Seed maturity differentially mediates metabolic responses in black soybean

Harnessing Multi-Omics Strategies and Bioinformatics Innovations for Advancing Soybean Improvement: A Comprehensive Review

Soybean improvement has entered a new era with the advent of multi-omics strategies and bioinformatics innovations, enabling more precise and efficient breeding practices. This comprehensive review examines the application of multi-omics approaches in soybean-encompassing genomics, transcriptomics, proteomics, metabolomics, epigenomics, and phenomics. We first explore pre-breeding and genomic selection as tools that have laid the groundwork for advanced trait improvement. Subsequently, we dig into the specific contributions of each -omics field, highlighting how bioinformatics tools and resources have facilitated the generation and integration of multifaceted data. The review emphasizes the power of integrating multi-omics datasets to elucidate complex traits and drive the development of superior soybean cultivars. Emerging trends, including novel computational techniques and high-throughput technologies, are discussed in the context of their potential to revolutionize soybean breeding. Finally, we address the challenges associated with multi-omics integration and propose future directions to overcome these hurdles, aiming to accelerate the pace of soybean improvement. This review serves as a crucial resource for researchers and breeders seeking to leverage multi-omics strategies for enhanced soybean productivity and resilience.

Unveiling the nutrient-wealth of black soybean: A holistic review of its bioactive compounds and health implications

Legumes, an essential component of staple diets, hold a prominent place in global cuisines. Soybean stands out as a widely cultivated legume and is valued for its high protein content, dietary fiber, and rich micronutrients. Several varieties of soybean are available, of which black and yellow varieties show dominance in varied countries and cultures. Over time, the cultivation and consumption of black soybeans have markedly reduced compared to the yellow variety. Despite its rich nutritional and therapeutic indices, it has lost its usage over time. Traditionally, it was utilized in oriental medicine for detoxification and anti-inflammatory potential. However, the antinutrients present in black soybean limit its utilization in the food sector due to their interference with overall nutrient absorption. Several studies in the last few decades have focused on reducing the content of antinutritional factors. However, the information on the use of different processing techniques, both singly and in blends, to reduce antinutrients and enhance the bioaccessibility, bioavailability, and bioactivity of bioactive compounds and varied nutrients is limited and fragmented. Furthermore, studies have highlighted black soybeans' protective effects against various degenerative diseases. However, the studies on the effect of processing to enhance its antioxidative properties to make them a sought-after food commodity with nutraceutical potential and therapeutic efficacy are limited and widely scattered. The review aims to consolidate knowledge of diverse processing methods to improve their nutritional and bioactive profile for wider applications in the food and pharmaceutical industries. Further, it has also highlighted its nutraceutical properties for developing varied functional foods against degenerative diseases to have better therapeutic efficacy.

LC-MS and MALDI-MSI-based metabolomic approaches provide insights into the spatial-temporal metabolite profiles of Tartary buckwheat achene development

Tartary buckwheat, celebrated as the "king of grains" for its flavonoid and phenolic acid richness, has health-promoting properties. Despite significant morphological and metabolic variations in mature achenes, research on their developmental process is limited. Utilizing Liquid chromatography-mass spectrometry and atmospheric pressure matrix-assisted laser desorption/ionization mass spectrometry imaging, we conducted spatial-temporal metabolomics on two cultivars during achene development. Metabolic profiles including 17 phenolic acids and 83 flavonoids are influenced by both varietal distinctions and developmental intricacies. Notably, flavonols, as major flavonoids, accumulated with achene ripening and showed a tissue-specific distribution. Specifically, flavonol glycosides and aglycones concentrated in the embryo, while methylated flavonols and procyanidins in the hull. Black achenes at the green achene stage have higher bioactive compounds and enhanced antioxidant capacity. These findings provide insights into spatial and temporal characteristics of metabolites in Tartary buckwheat achenes and serve as a theoretical guide for selecting optimal resources for food production.

