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

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.

Comparative Metabolomics Analysis of Different Perilla Varieties Provides Insights into Variation in Seed Metabolite Profiles and Antioxidant Activities

Perilla seeds are essential functional foods and key ingredients in traditional medicine. Herein, we investigated the variation in phytochemical profiles and antioxidant activities of twelve different perilla seeds. The seeds showed significant variations in total phenolic and flavonoid contents ranging from 16.92 to 37.23 mg GAE/g (GAE, gallic acid equivalent) and 11.6 to 19.52 mg CAE/g (CAE, catechin equivalent), respectively. LC-QqQ-MS (liquid chromatography triple quadrupole tandem mass spectrometry)-based widely targeted metabolic profiling identified a total of 975 metabolites, including 68-269 differentially accumulated metabolites (DAMs). Multivariate analyses categorized the seeds into four groups based on the seed coat and leaf colors. Most key bioactive DAMs, including flavonoids (quercetin-3'-O-glucoside, prunin, naringenin, naringenin chalcone, butin, genistin, kaempferol-3-O-rutinoside, etc.), amino acids (valine, lysine, histidine, glutamine, threonine, etc.), and vitamins (B1, B3, B6, U, etc.) exhibited the highest relative content in PL3 (brown seed, purple leaf), PL1 (white seed, green-purple leaf), and PL4 (white seed, green leaf) groups, respectively. Meanwhile, key differentially accumulated phenolic acids showed a higher relative content in PL1 and PL4 than in other groups. Both seeds exhibited high antioxidant activities, although those of PL2 (brown seed, green leaf) group seeds were the lowest. Our results may facilitate the comprehensive use of perilla seeds in food and pharmaceutical industries.

Distinct Effects of Seed Coat and Flower Colors on Metabolite Contents and Antioxidant Activities in Safflower Seeds

Safflower is an important oilseed crop cultivated primarily for its seeds, which have pharmaceutical properties. Color is an important agronomical trait that appears to be a prior parameter for evaluating the internal quality of plant seeds. This study employs 197 safflower accessions seeds to analyze how their seed coat and flower colors affect their total oil content, fatty acid composition, total phenolic content (TPC), N-(p-coumaroyl)serotonin (CS) and N-feruloylserotonin (FS) contents, and [2,2-diphenyl-1-picrylhydrazyl (DPPH) and 2,2'-azino-bis-(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS)] radical scavenging activities. Significant variations were observed in the targeted metabolite contents and antioxidant properties among genotypes. Notably, the linoleic acid content, total unsaturated fatty acid content, the ratio of total unsaturated fatty acid to total saturated fatty acid, CS, FS, ABTS, and DPPH scavenging capacities varied significantly based on seed coat color, with white-seeded genotypes having the highest average values of these parameters. Moreover, the linoleic acid content differed significantly (p < 0.05) among the genotypes with varying flower colors, with white-flowered accessions having the highest average content. Furthermore, genotypes K185105 (No. 75) and K175278 (No. 146) were identified as promising genetic resources with health benefits. Overall, these findings reveal that seed coat and flower colors distinctly affect metabolite contents and antioxidant properties in safflower seeds.

Origin and seed coat color differently affect the concentrations of metabolites and antioxidant activities in soybean (Glycine max (L.) Merrill) seeds

In this study, 54 soybean germplasms of different seed coat colors originated from America, China, Japan, and Korea were cultivated in Korea and analyzed for the contents of total oil, total protein, total phenolic, five fatty acids, and five isoflavones, and antioxidant activities using three assays. The soybeans showed significant variations (p < 0.05) of metabolite contents and antioxidant activities. Origin and seed coat color exhibited a slight or insignificant effect on total protein and total oil contents. In contrast, origin and seed coat color significantly affected the concentration of individual and total isoflavones, and total phenolics, with few exceptions. Whereas fatty acids were significantly affected by origin, seed coat color provided better information regarding the variations in antioxidant capacities. Together, multivariate and correlation analyses revealed important associations between biosynthetically-related metabolites. In general, origin and seed coat color differently influenced the concentration of different classes of metabolites and antioxidant activities.

