Seed isoflavone profiling of 1168 soybean accessions from major growing ecoregions in China

An R2R3-type MYB transcription factor, GmMYB77, negatively regulates isoflavone accumulation in soybean [Glycine max (L.) Merr.]

Soybean [Glycine max (L.) Merr.] is an exceptionally rich in isoflavones, and these compounds attach to oestrogen receptors in the human body, lessening the risk of breast cancer and effectively alleviating menopausal syndrome symptoms. Uncovering the molecular mechanisms that regulate soybean isoflavone accumulation is crucial for enhancing the production of these compounds. In this study, we combined bulk segregant analysis sequencing (BSA-seq) and a genome-wide association study (GWAS) to discover a novel R2R3-MYB family gene, GmMYB77, that regulates isoflavone accumulation in soybean. Using the soybean hairy root transient expression system, we verified that GmMYB77 inhibits isoflavone accumulation. Furthermore, knocking out GmMYB77 significantly increased total isoflavone (TIF) content, particularly malonylglycitin, while its overexpression resulted in a notable decrease in contents of malonylglycitin and TIF. We found that GmMYB77 can directly binds the core sequence GGT and suppresses the expression of the key isoflavone biosynthesis genes Isoflavone synthase 1 (GmIFS1), Isoflavone synthase 2 (GmIFS2), Chalcone synthase 7 (GmCHS7) and Chalcone synthase 8 (GmCHS8) by using dual-luciferase assays, electrophoretic mobility shift assays and yeast one-hybrid experiments. Natural variations in the promoter region of GmMYB77 affect its expression, thereby regulating the malonylglycitin and TIF contents. Hap-P2, an elite haplotype, plays a pivotal role in soybean breeding for substantially enhanced isoflavone content. These findings enhance our understanding of the genes influencing soybean isoflavone content and provide a valuable genetic resource for molecular breeding efforts in the future.

Occurrence and distribution of phytic acid and its degradation products in soybeans in China: Analytical challenges

Phytic acid (IP6) and its degradation products lower myo-inositol phosphates exert different impacts on nutrient bioavailability and product quality characteristics. However, information regarding the occurrence of IP6 and its degradation products is scarce. In this work, simultaneous determination of IP6 and its degradation products in soybeans was developed, with emphasis on analysis by UPLC-MS/MS and a BEH Amide column both with hybrid surface technology. The retention and analyte/metal surface interactions issues were effectively addressed without ion-pairing reagents addition or derivatization. This method was applied to analyze soybeans from China. Total contents were 0.44-13.2 mg/g, and IP6 and its degradation product myo-inositol pentakisphosphate (IP5) were the predominant analytes, accounting for over 99%. Accession type significantly affected IP5 content, and landraces had significantly higher IP5 than cultivars. Geographically, the lowest IP6 was concentrated in the Huanghuaihai region. Significant correlations existed between IP6 and longitude, altitude, and annual cumulative sunshine hours. This study provides comprehensive insights into the IP6 and its degradation product profile in soybeans, which will benefit breeding soybeans based on specific requirements.

Flavonoid localization in soybean seeds: Comparative analysis of wild (Glycine soja) and cultivated (Glycine max) varieties

Wild soybean (Glycine soja) is known for its high flavonoid contents, yet the distribution of flavonoids in the seeds is not well understood. Herein, we utilized matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) and metabolomics methods to systematically investigate flavonoid differences in the seed coats and embryos of G. soja and G. max. The results of flavonoid profiles and total flavonoid content analyses revealed that flavonoid diversity and abundance in G. soja seed coats were significantly higher than those in G. max whereas the levels were similar in embryos. Specifically, 23 unique flavonoids were identified in the seed coats of G. soja, including procyanidins, epicatechin derivatives, and isoflavones. Using MALDI-MSI, we further delineated the distribution of the important flavonoids in the cotyledons, hypocotyls, and radicles of the two species. These findings imply that G. soja holds considerable breeding potential to enhance the nutritional and stress resistance traits of G. max.

Microwave Irradiation as a Powerful Tool for Isolating Isoflavones from Soybean Flour

The use of microwave irradiation energy for isolating bioactive compounds from plant materials has gained popularity due to its ability to penetrate cells and facilitate extraction of intracellular materials, with the added benefits of minimal or no use of organic solvents. This is particularly significant due to the possibility of using extracts in the food and pharmaceutical industries. The aim of this work is to examine the effect of microwave irradiation on the extraction of three of the most important isoflavones from soybean flour, glycitin, genistin, and daidzin, as well as their aglycones, glycitein, genistein, and daidzein. By varying the extraction time, temperature, and microwave power, we have established the optimal parameters (irradiation power of 75 W for 5 min) for the most efficient extraction of individual isoflavones. Compared to conventional maceration and ultrasound-assisted extraction, the total phenol content of the extracts increased from 3.66 to 9.16 mg GAE/g dw and from 4.67 to 9.16 mg GAE/g dw, respectively. The total flavonoid content increased from 0.38 to 0.83 mg CE/g dw and from 0.48 to 0.83 mg CE/g dw, and the antioxidant activity increased from 96.54 to 185.04 µmol TE/g dw and from 158.57 to 185.04 µmol TE/g dw, but also from 21.97 to 37.16 µmol Fe2+/g dw and from 30.13 to 37.16 µmol Fe2+/g dw. The positive correlation between microwave extraction and increased levels of total phenols, flavonoids, and antioxidant activity demonstrates the method's effectiveness in producing bioactive compounds. Considering the growing recognition of glycitein's potential role in medical and pharmaceutical applications, microwave-assisted extraction under optimized conditions has proven highly efficient.

