Abstract
BackgroundRice is an important food source for humans worldwide. Because of its nutritional and agricultural significance, a number of studies addressed various aspects of rice grain development and grain filling. Nevertheless, the molecular processes underlying grain filling and development, and in particular the contributions of different grain tissues to these processes, are not understood.Main TextUsing RNA-sequencing, we profiled gene expression activity in grain tissues comprised of cross cells (CC), the nucellar epidermis (NE), ovular vascular trace (OVT), endosperm (EN) and the aleurone layer (AL). These tissues were dissected using laser capture microdissection (LCM) at three distinct grain development stages. The mRNA expression datasets offer comprehensive and new insights into the gene expression patterns in different rice grain tissues and their contributions to grain development. Comparative analysis of the different tissues revealed their similar and/or unique functions, as well as the spatio-temporal regulation of common and tissue-specific genes. The expression patterns of genes encoding hormones and transporters indicate an important role of the OVT tissue in metabolite transport during grain development. Gene co-expression network prediction on OVT-specific genes identified several distinct and common development-specific transcription factors. Further analysis of enriched DNA sequence motifs proximal to OVT-specific genes revealed known and novel DNA sequence motifs relevant to rice grain development.ConclusionTogether, the dataset of gene expression in rice grain tissues is a novel and useful resource for further work to dissect the molecular and metabolic processes during rice grain development.
Highlights
Rice (Oryza sativa L.) is the second most consumed crop worldwide, with nearly 3.5 billion people depending on it as a staple food
Spatio-Temporal Resolution of mRNA Profiles during Rice Grain Development Gene expression was analyzed in five sub-regions of the developing rice grain comprising the cross cells (CC), nucellar epidermis (NE), ovular vascular trace (OVT), EN and aleurone layer (AL) tissues that were collected by laser-capture micro dissection at 4, 8 and 16 days after flowering (DAF) (Fig. 1a, Fig. S1)
In order to further characterize the sub-region and stage-specific genes, gene ontology (GO) analysis was conducted on differentially expressed genes (DEGs) using PlantGSEA (Yi et al 2013)
Summary
Rice (Oryza sativa L.) is the second most consumed crop worldwide, with nearly 3.5 billion people depending on it as a staple food. The consumption of polished rice grains is extensive in Asian countries where it provides nearly 20% of the daily caloric intake (Thomson 2003). These facts emphasize the importance of understanding. Rice grains have been anatomically characterized and comprise the embryo and specific surrounding tissues, including the endosperm, nucellar epidermis, cross-cells, ovular vascular trace and aleurone layer (Krishnan and Dayanandan 2003). The endosperm (EN) is the major storage tissue for starch that nourishes the developing embryo and contributes most significantly to human nutrition. Because of its nutritional and agricultural significance, a number of studies addressed various aspects of rice grain development and grain filling. The molecular processes underlying grain filling and development, and in particular the contributions of different grain tissues to these processes, are not understood
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