RNA-seq analysis of different sub-regions of developing grains in rice

Popular rice mega varieties lack sufficient key micronutrients (e.g., Fe, Zn), vitamins and a balanced amino acid composition that are essential for a healthy diet. The major bottleneck for improving the nutritional quality of popular rice varieties through conventional breeding or gene technology is our lack of an integrated understanding of the biochemical and molecular processes that occur during rice grain filling (and their determining genes or loci). In this project, we will perform molecular expression profiling on specific tissue layers of the rice grain. To perform this experiment, the material will be developing rice seeds from plants grown hydroponically under controlled greenhouse conditions. Then, the laser microdissection approach will be applied to dissect different parts of the grain (i.e, vascular trace, aleurone, nucellar epidermis, etc). Total RNA will be extracted from these dissected parts and RNA sequencing will be performed. In this project, we will learn how the synthesis and deposition of grain nutrients is regulated, particularly, during grain filling. 47 samples were collected and 39 samples passed QC. Biological replicates of poor quality (i.e., with low correlation coefficients) were excluded, therefore, 28 samples in total were used for detailed analysis [NE_4DAF(3), OVT_4DAF(3), CC_4DAF(2), EN_4DAF(1), NE_8DAF(3), OVT_8DAF(2), CC_8DAF(1), EN_8DAF(2), NE_16DAF(3), OVT_16DAF(1), CC_16DAF(2), EN_16DAF(2), AL_16DAF(3)]