Bioinformatics Identification and Expression Analysis of Acetyl-CoA Carboxylase Reveal Its Role in Isoflavone Accumulation during Soybean Seed Development

Isoflavones belong to the class of flavonoid compounds, which are important secondary metabolites that play a crucial role in plant development and defense. Acetyl-CoA carboxylase (ACCase) is a biotin-dependent enzyme that catalyzes the conversion of Acetyl-CoA into Malonyl-CoA in plants. It is a key enzyme in fatty acid synthesis and also catalyzes the production of various secondary metabolites. However, information on the ACC gene family in the soybean (Glycine max L. Merr.) genome and the specific members involved in isoflavone biosynthesis is still lacking. In this study, we identified 20 ACC family genes (GmACCs) from the soybean genome and further characterized their evolutionary relationships and expression patterns. Phylogenetic analysis showed that the GmACCs could be divided into five groups, and the gene structures within the same groups were highly conserved, indicating that they had similar functions. The GmACCs were randomly distributed across 12 chromosomes, and collinearity analysis suggested that many GmACCs originated from tandem and segmental duplications, with these genes being under purifying selection. In addition, gene expression pattern analysis indicated that there was functional divergence among GmACCs in different tissues. The GmACCs reached their peak expression levels during the early or middle stages of seed development. Based on the transcriptome and isoflavone content data, a weighted gene co-expression network was constructed, and three candidate genes (Glyma.06G105900, Glyma.13G363500, and Glyma.13G057400) that may positively regulate isoflavone content were identified. These results provide valuable information for the further functional characterization and application of GmACCs in isoflavone biosynthesis in soybean.

Contextualized Metabolic Modelling Revealed Factors Affecting Isoflavone Accumulation in Soybean Seeds

Isoflavones, secondary metabolites with numerous health benefits, are predominantly found in legume seeds, especially soybean; however, their contents in domesticated soybean seeds are highly variable. Wild soybeans are known for higher seed isoflavone contents than cultivars. Here we used experimental and modelling approaches on wild soybean (W05) and cultivated soybean (C08) to delineate factors influencing isoflavone accumulation. We found imported nutrients were converted into storage compounds, with isoflavone accumulation in W05 seeds being faster than in C08 ones. The isoflavone accumulation during seed development was simulated using context-specific cotyledon metabolic models of four developmental stages on cultivar C08, and the metabolic burden imposed by increasing biomass was evaluated. Trade-off analyses between biomass and isoflavone suggest that high biomass requirement in cultivars could limit the reallocation of resources for secondary metabolite production. Isoflavone production in mature seeds was also influenced by biomass compositions. Seeds with higher carbohydrate contents favour isoflavone production, while those with highest protein and oil contents had lowest isoflavone contents. Although seeds could synthesize isoflavones on their own, the predicted fluxes from biosynthesis alone were lower than the empirical levels. Shadow price analyses indicated that isoflavone accumulation depended on both intrinsic biosynthesis and direct contribution from the plant.

Joint GWAS and WGCNA Identify Genes Regulating the Isoflavone Content in Soybean Seeds

Isoflavone is a secondary metabolite of the soybean phenylpropyl biosynthesis pathway with physiological activity and is beneficial to human health. In this study, the isoflavone content of 205 soybean germplasm resources from 3 locations in 2020 showed wide phenotypic variation. A joint genome-wide association study (GWAS) and weighted gene coexpression network analysis (WGCNA) identified 33 single-nucleotide polymorphisms and 11 key genes associated with soybean isoflavone content. Gene ontology enrichment analysis, gene coexpression, and haplotype analysis revealed natural variations in the Glyma.12G109800 (GmOMT7) gene and promoter region, with Hap1 being the elite haplotype. Transient overexpression and knockout of GmOMT7 increased and decreased the isoflavone content, respectively, in hairy roots. The combination of GWAS and WGCNA effectively revealed the genetic basis of soybean isoflavone and identified potential genes affecting isoflavone synthesis and accumulation in soybean, providing a valuable basis for the functional study of soybean isoflavone.

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.

Cytochrome GmGLY1 is Involved in the Biosynthesis of Glycitein in Soybean

Isoflavones, the major secondary metabolites of interest due to their benefits to both human and plant health, are exclusively produced by legumes. In this study, we profiled the isoflavone content in dry seeds from 211 soybean [Glycine max (L.) Merr.] accessions grown across five environments. Broad and discernible phenotypic variations were observed among accessions, regions, and years of growth. Twenty-six single-nucleotide polymorphisms (SNPs) associated with the sum of glycitein (GLE), glycitin (GL), 6″-O-acetylglycitin (AGL), and 6″-O-malonylglycitin (MGL) contents were detected in multiple environments via a genome-wide association study (GWAS). These SNPs were located on chromosome 11 (8,148,438 bp to 8,296,956 bp, renamed qGly11-01). Glyma.11g108300 (GmGLY1), a gene that encodes a P450 family protein, was identified via sequence variation analysis, functional annotation, weighted gene coexpression network analysis (WGCNA), and expression profile analysis of candidate gene, and hairy roots transformation in soybean. Overexpression of GmGLY1 increased the glycitein content (GLC) in soybean hairy roots and transgenic seeds, while CRISPR/Cas9-generated mutants exhibited decreased GLC and increased daidzein content (DAC). Haplotype analysis revealed that GmGLY1 allelic variations significantly affect the GLC accumulation. These findings enhance our understanding of genes influencing GLC in soybean and may guide breeding for lines with high and stable GLC.

Assessment of the salt tolerance of diverse bread wheat (Triticum aestivum L.) genotypes during the early growth stage under hydroponic culture conditions

Objectives

Soil salinity affects the growth of crop plants, leading to reduced productivity, and is a major challenge for wheat production worldwide. Various adaptations and mitigation approaches in combination with tolerant wheat genotypes can be useful for the sustainability of crop production in saline environments. However, the development of salt-tolerant wheat genotypes is one of the best and most efficient solutions for obtaining desirable yields. Considering these issues, an investigation was carried out under hydroponic nutrient culture conditions to assess the genetic variability and selection of salt-tolerant wheat genotypes by categorizing inequitable morphophysiological and genetic variability as well as multivariate analysis.

