State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China.
Plant Mol Biol. 2013 Mar;81(4-5):363-78. doi: 10.1007/s11103-013-0009-4. Epub 2013 Jan 16.
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 (log(2)Ratio ≥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.
胚乳在种子形成和萌发中起着重要作用，尤其是在水稻（Oryza sativa）中。我们使用高通量测序技术（RNA-Seq）来揭示参与水稻胚乳发育的分子机制。从授粉后 3、6 和 10 天的水稻胚乳中提取了三个 cDNA 文库，分别检测到 21596、20910 和 19459 个表达基因。通过 ERANGE，我们鉴定了 10371 个差异表达基因（log2Ratio ≥1，FDR ≤0.001）。将这些结果与三个公共数据库（基因本体论、京都基因与基因组百科全书和 MapMan）进行了比较，以注释基因描述，将它们与基因本体论术语相关联，并将每个术语分配到途径中。大量与核糖体、剪接体和氧化磷酸化相关的基因在早期和中期表达。植物激素、半乳糖代谢和碳固定相关基因在中期表达显著增加，而防御疾病或应对压力的基因以及淀粉/蔗糖代谢基因在胚乳发育的后期强烈表达。有趣的是，除了与物质积累相关的途径（如淀粉/蔗糖和蛋白质代谢）外，大多数代谢途径在 3 至 10 DAP 之间下调。我们还鉴定了胚乳发育过程中 1118 个潜在转录因子基因的表达。RNA-Seq 结果为水稻胚乳发育提供了更深入的系统理解，并为未来的研究奠定了基础。
