水稻超大籽粒形成的重要基因和调控通路的转录组分析

Transcriptome analysis on critical genes and key pathways in extra-large grain development of rice

以特大粒水稻品系TD70和小粒籼稻品种Kasalath不同发育时期的幼穗为材料,进行转录组测序。将获得的干净读长(Clean read)以日本晴(Nipponbare)基因组序列为参考序列进行比对得到唯一读长(即特异比对到参考基因组的read),利用FPKM(Fragments per kilobase of transcript per million fragments mapped)法计算基因的表达水平,用GO和KEGG数据库对差异表达基因(Differentially expressed genes,DEGs)进行功能注释、富集和代谢通路分析。结果表明,在水稻幼穗发育的早、中、后3个时期分别获得3618个、4183个和5254个差异表达基因,共有4374个差异表达基因得到基因本体(Gene ontology,GO)功能注释,主要涉及DNA结合、细胞进程、信号转导、细胞增殖、物质转运等方面。KEGG数据库分析结果显示,差异表达基因共涉及119条代谢通路,主要包括淀粉和蔗糖代谢通路、内质网中的蛋白质加工通路、激素信号转导通路、细胞周期蛋白通路等。

Using young panicles of extra-large grain rice TD70 and small grain indica rice Kasalath at different growth stages as materials,transcriptome sequencing was conducted.Unique read was acquired by comparing the obtained clean read with reference genome sequences from Nipponbare.Expression levels of genes were counted by fragments per kilobase of transcript per million fragments mapped(FPKM)method.Functional annotation,enrichment and metabolic pathway of the differentially expressed genes(DEGs)were analysed by using GO and KEGG databases.The results showed that 3618,4183 and 5254 DEGs were obtained in the early,middle and late stages of young panicle development,and a total of 4374 DEGs were annotated with gene ontology(GO),mainly involving DNA binding,cellular processes,signal transduction,cell proliferation and material transfer,etc.The analysis results of KEGG database analysis indicated that DEGs referred to 119 metabolic pathways,mainly including starch and sucrose metabolism,protein processing in endoplasmic reticulum,hormone signal transduction,cyclin and so on.