Transcriptome analysis of walnut quality formation and color change mechanism of pellicle during walnut development

Walnuts (including those covered with a pellicle) are loved for their rich nutritional value. And the popular varieties of walnut cultivation are Juglans sigillata L. The pellicle (seed coat) of these walnut cultivars has different colors and has an indispensable influence on the walnut quality formation. However, there are few reports on the pellicle color and quality formation in different developmental stages of walnut (Juglans sigillata L.). Therefore, in this study, three walnut cultivars (F, Q, and T) with different pellicle colors were selected for transcriptome sequencing and physiological index analysis of the color and quality formation mechanisms at different development stages. The results showed that with the development of walnut fruit, the starch sucrose metabolism pathway in the pellicle was activated and promoted starch hydrolysis. Meanwhile, the expression levels of genes related to the alpha-linolenic acid metabolism pathway were significantly increased during walnut maturation, especially in F2. Some physiological indicators related to lipid oxidation were also detected and analyzed in this study, such as MDA, CAT, POD and DPPH. These results were similar to the expression patterns of corresponding regulatory genes in the RNA-Seq profile. In addition, lignin synthesis genes were up-regulated in the phenylpropanoid metabolic pathway, while key genes enriched in the flavonoid and anthocyanin synthesis pathways were down-regulated. The results were consistent with the results of total anthocyanins and flavonoid content detection during walnut development. Therefore, this experiment suggested that with the maturation of walnut pellicle, the gene expression in the phenylpropanoid metabolic pathway flowed to the branch of lignin synthesis, especially in the Q variety, resulting in lower flavonoid and anthocyanin content at the maturity stage than immature. This is also the main reason for the pale pellicle of the three walnut varieties after mature. The findings of this study showed that changes in the expression levels of regulating genes for lipid, starch, sugar, and flavonoid synthesis during walnut development influenced the accumulation of the related metabolite for walnut quality formation and pellicle color. The results of this experiment provided the molecular basis and reference for the breeding of high nutritional quality walnut varieties.

MC03g0810, an Important Candidate Gene Controlling Black Seed Coat Color in Bitter Gourd (Momordica spp.)

Seed coat color is one of the most intuitive phenotypes in bitter gourd (Momordica spp.). Although the inheritance of the seed coat color has been reported, the gene responsible for it is still unknown. This study used two sets of parents, representing, respectively, the intersubspecific and intraspecific materials of bitter gourd, and their respective F₁ and F₂ progenies for genetic analysis and primary mapping of the seed coat color. A large F_2:3 population comprising 2,975 seedlings from intraspecific hybridization was used to fine-map the seed coat color gene. The results inferred that a single gene, named McSC1, controlled the seed coat color and that the black color was dominant over the yellow color. The McSC1 locus was mapped to a region with a physical length of ∼7.8 Mb and 42.7 kb on pseudochromosome 3 via bulked segregant analysis with whole-genome resequencing (BSA-seq) and linkage analysis, respectively. Subsequently, the McSC1 locus was further fine-mapped to a 13.2-kb region containing only one candidate gene, MC03g0810, encoding a polyphenol oxidase (PPO). Additionally, the variations of MC03g0810 in the 89 bitter gourd germplasms showed a complete correlation with the seed coat color. Expression and PPO activity analyses showed a positive correlation between the expression level of MC03g0810 and its product PPO and the seed coat color. Therefore, MC03g0810 was proposed as the causal gene of McSC1. Our results provide an important reference for molecular marker-assisted breeding based on the seed coat color and uncover molecular mechanisms of the seed coat color formation in bitter gourd.

Origin, Maturity Group and Seed Coat Color Influence Carotenoid and Chlorophyll Concentrations in Soybean Seeds

Soybean (Glycine max (L.) Merrill) seeds are abundant in physiologically active metabolites, including carotenoids and chlorophylls, and are used as an affordable source of functional foods that promote and maintain human health. The distribution and variation of soybean seed metabolites are influenced by plant genetic characteristics and environmental factors. Here, we investigated the effects of germplasm origin, genotype, seed coat color and maturity group (MG) on the concentration variation of carotenoid and chlorophyll components in 408 soybean germplasm accessions collected from China, Japan, the USA and Russia. The results showed that genotype, germplasm origin, seed color, and MG were significant variation sources of carotenoid and chlorophyll contents in soybean seeds. The total carotenoids showed about a 25-fold variation among the soybean germplasms, with an overall mean of 12.04 µg g⁻¹. Russian soybeans yielded 1.3-fold higher total carotenoids compared with Chinese and Japanese soybeans. Similarly, the total chlorophylls were substantially increased in Russian soybeans compared to the others. Soybeans with black seed coat color contained abundant concentrations of carotenoids, with mainly lutein (19.98 µg g⁻¹), β-carotene (0.64 µg g⁻¹) and total carotenoids (21.04 µg g⁻¹). Concentrations of lutein, total carotenoids and chlorophylls generally decreased in late MG soybeans. Overall, our results demonstrate that soybean is an excellent dietary source of carotenoids, which strongly depend on genetic factors, germplasm origin, MG and seed coat color. Thus, this study suggests that soybean breeders should consider these factors along with environmental factors in developing carotenoid-rich cultivars and related functional food resources.

