Dissecting seed pigmentation-associated genomic loci and genes by employing dual approaches of reference-based and k-mer-based GWAS with 438 Glycine accessions.

The soybean is agro-economically the most important among all cultivated legume crops, and its seed color is considered one of the most attractive factors in the selection-by-breeders. Thus, genome-wide identification of genes and loci associated with seed colors is critical for the precision breeding of crop soybeans. To dissect seed pigmentation-associated genomic loci and genes, we employed dual approaches by combining reference-based genome-wide association study (rbGWAS) and k-mer-based reference-free GWAS (rfGWAS) with 438 Glycine accessions. The dual analytical strategy allowed us to identify four major genomic loci (designated as SP1-SP4 in this study) associated with the seed colors of soybeans. The k-mer analysis enabled us to find an important recombination event that occurred between subtilisin and I-cluster B in the soybean genome, which could describe a special structural feature of ii allele within the I locus (SP3). Importantly, mapping analyses of both mRNAs and small RNAs allowed us to reveal that the subtilisin-CHS1/CHS3 chimeric transcripts generate and act as an initiator towards 'mirtron (i.e., intron-harboring miRNA precursor)'-triggered silencing of chalcone synthase (CHS) genes. Consequently, the results led us to propose a working model of 'mirtron-triggered gene silencing (MTGS)' to elucidate a long-standing puzzle in the genome-wide CHS gene silencing mechanism. In summary, our study reports four major genomic loci, lists of key genes and genome-wide variations that are associated with seed pigmentation in soybeans. In addition, we propose that the MTGS mechanism plays a crucial role in the genome-wide silencing of CHS genes, thereby suggesting a clue to currently predominant soybean cultivars with the yellow seed coat. Finally, this study will provide a broad insight into the interactions and correlations among seed color-associated genes and loci within the context of anthocyanin biosynthetic pathways.

Comparative metabolic profiling of cultivated and wild black soybeans reveals distinct metabolic alterations associated with their domestication.

Generally, cultivated black soybean (CBS) has been used as a major source of various nutrients for humans and animals. To assess the metabolic alterations induced by domestication in soybean, we performed a comprehensive metabolite profiling of 56 soybean varieties, including 28 CBS and 28 wild black soybean (WBS) varieties. A total of 48 metabolites were characterized, including 45 primary and 3 secondary metabolites, from CBS and WBS. The results of principal component analysis and hierarchical cluster analysis (HCA) revealed significant metabolic differences between CBS and WBS that were closely related to metabolic pathways. The results indicate that flavonoids correlated positively with phenylalanine, a precursor for phenylpropanoid biosynthesis; the contents of flavonoids and phenylpropanoids were higher in WBS. Pathway analysis revealed that CBS contained large amounts of TCA cycle intermediates, amino acids, and fatty acids as a result of increased energy metabolism, amino acid metabolism, and seed filling. The projection to latent structure method, using the partial least squares method, was applied to predict the flavonoid content in soybean seed, which indicated that sucrose, threonic acid, citric acid, and fatty acids are important in predicting the antioxidant content of samples. This work will provide important information for designing new soybean cultivars with enhanced nutritional and agricultural traits.

Simultaneous roasting and extraction of green coffee beans by pressurized liquid extraction.

Green coffee extracted by pressurized liquid extraction (PLE) was found to undergo a roasting process similar to traditional roasting. Liquid chromatography-tandem mass spectrometry was used to investigate the chlorogenic acid (CGA) composition and profiling changes by PLE under different extraction conditions and showed almost identical generation and degradation of CGAs occurring during traditional coffee roasting. Compared with the traditional extraction of roasted coffee, optimized PLE coffee showed three- and two-fold higher antioxidant activity and total CGA contents, respectively. Composition diversity and the content of volatile compounds in PLE coffee were found to increase as the PLE temperature increased but were lower than those of traditionally roasted coffee. The sensory attributes of PLE coffee were also evaluated to have be associated with a profile change in the volatile compounds and non-volatile CGA compounds.

Anti-neuroinflammatory Effects of 12-Dehydrogingerdione in LPS-Activated Microglia through Inhibiting Akt/IKK/NF-κB Pathway and Activating Nrf-2/HO-1 Pathway.

Ginger, one of worldwide consumed dietary spice, is not only famous as food supplements, but also believed to exert a variety of remarkable pharmacological activity as herbal remedies. In this study, a ginger constituent, 12-dehydrogingerdione (DHGD) was proven that has comparable anti-inflammatory activity with positive control 6-shogaol in inhibiting LPS-induced interleukin (IL)-6, tumor necrosis factor (TNF)-α, prostaglandin (PG) E2, nitric oxide (NO), inducible NO synthase (iNOS) and cyclooxygenase (COX)-2, without interfering with COX-1 in cultured microglial cells. Subsequent mechanistic studies indicate that 12-DHGD may inhibit neuro-inflammation through suppressing the LPS-activated Akt/IKK/NF-κB pathway. Furthermore, 12-DHGD markedly promoted the activation of NF-E2-related factor (Nrf)-2 and heme oxygenase (HO)-1, and we demonstrated that the involvement of HO-1 on the production of pro-inflammatory mediators such as NO and TNF-α by using a HO-1 inhibitor, Zinc protoporphyrin (Znpp). These results indicate that 12-DHGD may protect against neuro-inflammation by inhibiting Akt/IKK/IκB/NF-κB pathway and promoting Nrf-2/HO-1 pathway.

Differences in the metabolic profiles and antioxidant activities of wild and cultivated black soybeans evaluated by correlation analysis.

Wild soybeans are considered a potential resource for soybean domestication and an important source of genetic diversity for soybean crop improvement. Understanding metabolite-caused bioactivity differences between cultivated and wild soybeans is essential for designing a soybean with enhanced nutritional traits. In this study, the non-targeted metabolic profiling of 26 soybean varieties, 15 wild black soybeans (WBS) and 11 cultivated black soybeans (CBS), using liquid chromatography-mass spectrometry (LC-MS) in combination with multivariate analysis revealed significant differences in 25 differential metabolites. Among these, the soyasaponins Ab and Bb were found to be characteristic metabolites expressed more substantially in CBS than in WBS. Three different antioxidant assays and correlation analysis identified major and minor antioxidants that contributed to WBS having an antioxidant activity 4- to 8-fold stronger than that of CBS. Epicatechin, procyanidin B2, and cyanidin-3-O-glucoside were identified by both association analysis and the online LC-ABTS radical scavenging assay as being major antioxidants.