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 the contributions of different grain tissues to these processes, 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.

Gene expression variations and allele-specific expression of two rice and their hybrid in caryopses at single-nucleus resolution

“…To attribute nuclear identities to these clusters, the expression levels of marker genes whose patterns have been well studied in the endosperm, embryo, pericarp, and seed coat were evaluated for each cluster ( Figure 1C ). The average expression levels of previously reported tissue-specific genes helped us to identify nuclei clusters ( Zhou et al., 2013 ; Wu et al., 2020 ; Ram et al., 2021 ) ( Table S3 ). The results suggested that clusters 2 and 7 likely represented the pericarp and seed coat, clusters 3 and 5 could be represented the embryo, and the remaining clusters (including clusters 0, 1, 4, 6, and 8) were likely to be the endosperm.…”

“…The nucleus type in each cluster was further validated by correlation coefficiency analysis between the cluster-enriched genes and published seed cell-type expression profiles ( Figure S2 ) ( Wu et al., 2020 ; Ram et al., 2021 ). Furthermore, conserved and divergently expressed genes for each homologous cell type were compared among the three rice samples.…”

Evolution of plant cell-type-specificcis-regulatory elements

“…Upon completing the initial annotation process, which was based on a curated list of marker genes, we further expanded our marker repertoire by incorporating markers collected from published bulk RNA-seq data encompassing a diverse array of cell types, which were acquired via laser capture dissection. In brief, we collected the markers from several studies, including three distinct cell types within rice leaves 63 and ten cell types across rice seed organs 64,65 . From these sources, we selected the top 100 variably expressed markers for each cell type and employed them to compute cell identity enrichment scores.…”

The molecular basis of cereal grain proteostasis

“…Significant interest has been paid to understanding the role of protein synthesis and degradation during protein accumulation in cereal grains. The majority of this work is based on measuring changing patterns of protein abundance in time course proteomics experiments, and matching this to related changes in transcriptomics and metabolomics experiments [37][38][39][40][41][42][43]. Proteins that are required for cell division, cell wall formation, and cell growth, such as cytoskeleton proteins, histones, and xyloglucan endotransglucosylases/hydrolases accumulate in the early stage of grain development [42,44,45].…”