Effect of Origin, Seed Coat Color, and Maturity Group on Seed Isoflavones in Diverse Soybean Germplasm

Soybeans are grown worldwide owing to their protein, oil, and beneficial bioactive compounds. Genetic and environmental factors influence soybean seed isoflavones. In the present study, we profiled the seed isoflavones in world diverse soybean germplasm grown in two locations over two years in China. Significant differences (p < 0.001) were observed between the accessions, accession origins, seed coat colors, and maturity groups for individual and total isoflavone (TIF) content. TIF content of the soybean accessions ranged from 677.25 μg g-1 to 5823.29 μg g-1, representing an 8-fold difference. USA soybean accessions showed the highest mean TIF content (3263.07 μg g-1), followed by Japan (2521.26 μg g-1). Soybean with black seed coat showed the highest (3236.08 μg g-1) TIF concentration. Furthermore, isoflavone levels were significantly higher in late-maturity groups. Correlation analysis revealed significant positive associations between individual and TIF content. Malonyldaidzin and malonylgenistin showed higher correlations with TIF content (r = 0.92 and r = 0.94, respectively). The soybean accessions identified as having high and stable TIF content can be utilized in the food and pharmaceutical industries and breeding programs to develop soybean varieties with enhanced isoflavone content.

An integrated untargeted metabolomic approach reveals the quality characteristics of black soybeans from different geographical origins in China

Black soybeans are extensively planted and consumed in China due to their high nutritional value and numerous health benefits. However, very few is known about the characteristic metabolites of black soybeans from different geographical origins in China. In the present study, 31 black soybean samples were collected from 11 main producing provinces in China. A combined metabolomics approach using ultra-performance liquid chromatography/quadrupole time-of-flight mass spectrometry (UPLC-QTOF-MS) and gas chromatography coupled to an Orbitrap mass analyzer (GC-orbitrap-MS) was performed for the first time to comprehensively investigate the metabolite variability among the black soybeans from different geographical origins. A total of 48 differential non-volatile metabolites and 14 differential volatile metabolites were identified based on orthogonal partial least squares discriminant analysis (OPLS-DA) coupled with analysis of variance (ANOVA). Higher procyanidin B1, procyanidin B2, epicatechin, malonylated isoflavones, and β-pinene were observed in Gansu black soybeans. Guangxi black soybeans had higher amounts of linoleic acid and its oxidation products of hexanal and pentane. The black soybeans from Xinjiang and Yunnan were found to have higher delphinidin-derived anthocyanins, gamma-glutamyl peptides, and aromatic hydrocarbons. The characteristic metabolites of black soybeans from other geographical origins were also clarified. This study indicated that the integrated untargeted metabolomic approach can be a powerful tool to provide knowledge for developing specialty black soybeans.

Comparison of the Main Metabolites in Different Maturation Stages of Camelliavietnamensis Huang Seeds

Camellia vietnamensis Huang is an important woody oil crop in China, which has attracted much attention because of its abundant nutritional components and pharmaceutical value. Its seeds undergo a complex series of physiological and biochemical changes during maturation, with consequent alterations in metabolites. In order to investigate the endogenous metabolism of C. vietnamensis on Hainan Island during seed development, in this study, ultra-high-performance liquid tandem chromatography coupled with quadrupole time-of-flight mass spectrometry (UHPLC/Q-TOF-MS) and multivariate statistical analysis (MSA) were used to analyze the differences in the chemical compounds of C. vietnamensis seeds among the four maturation stages. A total of 293 metabolites were identified from the methanol extract of the seeds of C. vietnamensis. Five metabolites, belonging to benzene and substituted derivatives, 5′-deoxyribonucleosides and linear 1,3-diarylpropanoids, were found in all three comparison groups, with consistently down-regulated trends. The Kyoto Encyclopedia of Genes and Genomes (KEGG) results showed that phloretin and 5′-methylthioadenosine were the differentially expressed metabolites when seeds were in the growth periods of S2 and S3, and indole and L-tryptophan were the differentially expressed metabolites when seeds were in the growth periods of S3 and S4. In addition, 34 flavonoid metabolites were detected, of which 4 were differentially expressed. It was indicated that flavonoids dynamically change during all the oil-tea camellia seed development stages. The findings provide data for the better understanding of endogenous metabolic pathways during C. vietnamensis seed development.

