Abstract
Seed germination is a critical process for completion of the plant life cycle and for global food production. Comparing the germination transcriptomes of barley (Hordeum vulgare) to Arabidopsis thaliana revealed the overall pattern was conserved in terms of functional gene ontology; however, many oppositely responsive orthologous genes were identified. Conserved processes included a set of approximately 6000 genes that peaked early in germination and were enriched in processes associated with RNA metabolism, e.g., pentatricopeptide repeat (PPR)-containing proteins. Comparison of orthologous genes revealed more than 3000 orthogroups containing almost 4000 genes that displayed similar expression patterns including functions associated with mitochondrial tricarboxylic acid (TCA) cycle, carbohydrate and RNA/DNA metabolism, autophagy, protein modifications, and organellar function. Biochemical and proteomic analyses indicated mitochondrial biogenesis occurred early in germination, but detailed analyses revealed the timing involved in mitochondrial biogenesis may vary between species. More than 1800 orthogroups representing 2000 genes displayed opposite patterns in transcript abundance, representing functions of energy (carbohydrate) metabolism, photosynthesis, protein synthesis and degradation, and gene regulation. Differences in expression of basic-leucine zippers (bZIPs) and Apetala 2 (AP2)/ethylene-responsive element binding proteins (EREBPs) point to differences in regulatory processes at a high level, which provide opportunities to modify processes in order to enhance grain quality, germination, and storage as needed for different uses.
Highlights
Seed germination is the earliest process in the life cycle of flowering plants
The dry weight only increased less than twofold up to 36 h, but thereafter showed a large increase from ≈35 mg to ≈60 mg (Figure 1B). For both the barley grain used in this study and the Arabidopsis seed from previous studies [10], the germination rate was greater than 99% and germination was complete after 24 h on the basis of the observation that the radicle had emerged (Figure 1A)
When the over-representation analysis was carried out for the downregulated orthologous genes in barley that were upregulated in Arabidopsis (Figure 5Bi,ii), we identified protein biosynthesis functions; the major facilitator superfamily (MFS) of solute transporters; and carbohydrate metabolism, starch metabolism, as being enriched in the downregulated genes in barley that were orthologous to upregulated genes in Arabidopsis (Figure 5Bi,ii)
Summary
The quiescent seed imparts flowering plants with the advantage of being able to withstand periods where growth and survival may not be possible. This may last from weeks to decades and in favorable conditions vegetative growth can recommence rapidly. GA promotes germination by binding to the GA receptor, which results in the degradation of DELLA proteins (aspartic acid–glutamic acid–leucine–leucine–alanine), strong repressors of germination [5]. This results in the activation of a series of transcription factors (TFs) that increase the levels of various hydrolytic enzymes necessary for germination to proceed. In addition to ABA and GA, a variety of other hormones, including auxin and ethylene, likely play a role in germination via interacting signaling pathways [7]
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