Experimental Procedures for Studying Skotomorphogenesis in Arabidopsis thaliana

Metabolic network changes during skotomorphogenesis in Arabidopsis thaliana mutant (atdfb-3)

The metabolic networks underlying skotomorphogenesis in seedlings remain relatively unknown. On the basis of our previous study on the folate metabolism in seedlings grown in darkness, the plastidial folylpolyglutamate synthetase gene (AtDFB) T-DNA insertion Arabidopsis thaliana mutant (atdfb-3) was examined. Under the nitrate-sufficient condition, the mutant exhibited deficient folate metabolism and hypocotyl elongation, which affected skotomorphogenesis. Further analyses revealed changes to multiple intermediate metabolites related to carbon and nitrogen metabolism in the etiolated atdfb-3 seedlings. Specifically, the sugar, polyol, and fatty acid contents decreased in the atdfb-3 mutant under the nitrate-sufficient condition, whereas the abundance of various organic acids and amino acids increased. In response to nitrate-limited stress, multiple metabolites, including sugars, polyols, fatty acids, organic acids, and amino acids, accumulated more in the mutant than in the wild-type control. The differences in the contents of multiple metabolites between the atdfb-3 and wild-type seedlings decreased following the addition of exogenous 5-F-THF under both nitrogen conditions. Additionally, the mutant accumulated high levels of one-carbon metabolites, such as Cys, S-adenosylmethionine, and S-adenosylhomocysteine, under both nitrogen conditions. Thus, our data demonstrated that the perturbed folate metabolism in the atdfb-3 seedlings, which was caused by the loss-of-function mutation to AtDFB, probably altered carbon and nitrogen metabolism, thereby modulating skotomorphogenesis. Furthermore, the study findings provide new evidence of the links among folate metabolism, metabolic networks, and skotomorphogenesis.

Deciphering Novel Transcriptional Regulators of Soybean Hypocotyl Elongation Based on Gene Co-expression Network Analysis

Hypocotyl elongation is the key step of soybean seed germination, as well an important symbol of seedling vitality, but the regulatory mechanisms remain largely elusive. To address the problem, bioinformatics approaches along with the weighted gene co-expression network analysis (WGCNA) were carried out to elucidate the regulatory networks and identify key regulators underlying soybean hypocotyl elongation at transcriptional level. Combining results from WGCNA, yeast one hybridization, and phenotypic analysis of transgenic plants, a cyan module significantly associated with hypocotyl elongation was discerned, from which two novel regulatory submodules were identified as key candidates underpinning soybean hypocotyl elongation by modulating auxin and light responsive signaling pathways. Taken together, our results constructed the regulatory network and identified novel transcriptional regulators of soybean hypocotyl elongation based on WGCNA, which provide new insights into the global regulatory basis of soybean hypocotyl elongation and offer potential targets for soybean improvement to acquire cultivars with well-tuned hypocotyl elongation and seed germination vigor.