Abstract
Poor grain filling of inferior grains located on lower secondary panicle branch causes great drop in rice yield and quality. Dynamic gene expression patterns between superior and inferior grains were examined from the view of the whole transcriptome by using RNA-Seq method. In total, 19,442 genes were detected during rice grain development. Genes involved in starch synthesis, grain storage and grain development were interrogated in particular in superior and inferior grains. Of the genes involved in sucrose to starch transformation process, most were expressed at lower level in inferior grains at early filling stage compared to that of superior grains. But at late filling stage, the expression of those genes was higher in inferior grains and lower in superior grains. The same trends were observed in the expression of grain storage protein genes. While, evidence that genes involved in cell cycle showed higher expression in inferior grains during whole period of grain filling indicated that cell proliferation was active till the late filling stage. In conclusion, delayed expression of most starch synthesis genes in inferior grains and low capacity of sink organ might be two important factors causing low filling rate of inferior grain at early filling stage, and shortage of carbohydrate supply was a limiting factor at late filling stage.
Highlights
In rice seed development, the grain filling process is the most important factor related to the yield and quality of rice grains [1]
CYP78A13 was a cytochrome P450 gene which could promote cell proliferation, and over-expression of CYP78A13 or its paralogue (GL3.2) could increase grain size [37]. Expression of these two genes was checked in our RNA-Seq data and we found CYP78A13 (LOC_Os07g41240) in superior grains was expressed higher than inferior grains at 10DAF, but lower at afterward periods
Rice grain filling is a highly complicated process, and the accumulation of starch and storage proteins is regulated starting at the mRNA level [8]
Summary
The grain filling process is the most important factor related to the yield and quality of rice grains [1]. The reasons of poor grain filling of inferior spikelets are beneficial to improve rice yield for cultivars that have numerous spikelets on the panicle. RNA-Seq is a recently developed approach to study gene expression profiling that uses the generation sequencing technologies, and provides a more precise measurement of gene transcripts dynamics on global scale in different tissues and biological contexts [19,20]. We investigated the dynamics of gene expression in four developing periods of rice superior and inferior grains by using RNA-Seq technique. Genes involved in storage protein accumulation, sucrose and starch biosynthesis, plant hormone metabolism and cell cycle related genes were examined and the potential mechanisms of poor filling of inferior grains were discussed
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