Methods

To meet the objectives of this study, 100 wheat genotypes were tested hydroponically in 0 (control) and 15 dS m-1 salt solutions.

Conclusion

For all the wheat genotypes grown under saline conditions, the shoot length (SL), root length (RL), shoot fresh weight (SFW), root fresh weight (RFW), total fresh weight (TFW), shoot dry weight (SDW), root dry weight (RDW), and total dry weight (TDW) decreased significantly. Furthermore, significant variation was observed among the genotypes in terms of their characteristics only under saline conditions. In the case of genetic diversity analysis, a high genotypic coefficient of variation (GCV), phenotypic coefficient of variation (PCV), genetic advance in the percentage of the mean (GAM) and high heritability (h2b) were recorded for all tested wheat genotypes based on the SDW, RDW and TDW. Correlation analysis for both genotypic and phenotypic relationships revealed strong positive correlations for TDW, SDW, TFW and SFW. Principal component analysis (PCA) revealed that TDW, TFW, SDW, and SFW were the most discriminative variables for the wheat genotypes, which was confirmed by discriminant function analysis (DFA). PCA-biplot analysis also revealed significant positive correlations between SDW and SFW and between TDW and TFW. Hierarchical cluster analysis was performed for ten clusters based on the relative performance of the genotypes, where the genotypes were characterized into salt-tolerant, medium-salt-tolerant, medium-salt-susceptible and salt-susceptible groups. Among the genotypes, G11, G25 and G29 under cluster VII were categorized as salt tolerant based on their outstanding performance in terms of characteristics only under saline conditions. D2 analysis proved that the wheat genotypes of this cluster were highly divergent from the other cluster genotypes; as a result, these genotypes might be utilized as parents in the development of salt-tolerant wheat genotypes. The current study concluded that SDW and TDW could be employed as criteria for selecting and defining salt-tolerant genotypes during the early growth stage of wheat.

Influence of malting procedure on the isoflavonoid content of soybeans

The goal of this study was to analyse, whether malting technique (consisting of seed hydration, germination and drying) can be used to modify concentration of various isoflavonoids in soybean seeds. Seeds of three soybean varieties were germinated by different lengths of time (from 24 to 120 h) and dried by two different methods, typically used to produce so-called 'light' and 'caramel' malts. It was determined, that malting decreases concentration of 7-O-β-D-glucosides such as daidzin, genisitin and glycitin, while at the same time increasing concentration of aglycones (daidzein, genistein and glycitein). Increasing time of the germination period increased concentration of aglycones. 'Caramel' type malts were characterised with higher concentration of most of the isoflavonoids (daidzin, daidzein, genistin, genistein and glycitein) than 'light' type malts. Results of this study suggest that soybean malts can be an interesting substrate in the production of various food products with increased aglycone content.

Mechanism of action, benefits, and research gap in fermented soybean meal utilization as a high-quality protein source for livestock and poultry

Animal nutritionists have incessantly worked towards providing livestock with high-quality plant protein feed resources. Soybean meal (SBM) has been an essential and predominantly adopted vegetable protein source in livestock feeding for a long time; however, several SBM antinutrients could potentially impair the animal's performance and growth, limiting its use. Several processing methods have been employed to remove SBM antinutrients, including fermentation with fungal or bacterial microorganisms. According to the literature, fermentation, a traditional food processing method, could improve SBM's nutritional and functional properties, making it more suitable and beneficial to livestock. The current interest in health-promoting functional feed, which can enhance the growth of animals, improve their immune system, and promote physiological benefits more than conventional feed, coupled with the ban on the use of antimicrobial growth promoters, has caused a renewed interest in the use of fermented SBM (FSBM) in livestock diets. This review details the mechanism of SBM fermentation and its impacts on animal health and discusses the recent trend in the application and emerging advantages to livestock while shedding light on the research gap that needs to be critically addressed in future studies. FSBM appears to be a multifunctional high-quality plant protein source for animals. Besides removing soybean antinutrients, beneficial bioactive peptides and digestive enzymes are produced during fermentation, providing probiotics, antioxidants, and immunomodulatory effects. Critical aspects regarding FSBM feeding to animals remain uncharted, such as the duration of fermentation, the influence of feeding on digestive tissue development, choice of microbial strain, and possible environmental impact.

Differentially Expressed Genes Related to Isoflavone Biosynthesis in a Soybean Mutant Revealed by a Comparative Transcriptomic Analysis

Soybean [Glycine max (L.) Merr.] isoflavones, which are secondary metabolites with various functions, are included in food, cosmetics, and medicine. However, the molecular mechanisms regulating the glycosylation and malonylation of isoflavone glycoconjugates remain unclear. In this study, we conducted an RNA-seq analysis to compare soybean genotypes with different isoflavone contents, including Danbaek and Hwanggeum (low-isoflavone cultivars) as well as DB-088 (high-isoflavone mutant). The transcriptome analysis yielded over 278 million clean reads, representing 39,156 transcripts. The analysis of differentially expressed genes (DEGs) detected 2654 up-regulated and 1805 down-regulated genes between the low- and high-isoflavone genotypes. The putative functions of these 4459 DEGs were annotated on the basis of GO and KEGG pathway enrichment analyses. These DEGs were further analyzed to compare the expression patterns of the genes involved in the biosynthesis of secondary metabolites and the genes encoding transcription factors. The examination of the relative expression levels of 70 isoflavone biosynthetic genes revealed the HID, IFS, UGT, and MAT expression levels were significantly up/down-regulated depending on the genotype and seed developmental stage. These expression patterns were confirmed by quantitative real-time PCR. Moreover, a gene co-expression analysis detected potential protein-protein interactions, suggestive of common functions. The study findings provide valuable insights into the structural genes responsible for isoflavone biosynthesis and accumulation in soybean seeds.

QTL mapping reveals key factors related to the isoflavone contents and agronomic traits of soybean (Glycine max)

BACKGROUND

Soybean is a valuable source of edible protein and oil, as well as secondary metabolites that can be used in food products, cosmetics, and medicines. However, because soybean isoflavone content is a quantitative trait influenced by polygenes and environmental interactions, its genetic basis remains unclear.

