Genome wide analysis of the transcriptional profiles in different regions of the developing rice grains

Abstract

Background Rice 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 in different contributions of grain tissues to these process, are not understood. Main text Using 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. Conclusion Together, 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.

Integration of embryo-endosperm interaction into a holistic and dynamic picture of seed development using a rice mutant with notched-belly grains

“…Rice is a main contributor of dietary calories and nutrients for nearly half of the global population (Wu et al, 2020). Rice grain yield has to be sustainably improved both in quantity and quality, to solve formidable challenges including the ever-increasing population, climate change, and the quest for high-quality rice that has accompanied the rise in living standards (Sreenivasulu et al, 2015).…”

“…These comprehensive studies provided insights into the molecular networks and pathway interactions that function during the development of individual seed compartments for Arabidopsis (Belmonte et al, 2013), maize (Chen et al, 2014;Yi et al, 2019), wheat (Triticum aestivum; Xiang et al, 2019), and barley (Hordeum vulgare; Bian et al, 2019). In rice, laser-capture microdissection (LCM) has been employed to unravel the molecular mechanisms underpinning grain development and its response to abiotic stress (Ishimaru et al, 2019;Ram et al, 2020;Wu et al, 2020). Regardless of a large number of comprehensive studies on the transcriptome atlas for the developing seed with high spatio-temporal resolutions, detailed information about the communications between embryo and endosperm is still lacking, which is partly attributed to the complexity of seed structures (Doll et al, 2020).…”