Plant Molecular Biology

, Volume 81, Issue 4, pp 363–378

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


DOI: 10.1007/s11103-013-0009-4

Cite this article as:
Gao, Y., Xu, H., Shen, Y. et al. Plant Mol Biol (2013) 81: 363. doi:10.1007/s11103-013-0009-4


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.


Endosperm developmentRiceTranscriptomeHigh-throughput sequencingStorageProgrammed cell death

Supplementary material

11103_2013_9_MOESM1_ESM.xls (3.2 mb)
Supplementary material 1 (XLS 3314 kb). Supplemental Table 1 A total of 23,836 genes derived from three cDNA libraries. The GeneID, length of gene, RPKM of three stages and the expression pattern are presented in this table
11103_2013_9_MOESM2_ESM.xls (1.2 mb)
Supplementary material 2 (XLS 1246 kb). Supplemental Table 2 A table listing 10,371 differentially expressed genes (DEGs) during rice endosperm development. We use FDR < 0.001 and the absolute value of log2Ratio ≥ 1 as the threshold to judge the significance of gene expression difference. The RPKM of three stages and expression pattern for DEGs are presented in the table
11103_2013_9_MOESM3_ESM.xls (52 kb)
Supplementary material 3 (XLS 51 kb). Supplemental Table 3 Overview of all 123 KEGG pathways. All 10,371 DEGs are assigned to 123 KEGG pathways. The KEGG functional class, number, RPKM of three stages, expression type and expression pattern of members are presented in this table
11103_2013_9_MOESM4_ESM.xls (68 kb)
Supplementary material 4 (XLS 67 kb). Supplemental Table 4 Detail of all 211 branch pathways in 35 MapMan major pathways. The MapMan functional class, number, RPKM of three stages, expression type and expression pattern of members are presented in the table
11103_2013_9_MOESM5_ESM.xls (34 kb)
Supplementary material 5 (XLS 34 kb). Supplemental Table 5 All 55 transcription factor (TF) families found in the result. 1,118 putative TF genes are identified in all 23,836 genes. The TF family name, number, RPKM, expression pattern and expression pattern of TF family’s members are presented in the table
11103_2013_9_MOESM6_ESM.xls (2.8 mb)
Supplementary material 6 (XLS 2896 kb). Supplemental Table 6 Detail of top 100 up-regulated genes between R1 and R3. The gene ID, gene description and difference RPKM (R3-R1) are presented in the table
11103_2013_9_MOESM7_ESM.xls (25 kb)
Supplementary material 7 (XLS 25 kb). Supplemental Table 7 Thirteen PCD-related genes identified in the RNA-Seq result. The name of gene, gene ID, description and RPKM of three stages are presented in the table
11103_2013_9_MOESM8_ESM.doc (43 kb)
Supplementary material 8 (DOC 43 kb). Supplemental Table 8 Primers used in the analysis of rice endosperm development. UBQ5 is used as internal control to standardize the results

Copyright information

© Springer Science+Business Media Dordrecht 2013

Authors and Affiliations

  1. 1.State Key Laboratory of Hybrid Rice, College of Life SciencesWuhan UniversityWuhanChina