Multi-Omics Techniques for Soybean Molecular Breeding

Soybean is a major crop that provides essential protein and oil for food and feed. Since its origin in China over 5000 years ago, soybean has spread throughout the world, becoming the second most important vegetable oil crop and the primary source of plant protein for global consumption. From early domestication and artificial selection through hybridization and ultimately molecular breeding, the history of soybean breeding parallels major advances in plant science throughout the centuries. Now, rapid progress in plant omics is ushering in a new era of precision design breeding, exemplified by the engineering of elite soybean varieties with specific oil compositions to meet various end-use targets. The assembly of soybean reference genomes, made possible by the development of genome sequencing technology and bioinformatics over the past 20 years, was a great step forward in soybean research. It facilitated advances in soybean transcriptomics, proteomics, metabolomics, and phenomics, all of which paved the way for an integrated approach to molecular breeding in soybean. In this review, we summarize the latest progress in omics research, highlight novel findings made possible by omics techniques, note current drawbacks and areas for further research, and suggest that an efficient multi-omics approach may accelerate soybean breeding in the future. This review will be of interest not only to soybean breeders but also to researchers interested in the use of cutting-edge omics technologies for crop research and improvement.

iTRAQ and RNA-seq analyses provide an insight into mechanisms of recalcitrance in a medicinal plant Panax notoginseng seeds during the after-ripening process

Panax notoginseng (Burk) F.H. Chen is an important economic and medicinal plant from the family of Araliaceae, and its seed is characterised by the recalcitrance and after-ripening process. However, the molecular mechanism on the dehydration sensitivity is not clear in recalcitrant seeds. In the present study, isobaric tag for relative and absolute quantification (iTRAQ) and RNA-seq were used to analyse the proteomic and transcriptomic changes in seeds of P. notoginseng in days after-ripening (DAR). A total of 454 differentially expressed proteins (DEPs) and 12000 differentially expressed genes (DEGs) were obtained. The activity of enzymes related to antioxidant system were significantly increased, and the late embryogenesis abundant (LEA) protein family and most members of glutathione metabolism enzymes have been downregulated during the after-ripening process. The lack or inadequate accumulation of LEA proteins in the embryo and the low activity of antioxidant defense in glutathione metabolism might be the key factors leading to the dehydration sensitivity in recalcitrant seeds of P. notoginseng. In addition, the increased activity of elycolysis (EMP), citric acid cycle (TCA) and pentose phosphate pathway (PPP) pathways might be one of important signals to complete the after-ripening process. Overall, our study might provide a new insight into the molecular mechanism on dehydration sensitivity of recalcitrant seeds.

Metabolomics as a Tool to Study Underused Soy Parts: In Search of Bioactive Compounds

The valorization of agri-food by-products is essential from both economic and sustainability perspectives. The large quantity of such materials causes problems for the environment; however, they can also generate new valuable ingredients and products which promote beneficial effects on human health. It is estimated that soybean production, the major oilseed crop worldwide, will leave about 597 million metric tons of branches, leaves, pods, and roots on the ground post-harvesting in 2020/21. An alternative for the use of soy-related by-products arises from the several bioactive compounds found in this plant. Metabolomics studies have already identified isoflavonoids, saponins, and organic and fatty acids, among other metabolites, in all soy organs. The present review aims to show the application of metabolomics for identifying high-added-value compounds in underused parts of the soy plant, listing the main bioactive metabolites identified up to now, as well as the factors affecting their production.

Genetic Mapping and Identification of the Candidate Gene for White Seed Coat in Cucurbita maxima

Seed coat color is an important agronomic trait of edible seed pumpkin in Cucurbita maxima. In this study, the development pattern of seed coat was detected in yellow and white seed coat accessions Wuminglv and Agol. Genetic analysis suggested that a single recessive gene white seed coat (wsc) is involved in seed coat color regulation in Cucurbita maxima. An F₂ segregating population including 2798 plants was used for fine mapping and a candidate region containing nine genes was identified. Analysis of 54 inbred accessions revealed four main Insertion/Deletion sites in the promoter of CmaCh15G005270 encoding an MYB transcription factor were co-segregated with the phenotype of seed coat color. RNA-seq analysis and qRT-PCR revealed that some genes involved in phenylpropanoid/flavonoid metabolism pathway displayed remarkable distinction in Wuminglv and Agol during the seed coat development. The flanking InDel marker S1548 was developed to predict the seed coat color in the MAS breeding with an accuracy of 100%. The results may provide valuable information for further studies in seed coat color formation and structure development in Cucurbitaceae crops and help the molecular breeding of Cucurbita maxima.