Widely targeted metabolome profiling of different colored sesame (Sesamum indicum L.) seeds provides new insight into their antioxidant activities

Sesame seeds are considered worldwide as a functional food due to their nutritional and therapeutical values. Several physiological functions are being associated with sesame seeds and their derived products. However, the phytochemicals responsible for these various proprieties are not well understood. Thus, to acknowledge the diversity and variability of metabolites in sesame seeds of different colors and reveal key metabolites and pathways contributing to differences in antioxidant activities, black, brown, yellow, and white sesame seeds from 12 varieties were subjected to LC-MS/MS-based widely targeted metabolomics analysis. Totally, 671 metabolites were identified and chemically classified. The metabolic compounds varied significantly with the seed coat color and genotype. Many flavonoids, amino acids, and terpenoids were up-regulated in dark seeds. Sixty key differential metabolites were filtered out. Phenylpropanoid biosynthesis, amino acids biosynthesis, and tyrosine metabolism were the main differently regulated pathways. The DPPH, ABTS, and FRAP assays showed that the antioxidant activities of the seeds increased with the seed coat darkness. Therefore, the pharmacological proprieties of black seeds might be related to their high content of flavonoids and essential amino acids mostly. These findings expand phytochemicals composition information of different colored sesame seeds and provide resources for their comprehensive use and quality improvement.

Bio-Chemical Fertilizer Improves the Oil Yield, Fatty Acid Compositions, and Macro-Nutrient Contents in Nigella sativa L

The present study evaluated the effects of biofertilizers on qualitative and quantitative traits of Nigella sativa L. The experiment was conducted based on a randomized complete block design with 10 treatments and three replications. The treatments included control (no fertilization), U (100% chemical fertilizer as urea at 53.3 kg ha−1, Nb (Biofertilizer, Azotobacter vinelandii), Pb (Biofertilizer, Pantoea agglomerans and Pseudomonas putida), Kb (Biofertilizer, Bacillus spp.), NPKb (NPK combined biofertilizers), Nb + 50% U, Pb + 50% U, Kb + 50% U, and NPKb + 50% U. The highest oil percentage was 46.33 percent related to NPK(b) + U50%, and the highest oil yield was 466.43 kg/ha related to NPK(b) + U50%. The highest seed yield (1006.64 kg/ha) was observed in the plants treated with NPK(b) + U50%. The treatment of K(b) + U50% increased myristic acid by 0.35%. The NPK(b) + U50% treatment reduced palmitic, stearic, and linolenic acid by 11.3, 2.01, and 0.31%, respectively. The highest oleic acid (27.85%) and linoleic acid (56.6%) were obtained from the treatment of NPK(b) + U50%, respectively. The plants treated with NPK(b) + U50% showed the highest seed N percentage (%), P content (mg g−1) and K content (mg g−1). In general, NPK(b) + U50% is the best treatment in line with sustainable agriculture.

Benchmarking Nutraceutical Soybean Composition Relative to Protein and Oil

The aim of this study was to explore relationships between protein, oil, and seed weight with seed nutraceutical composition, focused on total isoflavone (TI) and total tocopherol (TT) contents across genotypic and environmental combinations in soybean. We conducted a synthesis-analysis of peer-reviewed published field studies reporting TI, TT, protein, oil, and seed weight (n = 1,908). The main outcomes from this synthesis-analysis were: (i) relationship of TI-to-protein concentration was positive, though for the upper boundary, TI decreases with increases in protein; (ii) relationship of TT-to-oil concentration was positive, but inconsistent when oil was expressed in mg per seed; and (iii) as seed weight increased, TI accumulation was less than proportional relative to protein concentration and TT decreased more proportional relative to oil concentration. Association between nutraceuticals and protein, oil, and seed weight for soybean reported in the present study can be used as a foundational knowledge for soybean breeding programs interested on predicting and selecting enhanced meal isoflavone and/or oil tocopherol contents.

