Abstract
Soybean (Glycine max) seeds are an important source of seed storage compounds, including protein, oil, and sugar used for food, feed, chemical, and biofuel production. We assessed detailed temporal transcriptional and metabolic changes in developing soybean embryos to gain a systems biology view of developmental and metabolic changes and to identify potential targets for metabolic engineering. Two major developmental and metabolic transitions were captured enabling identification of potential metabolic engineering targets specific to seed filling and to desiccation. The first transition involved a switch between different types of metabolism in dividing and elongating cells. The second transition involved the onset of maturation and desiccation tolerance during seed filling and a switch from photoheterotrophic to heterotrophic metabolism. Clustering analyses of metabolite and transcript data revealed clusters of functionally related metabolites and transcripts active in these different developmental and metabolic programs. The gene clusters provide a resource to generate predictions about the associations and interactions of unknown regulators with their targets based on “guilt-by-association” relationships. The inferred regulators also represent potential targets for future metabolic engineering of relevant pathways and steps in central carbon and nitrogen metabolism in soybean embryos and drought and desiccation tolerance in plants.
Highlights
Seeds are an important source of food, feed, biodiesel, and chemicals, because they are rich in oils, proteins, and carbohydrates [1,2]
We followed changes in the levels of proteins and lipid-derived fatty acids during seed filling, starting with young embryos and ending with maturing and desiccating embryos. The accumulation of these major seed storage compounds increased in a nearly linear manner in developing soybean embryos until day 25 when a plateau was reached for both fatty acids and proteins
With respect to protein levels, the plateau was maintained until the end of the time course, while the levels of individual fatty acids started to decrease after day 40 in the time course in desiccating embryos (Figure 1, Table 1)
Summary
Seeds are an important source of food, feed, biodiesel, and chemicals, because they are rich in oils, proteins, and carbohydrates [1,2]. Seed development in general encompasses a chronological series of developmental, metabolic, and physiological processes, controlled by relevant, and only partially understood, regulatory events In soybean, these processes take place during the reproductive R3 (beginning pod) through R8 (full maturity) developmental stages at the whole plant, organ, tissue, cell, and molecular levels [6,7,8]. Nutrient supply by maternal source tissues continues even in green seeds, as they show a very active photoheterotrophic type of metabolism [11,12,13,14,15] During this seed-filling stage (R4–7 reproductive stages), cell elongation and accumulation of seed storage compounds represent the major developmental and metabolic processes [11,16,17,18,19]. This allowed gaining a better understanding of transitions between these developmental stages and identifying seed filling- and desiccation tolerance-specific genes
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