RESULTS

This study was conducted to identify causal quantitative trait loci (QTLs) associated with soybean isoflavone contents. A mutant-based F2 population (190 individuals) was created by crossing the Korean cultivar Hwanggeum with low isoflavone contents (1,558 µg g-1) and the soybean mutant DB-088 with high isoflavone contents (6,393 µg g-1). A linkage map (3,049 cM) with an average chromosome length of 152 cM was constructed using the 180K AXIOM® SoyaSNP array. Thirteen QTLs related to agronomic traits were mapped to chromosomes 2, 3, 11, 13, 19, and 20, whereas 29 QTLs associated with isoflavone contents were mapped to chromosomes 1, 3, 8, 11, 14, 15, and 17. Notably, the qMGLI11, qMGNI11, qADZI11, and qTI11, which located Gm11_9877690 to Gm11_9955924 interval on chromosome 11, contributed to the high isoflavone contents and explained 11.9% to 20.1% of the phenotypic variation. This QTL region included four candidate genes, encoding β-glucosidases 13, 14, 17-1, and 17-2. We observed significant differences in the expression levels of these genes at various seed developmental stages. Candidate genes within the causal QTLs were functionally characterized based on enriched GO terms and KEGG pathways, as well as the results of a co-expression network analysis. A correlation analysis indicated that certain agronomic traits (e.g., days to flowering, days to maturity, and plant height) are positively correlated with isoflavone content.

CONCLUSIONS

Herein, we reported that the major QTL associated with isoflavone contents was located in the interval from Gm11_9877690 to Gm11_9955924 (78 kb) on chromosome 11. Four β-glucosidase genes were identified that may be involved in high isoflavone contents of soybean DB-088. Thus, the mutant alleles from soybean DB-088 may be useful for marker-assisted selection in developing soybean lines with high isoflavone contents and superior agronomic traits.

Evaluation of sugarcane promising clones based on the morphophysiological traits developed from fuzz

Sugarcane is one of the critical commercial crops and principal sources of ethanol and sugar worldwide. Unfavorable conditions and poor seed setting rates hinder variety development in sugarcane. Countries like Pakistan directly import fuzz (true seed) and other propagation material from the USA, China, Brazil, etc. In this study, we imported fuzz from China, developed 29 genotypes germinating in the glasshouse, and evaluated at field conditions along with two local checks (CPF-251 and HSF-240). Morphophysiological data were recorded, including plant height (PH), cane length (CL), internodal length (IL), tiller number (TN), brix percentage (B), cane diameter (CD), chlorophyll a (Chl. a), chlorophyll b (Chl. b), and total chlorophyll (T. Chl). Results showed highly significant (p < 0.001) differences among the sugarcane accessions for all the studied traits. High broad-sense heritability (81.89% to 99.91%) was recorded for all the studied parameters. Genetic Advance (GA) ranges from 4.6% to 65.32%. The highest GA was observed for PH (65.32%), followed by CL (63.28%). Chlorophyll leaching assay was also performed at different time points (0, 50, 100, 150, and 200 min). All the genotypes showed the same leaching trend at all times, and better performing genotypes showed less leaching compared to poor performing, indicating the high amount of cutin and wax on the leaf surface. Correlation analysis showed that PH, CL, IL, and TN had significant associations. Principal components analysis (PCA) further confirms these results. Based on PCA and correlation results, PH, CL, IL, and TN can be utilized as a selection criterion for sugarcane improvement. Genotypes such as NS-4a, NS-5, NS-6, NS-8, NS-9, and NS-15 are recommended for future breeding programs related to sugarcane variety development.

Dual-function C2H2-type zinc-finger transcription factor GmZFP7 contributes to isoflavone accumulation in soybean

Isoflavones are a class of secondary metabolites produced by legumes and play important roles in human health and plant stress tolerance. The C2H2 zinc-finger transcription factor (TF) functions in plant stress tolerance, but little is known about its function in isoflavone regulation in soybean (Glycine max). Here, we report a C2H2 zinc-finger TF gene, GmZFP7, which regulates isoflavone accumulation in soybean. Overexpressing GmZFP7 increased the isoflavone concentration in both transgenic hairy roots and plants. By contrast, silencing GmZFP7 expression significantly reduced isoflavone levels. Metabolomic and qRT-PCR analysis revealed that GmZFP7 can increase the flux of the phenylpropanoid pathway. Furthermore, dual-luciferase and electrophoretic mobility shift assays showed that GmZFP7 regulates isoflavone accumulation by influencing the expression of Isoflavone synthase 2 (GmIFS2) and Flavanone 3 β-hydroxylase 1 (GmF3H1). In this study, we demonstrate that GmZFP7 contributes to isoflavone accumulation by regulating the expression of the gateway enzymes (GmIFS2 and GmF3H1) of competing phenylpropanoid pathway branches to direct the metabolic flux into isoflavone. A haplotype analysis indicated that important natural variations were present in GmZFP7 promoters, with P-Hap1 and P-Hap3 being the elite haplotypes. Our findings provide insight into how GmZFP7 regulates the phenylpropanoid pathway and enhances soybean isoflavone content.

Identification of hub genes regulating isoflavone accumulation in soybean seeds via GWAS and WGCNA approaches

INTRODUCTION

Isoflavones are the secondary metabolites synthesized by the phenylpropanoid biosynthesis pathway in soybean that benefits human and plant health.

METHODS

In this study, we have profiled seed isoflavone content by HPLC in 1551 soybean accessions grown in Beijing and Hainan for two consecutive years (2017 and 2018) and in Anhui for one year (2017).