Protein, Amino Acid, Oil, Fatty Acid, Sugar, Anthocyanin, Isoflavone, Lutein, and Antioxidant Variations in Colored Seed-Coated Soybeans

Different physiological and genetic studies show that the variations in the accumulation of pigment-stimulating metabolites result in color differences in soybean seed coats. The objective of this study was to analyze the nutrient contents and antioxidant potential in black, brown, and green seed-coated soybeans. Significant variations in protein (38.9-43.3%), oil (13.9-20.4%), total sugar (63.5-97.0 mg/g seed), total anthocyanin (3826.0-21,856.0 μg/g seed coat), total isoflavone (709.5-3394.3 μg/g seed), lutein (1.9-14.8 μg/g), total polyphenol (123.0-385.8 mg gallic acid/100 g seed), total flavonoid (22.1-208.5 mg catechin/100 g seed), 2,2'-azino-bis(3-ethylbenzthiazoline-6-sulphonic acid (ABTS; 275.0-818.8 mg Trolox/100 g seed), and 2,2-diphenyl-1-picrylhydrazyl (DPPH; 96.3-579.7 mg Trolox/100 g seed) were found among the soybean genotypes. Ilpumgeomjeong2 contained the lowest protein but the highest oil and total sugar. The lowest oil-containing Wonheug had the highest protein content. Socheong2 was rich in all four variables of antioxidants. Anthocyanins were detected only in black soybeans but not in brown and green soybeans. The variation in isoflavone content was up to 5-fold among the soybean genotypes. This study could be a valuable resource for the selection and improvement of soybean because an understanding of the nutrient content and antioxidant potentials is useful to develop effective strategies for improving the economic traits; for example, the major emphasis of soybean breeding for fatty acids is to enhance the oleic and linoleic acid contents and to decrease linolenic acid content.

Metabolite Contents and Antioxidant Activities of Soybean (Glycine max (L.) Merrill) Seeds of Different Seed Coat Colors

Seed coat color is one of the main agronomical traits that determine the chemical quality of soybean seeds and has been used as a parameter during cultivar development. In this study, seeds of yellow (n = 10), greenish-yellow (n = 5), and light-yellow (n = 4) soybean accessions were evaluated for their contents of total protein, total oil, total phenolic (TPC), and five prominent fatty acids including palmitic acid (PA), stearic acid (SA), oleic acid (OA), linoleic acid (LA), and linolenic acid (LLA), relative to a control cultivar, and the effect of seed coat color on each was investigated. Antioxidant activity was also evaluated using 1,1-diphenyl-1-picrylhydrazyl (DPPH) radical scavenging activity, Trolox equivalent antioxidant capacity (TEAC), and ferric reducing antioxidant power (FRAP). The results showed significant variations of metabolite contents and antioxidant activities between the soybeans. The average TPC, DPPH-radical scavenging activity, and FRAP were each in the order of greenish-yellow > yellow > light-yellow soybeans. In contrast, light-yellow soybeans contained a high level of OA and low levels of SA, LA, and LLA, each except LA differing significantly from yellow and greenish-yellow soybeans (p < 0.05). Our findings suggest that greenish-yellow and light-yellow soybeans could be good sources of antioxidants and high-quality soybean oil, respectively.

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.

Antioxidant Contributors in Seed, Seed Coat, and Cotyledon of γ-ray-Induced Soybean Mutant Lines with Different Seed Coat Colors

The development of soybean with high antioxidant activities for use in the food and cosmetics industries is a target of breeding programs. In soybean, antioxidants are associated with seed color, although the metabolic basis for seed coloration remains incompletely understood. We selected six γ-ray-induced mutant lines that exhibited black, partially black, brown, partially brown, or yellowish-white pigmentation in the seed coat. Antioxidant activity and contents of anthocyanins, flavan-3-ols, and isoflavones were evaluated in the seed coat and cotyledons. The lines with black or brown seeds showed the highest antioxidant activities. The cotyledons showed no significant differences in seed coat components or antioxidant activities among lines. Black and brown seed coat components showed the highest antioxidant activities. The black seed coat contained five anthocyanins, whereas seed coats of brown- and yellow-seeded lines entirely lacked anthocyanins. Both black and brown seeds were rich in flavan-3-ols, including catechin and epicatechin, which were the predominant antioxidant contributors in brown seeds. Isoflavone contents showed weaker correlations with antioxidant activity than anthocyanins and flavan-3-ols. These results demonstrated that antioxidant activities were determined by anthocyanins in black seeds and flavan-3-ols in brown and black seeds, whereas relatively low antioxidant activities in yellow seeds reflected their high isoflavone contents.