Isoflavones, anthocyanins, phenolic content, and antioxidant activities of black soybeans (Glycine max (L.) Merrill) as affected by seed weight

Seed weight is regulated by several genes which in turn could affect the metabolite contents, yield, and quality of soybean seeds. Due to these, seed weight is receiving much attention in soybean breeding. In this study, seeds of 24 black soybean varieties and a reference genotype were grown in Korea, and grouped as small (< 13 g), medium (13-24 g), and large (> 24 g) seeds based on their seed weight. The contents of six anthocyanins, twelve isoflavones, and total phenolic, and the antioxidant activities were determined, and the association of each with seed weight was analyzed. The total anthocyanin (TAC) and total isoflavone (TIC) contents were in the ranges of 189.461-2633.454 mg/100 g and 2.110-5.777 mg/g, respectively and were significantly different among the black soybean varieties. By comparison, the average TAC and TIC were the highest in large seeds than in small and medium seeds while the total phenolic content (TPC) was in the order of small seeds > large seeds > medium seeds. Besides, large seeds showed the maximum 1,1-diphenyl-2-picrylhydrazyl radical (DPPH) scavenging activity, whereas small seeds showed the maximum ferric reducing antioxidant power (FRAP) and 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) radical (ABTS) scavenging activities. FRAP activity was positively associated with TIC and TAC, the former association being significant. On the other hand, ABTS and DPPH activities were positively correlated to TPC, the later association being significant. Overall, our findings demonstrated the influence of seed weight on anthocyanin, isoflavone, and phenolic contents and antioxidant activities in black soybeans. Besides, the dominant anthocyanins and isoflavones were the principal contributors to the variations observed in the black soybean varieties, and hence, these components could be selectively targeted to discriminate a large population of black soybean genetic resources.

5,7,3',4'-Tetrahydroxyflav-2-en-3-ol 3-O-glucoside, a new biosynthetic precursor of cyanidin 3-O-glucoside in the seed coat of black soybean, Glycine max

The seed coat of mature black soybean, Glycine max, accumulates a high amount of cyanidin 3-O-glucoside (Cy3G), which is the most abundant anthocyanin in nature. In the pod, it takes two months for the seed coat color change from green to black. However, immature green beans rapidly adopt a black color within one day when the shell is removed. We analyzed the components involved in the color change of the seed coat and detected a new precursor of Cy3G, namely 5,7,3',4'-tetrahydroxyflav-2-en-3-ol 3-O-glucoside (2F3G). Through quantitative analysis using purified and synthetic standard compounds, it was clarified that during this rapid color change, an increase in the Cy3G content was observed along with the corresponding decrease in the 2F3G content. Chemical conversion from 2F3G to Cy3G at pH 5 with air and ferrous ion was observed. Our findings allowed us to propose a new biosynthetic pathway of Cy3G via a colorless glucosylated compound, 2F3G, which was oxidized to give Cy3G.

Improvement of Soybean Products Through the Response Mechanism Analysis Using Proteomic Technique

Soybean is rich in protein/vegetable oil and contains several phytochemicals such as isoflavones and phenolic compounds. Because of the predominated nutritional values, soybean is considered as traditional health benefit food. Soybean is a widely cultivated crop; however, its growth and yield are markedly affected by adverse environmental conditions. Proteomic techniques make it feasible to map protein profiles both during soybean growth and under unfavorable conditions. The stress-responsive mechanisms during soybean growth have been uncovered with the help of proteomic studies. In this review, the history of soybean as food and the morphology/physiology of soybean are described. The utilization of proteomics during soybean germination and development is summarized. In addition, the stress-responsive mechanisms explored using proteomic techniques are reviewed in soybean.