RESULTS

A broad range of phenotypic variations was observed for individual and total isoflavone (TIF) content. The TIF content ranged from 677.25 to 5823.29 µg g^-1 in the soybean natural population. Using a genome-wide association study (GWAS) based on 6,149,599 single nucleotide polymorphisms (SNPs), we identified 11,704 SNPs significantly associated with isoflavone contents; 75% of them were located within previously reported QTL regions for isoflavone. Two significant regions on chromosomes 5 and 11 were associated with TIF and malonylglycitin across more than 3 environments. Furthermore, the WGCNA identified eight key modules: black, blue, brown, green, magenta, pink, purple, and turquoise. Of the eight co-expressed modules, brown (r = 0.68***), magenta (r = 0.64***), and green (r = 0.51**) showed a significant positive association with TIF, as well as with individual isoflavone contents. By combining the gene significance, functional annotation, and enrichment analysis information, four hub genes Glyma.11G108100, Glyma.11G107100, Glyma.11G106900, and Glyma.11G109100 encoding, basic-leucine zipper (bZIP) transcription factor, MYB4 transcription factor, early responsive to dehydration, and PLATZ transcription factor respectively were identified in brown and green modules. The allelic variation in Glyma.11G108100 significantly influenced individual and TIF accumulation.

DISCUSSION

The present study demonstrated that the GWAS approach, combined with WGCNA, could efficiently identify isoflavone candidate genes in the natural soybean population.

Soybean (Glycine max) isoflavone conjugate hydrolysing β-glucosidase (GmICHG): a promising candidate for soy isoflavone bioavailability enhancement

Isoflavones are a sub-class of phenylpropanoids having health benefits and a role in plant defence and plant-rhizobium interaction. Isoflavone conjugate hydrolysis is crucial in determining the bioactivity and bioavailability of these isoflavones inside the human body. This study examined the different characteristics of soy isoflavone conjugate hydrolysing β-glucosidase (GmICHG) to explore its potential for isoflavone bioavailability enhancement. We cloned the full-length GmICHG cDNA from the soybean seedling roots from the DS2706 variety of 1545 bp. The bioinformatics analysis revealed secretion and glycosylation of this protein. The evolutionary relatedness of this gene to the other glucosidases interestingly had related sequences outside the Papilionaceae family. The protein had a pI above neutral of 7.62 and optimum pH of 6.0, indicating its activity in the extracellular acidic environment. The GmICHG gene expression at three stages of seedling roots gradually rose to 1.84 ± 0.54 fold and a concomitant increase in the β-glucosidase activity. The enzyme kinetics of GmICHG showed a K m of 6.38 mM and V max of 2.82 U/ml and an optimum temperature of 40 °C. These hint that soy ICHG can be a potent candidate for the isoflavone bioavailability enhancement by hydrolysing their β-glycosidic bonds.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-022-03427-5.

Geographic distributions and the regionalization of soybean seed compositions across China

As one of major food crops, soybean is grown over a broad ecological region in China with considerable variations in environmental conditions, and the seed compositions of soybeans are diverse among different regions. To clarify the spatial patterns of soybean seed compositions, crude oil, protein, and 11 categories of functional components were quantified in 1792 soybean samples collected from a vast range of soybean planting regions across China spanning from 2010 to 2017. The Kriging interpolation maps presented a clear north-to-south (high latitude to low latitude) increasing trend in contents of crude protein and dietary fiber and decreasing trend in contents of crude oil, phospholipids, saponins, and carotenoids. Soybeans with high-level of total oligosaccharide were concentrated in the central region. Based on the geographical distribution of soybean nutritional components, weather conditions, and cultivation systems, the soybean production areas in China were divided into three regions and 10 subregions. This study highlights the geographic distribution of soybean nutritional compositions and provides scientific evidence for guiding the construction of high-quality edible soybean production bases in China.

Identification of genes for seed isoflavones based on bulk segregant analysis sequencing in soybean natural population

We identified four hub genes for isoflavone biosynthesis based on BSA-seq and WGCNA methods and validated that GmIE3-1 positively contribute to isoflavone accumulation in soybean. Soybean isoflavones are secondary metabolites of great interest owing to their beneficial impact on human health. Herein, we profiled the seed isoflavone content by HPLC in 1551 soybean accessions grown in two locations for two years and constructed two extreme pools with high (4065.1 µg g^-1) and low (1427.23 µg g^-1) isoflavone contents to identify candidate genes involved in isoflavone biosynthesis pathways using bulk segregant analysis sequencing (BSA-seq) approach. The results showed that the average sequencing depths were 50.3× and 65.7× in high and low pools, respectively. A total of 23,626 polymorphic SNPs and 5299 InDels were detected between both pools and 1492 genes with different variations were identified. Based on differential genes in BSA-seq and weighted gene co-expression network analysis (WGCNA), four hub genes, Glyma.06G290400 (designated as GmIE3-1), Glyma.01G239200, Glyma.01G241500, Glyma.13G256100 were identified, encoding E3 ubiquitin-protein ligase, arm repeat protein interacting with ABF2, zinc metallopeptidase EGY3, and dynamin-related protein 3A, respectively. The allelic variation in GmIE3-1 showed a significant influence on isoflavone accumulation. The virus-induced gene silencing (VIGS) and RNAi hairy root transformation of GmIE3-1 revealed partial suppression of this gene could cause a significant decrease (P < 0.0001) of total isoflavone content, suggesting GmIE3-1 is a positive regulator for isoflavones. The present study demonstrated that the BSA-seq approach combined with WGCNA, VIGS and hairy root transformation can efficiently identify isoflavone candidate genes in soybean natural population.

A pilot study characterizing longitudinal changes in fecal microbiota of patients with Hirschsprung-associated enterocolitis

PURPOSE

Hirschsprung disease is a neurointestinal disease that occurs due to failure of enteric neural crest-derived cells to complete their rostrocaudal migration along the gut mesenchyme, resulting in aganglionosis along variable lengths of the distal bowel. Despite the effective surgery that removes the aganglionic segment, children with Hirschsprung disease remain at high risk for developing a potentially life-threatening enterocolitis (Hirschsprung-associated enterocolitis). Although the etiology of this enterocolitis remains poorly understood, several recent studies in both mouse models and in human subjects suggest potential involvement of gastrointestinal microbiota in the underlying pathogenesis of Hirschsprung-associated enterocolitis.

