Transcriptional Dynamics of Grain Development in Barley (Hordeum vulgare L.)

Abstract

Grain development, as a vital process in the crop’s life cycle, is crucial for determining crop quality and yield. However, the molecular basis and regulatory network of barley grain development is not well understood at present. Here, we investigated the transcriptional dynamics of barley grain development through RNA sequencing at four developmental phases, including early prestorage phase (3 days post anthesis (DPA)), late prestorage or transition phase (8 DPA), early storage phase (13 DPA), and levels off stages (18 DPA). Transcriptome profiling found that pronounced shifts occurred in the abundance of transcripts involved in both primary and secondary metabolism during grain development. The transcripts’ activity was decreased during maturation while the largest divergence was observed between the transitions from prestorage phase to storage phase, which coincided with the physiological changes. Furthermore, the transcription factors, hormone signal transduction-related as well as sugar-metabolism-related genes, were found to play a crucial role in barley grain development. Finally, 4771 RNA editing events were identified in these four development stages, and most of the RNA editing genes were preferentially expressed at the prestore stage rather than in the store stage, which was significantly enriched in “essential” genes and plant hormone signal transduction pathway. These results suggested that RNA editing might act as a ‘regulator’ to control grain development. This study systematically dissected the gene expression atlas of barley grain development through transcriptome analysis, which not only provided the potential targets for further functional studies, but also provided insights into the dynamics of gene regulation underlying grain development in barley and beyond.

Genome Wide Analysis of the Transcriptional Profiles in Different Regions of the Developing Rice Grains

“…Strong temporal specificity for expression of several genes including transcription factors were also reported during early stages of maize seed development (Yi et al 2019). A time course analysis of transcription in barley grain revealed expression changes for genes encoding transcription factors and hormone signal transduction-related proteins, as well as genes encoding sugar-metabolism-related proteins (Bian et al 2019). In rice seeds, embryo and endosperm regions are the most studied grain tissues for gene expression patterns (Zhu et al 2002;Xu et al 2012b;Xue et al 2012;Gao et al 2013;Ishimaru et al 2019).…”

Heritable temporal gene expression patterns correlate with metabolomic seed content in developing hexaploid oat seed

“…A GO category of nutrient reservoir activity was found enriched between 28 and 33 DAA, which suggested the importance of nutrient accumulation and storage at the late seed development stage. This GO term was also found to be enriched at storage phase of barley seed development (Bian et al , ).…”

“…Photosynthesis is the dominant biological process ontology identified at 14 DAA in wheat grain development (Rangan et al , ). Expression of 20 of 29 (68.97%) photosynthesis‐related genes peaked at 8 DAA in developing barley grains (Bian et al , ). Here, photosynthesis‐related GO terms were enriched in time intervals of 13–18 DAA and 18–23 DAA, which suggests immature oat seeds at early and middle development stages contain functional chloroplasts capable of photosynthesis during grain filling.…”

Harnessing Transcription Factors as Potential Tools to Enhance Grain Size Under Stressful Abiotic Conditions in Cereal Crops

“…In general, grain size is co-ordinately controlled by cell expansion and proliferation in the developing endosperm and floral tissues (lemma, palea) surrounding the developing grain, determining the ‘sink’ capacity of the grain ( Li et al., 2018 ). In cereals, cell proliferation precedes cell expansion to some extent, beginning at fertilization and ceasing 15–25 days later ( Evers and Millar, 2002 ; Farooq et al., 2014 ; Li et al., 2018 ; Bian, 2019 ). This period of grain development predetermines the maximum size of the grain along the longitudinal and transverse axes and is quite sensitive to abiotic stress; for example in wheat, drought decreases endosperm cell proliferation reducing this ‘sink’ capacity ( Setter and Flannigan, 2001 ).…”