for starch/sucrose metabolism were strongly expressed during the later stages of endosperm development. Interestingly, most metabolic pathways were down-regulated between 3 and 10 DAP except for those involved in the accumulation of material, such as starch/sucrose and protein metabolism. We also identified the expression of 1,118 putative transcription factor genes in endosperm development. The RNA-Seq results provide further systematic understanding of rice endosperm development at a fine scale and a foundation for future studies.

Keywords

Endosperm development Rice Transcriptome High-throughput sequencing Storage Programmed cell death