METHODS

We present the first study to exploit the Illumina MiSeq next-generation sequencing platform within a longitudinal framework focused on microbiomes of Hirschsprung-associated enterocolitis in five patients. We analyzed bacterial communities from fecal samples collected at different timepoints starting from active enterocolitis and progressing into remission.

RESULTS

We observed compositional differences between patients largely attributable to variability in age at the time of sample collection. Remission samples across patients exhibited compositional similarity, including enrichment of Blautia, while active enterocolitis samples showed substantial variability in composition.

CONCLUSIONS

Overall, our findings provide continued support for the role of GI microbiota in the pathogenesis of Hirschsprung-associated enterocolitis.

Genome wide association study to detect genetic regions related to isoflavone content in a mutant soybean population derived from radiation breeding

Isoflavones are major secondary metabolites that are exclusively produced by legumes, including soybean. Soy isoflavones play important roles in human health as well as in the plant defense system. The isoflavone content is influenced by minor-effect quantitative trait loci, which interact with polygenetic and environmental factors. It has been difficult to clarify the regulation of isoflavone biosynthesis because of its complex heritability and the influence of external factors. Here, using a genotype-by-sequencing-based genome-wide association mapping study, 189 mutant soybean genotypes (the mutant diversity pool, MDP) were genotyped on the basis of 25,646 high-quality single nucleotide polymorphisms (SNPs) with minor allele frequency of >0.01 except for missing data. All the accessions were phenotyped by determining the contents of 12 isoflavones in the soybean seeds in two consecutive years (2020 and 2021). Then, quantitative trait nucleotides (QTNs) related to isoflavone contents were identified and validated using multi-locus GWAS models. A total of 112 and 46 QTNs related to isoflavone contents were detected by multiple MLM-based models in 2020 and 2021, respectively. Of these, 12 and 5 QTNs were related to more than two types of isoflavones in 2020 and 2021, respectively. Forty-four QTNs were detected within the 441-Kb physical interval surrounding Gm05:38940662. Of them, four QTNs (Gm05:38936166, Gm05:38936167, Gm05:38940662, and Gm05:38940717) were located at Glyma.05g206900 and Glyma.05g207000, which encode glutathione S-transferase THETA 1 (GmGSTT1), as determined from previous quantitative trait loci annotations and the literature. We detected substantial differences in the transcript levels of GmGSTT1 and two other core genes (IFS1 and IFS2) in the isoflavone biosynthetic pathway between the original cultivar and its mutant. The results of this study provide new information about the factors affecting isoflavone contents in soybean seeds and will be useful for breeding soybean lines with high and stable concentrations of isoflavones.

Profiling of naturally occurring folates in a diverse soybean germplasm by HPLC-MS/MS

Soybean is a rich source of folates. We optimised the extraction and detection of folates from soybean seeds by HPLC-MS/MS and analysed the folate content and composition of 1074 accessions. Total folate content ranged from 64.51 to 691.24 μg/100 g fresh weight, with 10-fold variation, and 60 elite accessions with over 400 μg/100 g of total folate were identified. The most abundant component was 5-CHO-H4folate, which accounted for an average of 60% of total folate content. Seed-coat colour, seed weight, ecoregion, and accession type significantly affected soybean folate content. Furthermore, 5-CH3-H4folate correlated positively with seed protein (r = 0.24***) and negatively with oil (r = -0.26***). The geographical distribution of folate according to accession origin revealed that accessions from Northeast China contain higher amounts of total folate and 5-CHO-H4folate. This study provides comprehensive and novel insights into the folate profile of soybean, which will benefit soybean breeding for folate enhancement.

Soybean Processing Wastes: Novel Insights on Their Production, Extraction of Isoflavones, and Their Therapeutic Properties

Soybean processing waste (SPW) has potential as a sustainable source of phytochemicals and functional foods. A variety of phytochemicals, nutrients, and minerals have been characterized from SPW using various analytical methods. SPW utilization strategies may provide a new way to increase production of bioactive compounds, nutritional supplements, and cosmetic ingredients. SPW has the potential for value-added processing, to improve commercial use, and to lower environmental pollution through proper use. Okara, a byproduct generated during soybean processing of tofu and soy milk, is rich in dietary fiber, isoflavones, and saponins. Isoflavones, an important class of biologically active compounds owing to their multifunctional and therapeutic effects, are extracted from SPW. Further, studies have shown that okara has potential prebiotic and therapeutic value in lowering the risk of noncommunicable diseases. Therefore, in this review, we focus on several extraction methods and pharmacotherapeutic effects of different SPWs. Their effective uses in functional foods, nutraceuticals, and health applications, as biocatalysts, and as value-added resources have been discussed.

Evaluation of Green Super Rice Lines for Agronomic and Physiological Traits under Salinity Stress

Rice (Oryza sativa) is an important staple food crop worldwide, especially in east and southeast Asia. About one-third of rice cultivated area is under saline soil, either natural saline soils or irrigation with brackish water. Salinity stress is among the devastating abiotic stresses that not only affect rice growth and crop productivity but also limit its cultivation area globally. Plants adopt multiple tolerance mechanisms at the morphological, physiological, and biochemical levels to tackle salinity stress. To identify these tolerance mechanisms, this study was carried out under both a controlled glass house as well as natural saline field conditions using 22 green super rice (GSR) lines along with two local varieties (“IRRI 6 and Kissan Basmati”). Several morpho-physiological and biochemical parameters along with stress-responsive genes were used as evaluation criteria under normal and salinity stress conditions. Correlation and Principal Component Analysis (PCA) suggested that shoot-related parameters and the salt susceptible index (SSI) can be used for the identification of salt-tolerant genotypes. Based on Agglomerative Hierarchical Cluster (AHC) analysis, two saline-tolerant (“S19 and S20”) and saline-susceptible (“S3 and S24”) lines were selected for further molecular evaluation. Quantitative RT-PCR was performed, and results showed that expression of 1-5-phosphoribosyl -5-5-phosphoribosyl amino methylidene amino imidazole-4-carboxamide isomerase, DNA repair protein recA, and peptide transporter PTR2 related genes were upregulated in salt-tolerant genotypes, suggesting their potential role in salinity tolerance. However, additional validation using reverse genetics approaches will further confirm their specific role in salt tolerance. Identified saline-tolerant lines in this study will be useful genetic resources for future salinity breeding programs.

