Comparative Metabolomics Reveals Two Metabolic Modules Affecting Seed Germination in Rice (Oryza sativa)

Abstract

The process of seed germination is crucial not only for the completion of the plant life cycle but also for agricultural production and food chemistry; however, the underlying metabolic regulation mechanism involved in this process is still far from being clearly revealed. In this study, one indica variety (Zhenshan 97, with rapid germination) and one japonica variety (Nipponbare, with slow germination) in rice were used for in-depth analysis of the metabolome at different germination stages (0, 3, 6, 9, 12, 24, 36, and 48 h after imbibition, HAI) and exploration of key metabolites/metabolic pathways. In total, 380 annotated metabolites were analyzed by using a high-performance liquid chromatography (HPLC)-based targeted method combined with a nontargeted metabolic profiling method. By using bioinformatics and statistical methods, the dynamic changes in metabolites during germination in the two varieties were compared. Through correlation analysis, coefficient of variation analysis and differential accumulation analysis, 74 candidate metabolites that may be closely related to seed germination were finally screened. Among these candidates, 29 members belong to the ornithine–asparagine–polyamine module and the shikimic acid–tyrosine–tryptamine–phenylalanine–flavonoid module. As the core member of the second module, shikimic acid’s function in the promotion of seed germination was confirmed by exogenous treatment. These results told that nitrogen flow and antioxidation/defense responses are potentially crucial for germinating seeds and seedlings. It deepens our understanding of the metabolic regulation mechanism of seed germination and points out the direction for our future research.

Transcriptomics and metabolomics changes triggered by exogenous 6-benzylaminopurine in relieving epicotyl dormancy of Polygonatum cyrtonema Hua seeds

“…We note that most of the genes and metabolites involved in arginine biosynthesis were downregulated in three stages. Research shows that ornithine and L-asparagine showed consumption patterns during rice germination according to our results (Guo et al, 2021). This indicates that arginine was always used as a donor to provide proline during the dormancy release of epicotyl of P. cyrtonema seeds.…”

Comparative Metabolomics Reveals Key Determinants in the Flavor and Nutritional Value of Coconut by HS-SPME/GC-MS and UHPLC-MS/MS

“…Amino acid levels fluctuate greatly in rice seed populations, and some amino acids could not be detected in a few varieties [ 21 ]. There are also significant differences in the content of vitamins such as nicotinamide among different varieties of rice and tomato [ 22 , 23 ]. In addition, the content of metabolites varies between different growth stages of the same fruit; therefore, selecting a fruit variety at the specific development stage that provides flavor and nutritional value remains a challenge [ 24 , 25 ].…”

Comparative Metabolomics Profiling Reveals Key Metabolites and Associated Pathways Regulating Tuber Dormancy in White Yam (<em>Dioscorea rotundata</em>)

“…The typical example is phytohormones, whose involvement in seed dormancy regulation has always been a popular topic in seed physiology and biochemistry research [17]. The most reported phytohormone influencing dormancy induction in crops is abscisic acid (ABA), it inhibits the process of seed germination, though complex interactions exist between ABA and other phytohormones [18]. Gibberellic acid (GA) is another important phytohormones known to be involved in dormancy regulation.…”

“…Asparagine, arginine, and γ-aminobutyric (GABA) are the three most common amino compounds in the mobilization of nitrogen reserves in dormancy breaking chestnut seeds [27]. Therefore, as the major transporter of all forms of nitrogen and the key factor of carbon/nitrogen balance in the plants, the role of amino acids in dormancy regulation may not be ignored [18].…”

“…The development of metabolomics technologies has improved our understanding of the complex molecular interaction of biological systems. Due to its high throughput and efficiency, metabolomics has been applied to research on the mechanism of dormancy in several plant species [18]. However, in yam crop only few metabolomics studies exist, and to the best of our knowledge this is the first time, metabolomics approach is being applied to study yam tuber dormancy.…”