Specialized phenolic compounds in seeds: structures, functions, and regulations

Plants produce a huge diversity of specialized metabolites (SM) throughout their life cycle that play important physiological and ecological functions. SM can protect plants and seeds against diseases, predators, and abiotic stresses, or support their interactions with beneficial or symbiotic organisms. They also have strong impacts on human nutrition and health. Despite this importance, the biosynthesis and biological functions of most of the SM remain elusive and their diversity and/or quantity have been reduced in most crops during domestication. Seeds present a large number of SM that are important for their physiological, agronomic, nutritional or industrial qualities and hence, provide interesting models for both studying biosynthesis and producing large amounts of specialized metabolites. For instance, phenolics are abundant and widely distributed in seeds. More specifically, flavonoid pathway has been instrumental for understanding environmental or developmental regulations of specialized metabolic pathways, at the molecular and cellular levels. Here, we summarize current knowledge on seed phenolics as model, and discuss how recent progresses in omics approaches could help to further characterize their diversity, regulations, and the underlying molecular mechanisms involved.

Natural Variation in Fatty Acid Composition of Diverse World Soybean Germplasms Grown in China

Soybean (Glycine max L. Merr.) is one of the most important crops in the world. Its major content of vegetable oil made it widely used for human consumption and several food industries. To investigate the variation in seed fatty acid composition of soybeans from different origins, a set of 633 soybean accessions originated from four diverse germplasm collections—including China, United States of America (USA), Japan, and Russia—were grown in three locations, Beijing, Anhui, and Hainan for two years. The results showed significant differences (P < 0.001) among the four germplasm origins for all fatty acid contents investigated. Higher levels, on average, of palmitic acid (PA) and linolenic acid (LNA) were observed in Russian germplasm (12.31% and 8.15%, respectively), whereas higher levels of stearic acid (SA) and oleic acid (OA) were observed in Chinese germplasm (3.95% and 21.95%, respectively). The highest level of linoleic acid (LA) was noticed in the USA germplasm accessions (56.34%). The largest variation in fatty acid composition was found in LNA, while a large variation was observed between Chinese and USA germplasms for LA level. Maturity group (MG) significantly (P < 0.0001) affected all fatty acids and higher levels of PA, SA, and OA were observed in early maturing accessions, while higher levels of LA and LNA were observed in late maturing accessions. The trends of fatty acids concentrations with different MG in this study further provide an evidence of the importance of MG in breeding for such soybean seed components. Collectively, the unique accessions identified in this study can be used to strengthen the soybean breeding programs for meeting various human nutrition patterns around the globe.

Studying the link between physiological performance of Crotalaria ochroleuca and the distribution of Ca, P, K and S in seeds with X-ray fluorescence

This study describes the use of X-ray fluorescence spectroscopy in Crotalaria ochroleuca seed technology. This work evaluated X-ray fluorescence techniques to estimate the physiological performance of different C. ochroleuca seed coat colours based on the concentration and distribution of Ca, P, K, and S in seed structures. The treatments consisted of seeds separated by coat colours (yellow, green, and red) and a control treatment (colour mix according to their natural occurrence in commercial lots), and was carried out in a completely randomized design, with four replications. The physiological performance was evaluated by analyzing the water content, germination, first germination count, germination speed index, electrical conductivity, seedling emergence, and seedling length and dry mass. X-ray fluorescence spectroscopy techniques were carried out with quantitative analyses (Ca, P, K, and S concentration in the seed coat and the whole seed) and qualitative analyses (macronutrient mapping). The EDXRF and μ-XRF techniques are efficient and promising to differentiate the physiological performance of C. ochroleuca seeds, based on the concentration and distribution of Ca, P, K, and S in different structures. Ca is predominant in the seed coat, and K, S, and P are found throughout the embryonic axis. Seeds of yellow and green coats have higher nutrients concentration and distribution in the embryonic axis, revealing high germinative capacity and physiological performance. Seeds of red coat have higher nutrients concentration in the seed coat and lower assimilation, showing less vigour, which interferes directly in the quality of commercial lots.