Fine-Mapping and Functional Analyses of a Candidate Gene Controlling Isoflavone Content in Soybeans Seed

Isoflavones, one of the most important secondary metabolites produced by soybeans (Glycine max (L.) Merr.), are important for a variety of biological processes, and are beneficial for human health. To identify genetic loci underlying soybean isoflavone content, a mapping population containing 119 F_5:18 recombinant inbred lines, derived by crossing soybean cultivar "Zhongdou27" with "Dongong8004," was used. We identified 15 QTLs associated with isoflavone contents. A novel loci, qISO19-1, was mapped onto soybean chromosome 19 and was fine-mapped to a 62.8 kb region using a BC₂F₂ population. We considered GmMT1 as a candidate gene for the qISO19-1 locus due to the significant positive correlation recovered between its expression level and isoflavone content in the seeds of 43 soybean germplasms. Overexpression of GmMT1 in Arabidopsis and soybean cultivars increased isoflavone contents. Transgenic soybeans overexpressing GmMT1 also exhibited improved resistance to pathogenic infection, while transgenic Arabidopsis resisted salt and drought stress.

The Characterization of Wheat Genotypes for Salinity Tolerance Using Morpho-Physiological Indices under Hydroponic Conditions

Salinity affects plant growth, development, yield, and is a big challenge for wheat growth across the globe. Possible feasible solution is creation of salt-tolerant material, genetic variation is a criterion to developing genetically superior individuals. To assess the genetic variation for salt tolerance, nationally and internationally-derived 81 wheat genotypes were selected and evaluated in 0- and 150-mM salt in nutritional culture at seedling stage. Results indicate that salinity levels reveal significant (p ≤ 0.01) differences for fresh root weight (RW), shoot length (SL), fresh shoot weight (SW), total plant length (TL), total fresh weight (TW), root/shoot weight ratio (RSWR), root/shoot length ratio (RSLR), and relative growth rate for weight (RGR-Wt). While, there was no difference for root length (RL). Hierarchical Clustering and Pairwise correlation analysis showed TW, RGR-Wt, SL, SW, and RW were positively correlated among themselves, whereas RL had poor correlations with all the traits except TL and RSLR. Hence, selection of SL can improve the performance of other parameters. Based on PCA analysis, SW and RGR-Wt were the major discriminative components for wheat genotypes. Present study explained that shoot related parameters could be used as a selection criterion to categorize salt-tolerant genotypes. Outperforming genotypes 1104 and 1106 in saline conditions could be used as parents in creation of salt-tolerant wheat genotypes, and parameters such as SL, SW, TW, and RGR-Wt for early screening will be important for creating salt-tolerant and high yielding wheat genotypes.

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.

Nutritional quality of different potassium efficiency types of vegetable soybean as affected by potassium nutrition

Pot experiments were conducted in 2017, 2019, and 2020 to examine the effects of potassium nutrition on the nutritional components of vegetable soybeans with different K efficiency at immature and mature stages. Two vegetable soybean varieties with higher K efficiency and two varieties with lower K efficiency were studied in the low available K soil under the condition of no K and normal K fertilization. The results indicated that almost all nutritional components in vegetable soybean were affected by K, genotypes, inter-annual differences, and their interactions. In general, no K fertilization increased protein and amino acid concentrations but decreased oil, soluble sugar, sucrose, K, Mg, and Fe concentrations in immature and mature vegetable soybean. The sensitivity of nutritional components to K nutrition differed among varieties. For instance, K high-efficiency varieties generally exhibited higher protein and amino acid concentrations without K application. K high-efficiency vegetable soybeans are low-K tolerance varieties to isoflavones. The results of this study provide insights for high yield and quality vegetable soybean breeding against soil K deficiency.

Isoflavones in Animals: Metabolism and Effects in Livestock and Occurrence in Feed

Soybeans are a common ingredient of animal feed. They contain isoflavones, which are known to act as phytoestrogens in animals. Isoflavones were described to have beneficial effects on farm animals. However, there are also reports of negative outcomes after the consumption of isoflavones. This review summarizes the current knowledge of metabolization of isoflavones (including the influence of the microbiome, phase I and phase II metabolism), as well as the distribution of isoflavones and their metabolites in tissues. Furthermore, published studies on effects of isoflavones in livestock species (pigs, poultry, ruminants, fish) are reviewed. Moreover, published studies on occurrence of isoflavones in feed materials and co-occurrence with zearalenone are presented and are supplemented with our own survey data.

The Soybean High Density 'Forrest' by 'Williams 82' SNP-Based Genetic Linkage Map Identifies QTL and Candidate Genes for Seed Isoflavone Content

Isoflavones are secondary metabolites that are abundant in soybean and other legume seeds providing health and nutrition benefits for both humans and animals. The objectives of this study were to construct a single nucleotide polymorphism (SNP)-based genetic linkage map using the ‘Forrest’ by ‘Williams 82’ (F×W82) recombinant inbred line (RIL) population (n = 306); map quantitative trait loci (QTL) for seed daidzein, genistein, glycitein, and total isoflavone contents in two environments over two years (NC-2018 and IL-2020); identify candidate genes for seed isoflavone. The FXW82 SNP-based map was composed of 2075 SNPs and covered 4029.9 cM. A total of 27 QTL that control various seed isoflavone traits have been identified and mapped on chromosomes (Chrs.) 2, 4, 5, 6, 10, 12, 15, 19, and 20 in both NC-2018 (13 QTL) and IL-2020 (14 QTL). The six QTL regions on Chrs. 2, 4, 5, 12, 15, and 19 are novel regions while the other 21 QTL have been identified by other studies using different biparental mapping populations or genome-wide association studies (GWAS). A total of 130 candidate genes involved in isoflavone biosynthetic pathways have been identified on all 20 Chrs. And among them 16 have been identified and located within or close to the QTL identified in this study. Moreover, transcripts from four genes (Glyma.10G058200, Glyma.06G143000, Glyma.06G137100, and Glyma.06G137300) were highly abundant in Forrest and Williams 82 seeds. The identified QTL and four candidate genes will be useful in breeding programs to develop soybean cultivars with high beneficial isoflavone contents.