Seed coat color and seed weight contribute differential responses of targeted metabolites in soybean seeds

The distribution and variation of targeted metabolites in soybean seeds are affected by genetic and environmental factors. In this study, we used 192 soybean germplasm accessions collected from two provinces of Korea to elucidate the effects of seed coat color and seeds dry weight on the metabolic variation and responses of targeted metabolites. The effects of seed coat color and seeds dry weight were present in sucrose, total oligosaccharides, total carbohydrates and all measured fatty acids. The targeted metabolites were clustered within three groups. These metabolites were not only differently related to seeds dry weight, but also responded differentially to seed coat color. The inter-relationship between the targeted metabolites was highly present in the result of correlation analysis. Overall, results revealed that the targeted metabolites were diverged in relation to seed coat color and seeds dry weight within locally collected soybean seed germplasm accessions.

Metabolite profiling of somatic embryos of Cyclamen persicum in comparison to zygotic embryos, endosperm, and testa

Somatic embryogenesis has been shown to be an efficient in vitro plant regeneration system for many crops such as the important ornamental plant Cyclamen persicum, for which this regeneration pathway of somatic embryogenesis is of interest for the vegetative propagation of parental lines as well as elite plants. However, somatic embryogenesis is not commercially used in many crops due to several unsolved problems, such as malformations, asynchronous development, deficiencies in maturation and germination of somatic embryos. In contrast, zygotic embryos in seeds develop and germinate without abnormalities in most cases. Instead of time-consuming and labor-intensive experiments involving tests of different in vitro culture conditions and plant growth regulator supplements, we follow a more directed approach. Zygotic embryos served as a reference and were compared to somatic embryos in metabolomic analyses allowing the future optimization of the in vitro system. The aims of this study were to detect differences in the metabolite profiles of torpedo stage somatic and zygotic embryos of C. persicum. Moreover, major metabolites in endosperm and testa were identified and quantified. Two sets of extracts of two to four biological replicates each were analyzed. In total 52 metabolites were identified and quantified in the different tissues. One of the most significant differences between somatic and zygotic embryos was that the proline concentration in the zygotic embryos was about 40 times higher than that found in somatic embryos. Epicatechin, a scavenger for reactive oxygen species, was found in highest abundance in the testa. Sucrose, the most abundant metabolite was detected in significantly higher concentrations in zygotic embryos. Also, a yet unknown trisaccharide, was significantly enriched in zygotic embryos.

Seed metabolomic study reveals significant metabolite variations and correlations among different soybean cultivars

Soybean [Glycine max (L.) Merr.] is one of the world's major crops, and soybean seeds are a rich and important resource for proteins and oils. While "omics" studies, such as genomics, transcriptomics, and proteomics, have been widely applied in soybean molecular research, fewer metabolomic studies have been conducted for large-scale detection of low molecular weight metabolites, especially in soybean seeds. In this study, we investigated the seed metabolomes of 29 common soybean cultivars through combined gas chromatography-mass spectrometry and ultra-performance liquid chromatography-tandem mass spectrometry. One hundred sixty-nine named metabolites were identified and subsequently used to construct a metabolic network of mature soybean seed. Among the 169 detected metabolites, 104 were found to be significantly variable in their levels across tested cultivars. Metabolite markers that could be used to distinguish genetically related soybean cultivars were also identified, and metabolite-metabolite correlation analysis revealed some significant associations within the same or among different metabolite groups. Findings from this work may potentially provide the basis for further studies on both soybean seed metabolism and metabolic engineering to improve soybean seed quality and yield.

Differential responses of B vitamins in black soybean seeds

This study was aimed to determine the contents and the association of B vitamins from seeds of 10 black and one yellow soybean (Glycine max (L.) Merr.) varieties with either green or yellow cotyledon. Thiamine, flavin adenine dinucleotide (FAD), riboflavin and total riboflavin were found highest in 'Chengjakong', while flavin mononucleotide (FMN) was greatest in 'Mirang'. Nicotinic acid and total vitamin B3 were highest in 'Shingi' as a yellow soybean variety but pantothenic acid and pyridoxine contents were greatest in 'Tawon' and 'Mirang', respectively. These content variations of B vitamins directly reflected the wide segregation of soybean varieties on the principal component analysis (PCA) scores plot, indicating that these 4 soybean varieties appeared to be least associated with other soybean varieties based on the different responses of B vitamins. The results of cluster and correlation analyses presented that the cotyledon colour of soybean seed contributed to a variation of B vitamin contents. Overall, the results suggest that a wide range of B vitamin contents would be affected by genotypic factors alongside the difference of cotyledon colour.