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.

Differential Gene Expression Associated with Altered Isoflavone and Fatty Acid Contents in Soybean Mutant Diversity Pool

Soybean seeds are consumed worldwide owing to their nutritional value and health benefits. In this study we investigated the metabolic properties of 208 soybean mutant diversity pool (MDP) lines by measuring the isoflavone and fatty acid contents of the seed. The total isoflavone content (TIC) ranged from 0.88 mg/g to 7.12 mg/g and averaged 3.08 mg/g. The proportion of oleic acid among total fatty acids (TFA) ranged from 0.38% to 24.66% and averaged 11.02%. Based on the TIC and TFA among the 208 MDP lines, we selected six lines with altered isoflavone content and six lines with altered oleic acid content compared with those of the corresponding wild-types for measuring gene expression. Each of twelve genes from the isoflavone and fatty acid biosynthesis pathways were analyzed at three different seed developmental stages. Isoflavone biosynthetic genes, including CHI1A, IFS1, and IFS2, showed differences in stages and expression patterns among individuals and wild-types, whereas MaT7 showed consistently higher expression levels in three mutants with increased isoflavone content at stage 1. Expression patterns of the 12 fatty acid biosynthetic genes were classifiable into two groups that reflected the developmental stages of the seeds. The results will be useful for functional analysis of the regulatory genes involved in the isoflavone and fatty acid biosynthetic pathways in soybean.

Screening of Novel Source for Genistein by Rapid and Sensitive UPLC-APCI-TOF Mass Spectrometry

Genistein has been shown to have a broad spectrum of health advantages. Only legumes were reported to have a significant amount of genistein with the highest concentration in Soybean. Soybean was found to cause allergies in children with atopic dermatitis and in adults. Limited food sources have hindered the use of genistein in daily diets, medications, and nutraceuticals. The main objective of the current research work was to discover the novel source for genistein by the simple method of extraction and quantification. Genistein was extracted by solid-liquid extraction technique. Extraction parameters were optimized by a single factor test. Identification and quantification of genistein from the selected seeds of Apiaceae were carried out using UPLC-APCI-TOF-MS. UPLC-APCI-TOF-MS method was successfully developed, validated (linearity (R² = 0.999), precision (R.S.D. <5%), and accuracy (107.23%)), and used for the study. Remarkably, a high concentration of the genistein (811.57 μg/g) was found in the Cuminum cyminum. Solvent mixture (50 mL Methanol+25 mL Dimethyl sulphoxide+25 mL Water (v/v/v)), temperature (80°C), and time (1 h) were found to be the optimum extraction conditions. The concentration of genistein before optimization was 226.67 μg/g and after optimization is 811.57 μg/g. This shows the efficiency of the extraction method in the extraction of genistein without the need for hydrolysis. Novel source for genistein is identified in regular human food can be consumed in a regular diet which increases wellness of human health along with enhancing the taste of the food. The developed extraction method coupled with high throughput, sensitive, and selective UPLC-APCI-TOF-MS technique facilitates rapid quantification (8 minutes of run time) without primary purification of complex extract.

A brief history and spectroscopic analysis of soy isoflavones

The production of soybean continues to increase worldwide. People are showing more interest in the beneficial health effects of soybeans than before. However, the origin and history of soybeans are still being discussed among many researchers. Chromatographic methods enable the desirable separation of a variety of isoflavones from soybeans. The structures of isolated soy isoflavones have been successfully identified in tandem with spectroscopic analytical instruments and technologies such as liquid chromatography, mass spectrometry, and nuclear magnetic resonance spectroscopy. The theoretical background behind spectroscopy may help improve the understanding for the analysis of isoflavones in soybeans and soy-derived foods. This review covers the origin of the English name of soybean and its scientific name, Glycine max (L.) Merrill, based on the evidence reported to date. Moreover, the reports of soy isoflavones discovered over a period of about 100 years have been briefly reviewed.

The Effects of Domestication on Secondary Metabolite Composition in Legumes

Legumes are rich in secondary metabolites, such as polyphenols, alkaloids, and saponins, which are important defense compounds to protect the plant against herbivores and pathogens, and act as signaling molecules between the plant and its biotic environment. Legume-sourced secondary metabolites are well known for their potential benefits to human health as pharmaceuticals and nutraceuticals. During domestication, the color, smell, and taste of crop plants have been the focus of artificial selection by breeders. Since these agronomic traits are regulated by secondary metabolites, the basis behind the genomic evolution was the selection of the secondary metabolite composition. In this review, we will discuss the classification, occurrence, and health benefits of secondary metabolites in legumes. The differences in their profiles between wild legumes and their cultivated counterparts will be investigated to trace the possible effects of domestication on secondary metabolite compositions, and the advantages and drawbacks of such modifications. The changes in secondary metabolite contents will also be discussed at the genetic level to examine the genes responsible for determining the secondary metabolite composition that might have been lost due to domestication. Understanding these genes would enable breeding programs and metabolic engineering to produce legume varieties with favorable secondary metabolite profiles for facilitating adaptations to a changing climate, promoting beneficial interactions with biotic factors, and enhancing health-beneficial secondary metabolite contents for human consumption.