3.1 Content and composition analysis of isoflavones in soybean genotypes
A large amount of variation exists for isoflavone content and composition in the soybean genotypes (Azam et al. 2020), with malonylated derivatives of genistin and daidzin being the most dominant (Tepavčević et al. 2021). Health benefits (including bioavailability) of these different isoflavones and their lox inhibitors potential could also vary with structural characteristics. Due to the prevalence of these substituted derivatives, we decided to undertake a comparison of isoflavone aglycones. For this, the acidic hydrolysis of isoflavones was carried out. 17 soybean genotypes were assessed for total isoflavone content and composition to explore its relationship with indices of off-flavour generation (TBA number and carbonyl value) in soybean. Enormous variation was observed amongst cultivars in the total isoflavone content and the content of individual forms of these isoflavones (Table 1). The total isoflavone content was expressed as μg/g of soy flour, ranging between 153.53 ± 7.22 (µg/g) for PUSA 40 to 1146.42 ± 43.47 (µg/g) for Bragg (fig. 1). Bragg and PUSA 40 were identified as the high and low isoflavone containing genotypes of soybean, respectively and thus selected for gene expression analysis of isoflavone synthase (IFS). Similarly, earlier studies have observed enormous variation in isoflavone content and composition for soybean genotypes grown in different ecoregions (Azam et al. 2020). PK 1042 and PK 416 were identified as the soybean genotypes having a maximum (1.64) and minimum (0.33) Genistein: Daidzein ratio, respectively.
3.2 The assessment of the extent of lipid peroxidation in different soybean genotypes
TBA number is a well-established measure of lipid peroxidation (Ganhão et al. 2011). It detects lipid hydroperoxides produced during this oxidation, and its amount is expressed in nmoles/g of seed. The soybean genotypes tested for TBA number ranged from 46.67 ±4.16 nmol/g for BS1 to 307.33 ± 8.08 nmol/g for UPSL 340 (Fig. 2). Similarly, the carbonyl value measures the number of aldehydes and ketone, which is associated with the generation of off-flavour. Its values were expressed in nmoles/g of seed and ranged from 378.95 ± 4.64 nmol/g for EC 109514 to 674.54 ± 4.64 nmol/g for UPSL 340 (Fig. 3). The extent of correlation present between isoflavone content and parameters taken as indices of off-flavour was measured in terms of Pearson's correlation coefficients. The observed value for the correlation coefficient between total isoflavone content and carbonyl value was 0.089, and that of TBA number and total isoflavone content was 0.016 (Table 2). Amongst the various soy isoflavones, genistein has been reported to have the maximum antioxidant activity (Mahesha et al. 2007). Therefore, the correlation of particular forms of isoflavones with these parameters is expected to differ. Hence, the correlation coefficients of off-flavour-determining parameters were also calculated for the genistein and genistein: daidzein ratio. The correlation between genistein content and carbonyl value was -0.12 and between TBA number and genistein content was -0.15. In the genistein: daidzein ratio, the value of the correlation coefficient for TBA number and carbonyl value were -0.41 and -0.42, respectively. The higher antioxidant potential of genistein compared to daidzein can be the reason behind this observation (Ruiz‑Larrea et al. 1997). Genistein is also a more potent inhibitor of soybean LOX, with a half inhibitory concentration (IC50) value of 107µM compared to 140µM for daidzein (Mahesha et al. 2007; Vicaş et al. 2011). Previously, Dahuja and Madaan (2004) also observed an inverse relationship between the levels of antioxidant enzymes and the values of off-flavour determining parameters like TBA number and carbonyl value. So, the ability of genistein as an inhibitor of LOX and a general antioxidant seems to be responsible for a reduction in indices of off-flavour generation.
3.3 Quantitative gene expression analysis of IFS and isoflavone profile at three stages of seed development
Isoflavone synthase is the key enzyme of isoflavone biosynthesis responsible for synthesising isoflavone aglycone backbones. There exist two different isoforms of IFS in soybean. In order to determine the relative contribution of these isoforms towards isoflavone accumulation in soybean seeds, we carried out the gene expression analysis of IFS1 and IFS2 in two contrasting soybean genotypes, i.e., Bragg (high isoflavone) & PUSA 40 (low isoflavone) at 3 stages of seed development. Expression profiling suggests that the expression level of IFS1 increased with the advancement in the developmental stage in PUSA 40 (Fig. 4). However, a non-linear and irregular trend was observed in the expression of IFS1 in Bragg; it first increased 2.34-fold from 35 DAF (Days After Flowering) to 45 DAF and then decreased to 2.22-fold at 55 DAF. An increasing trend was observed for IFS2 throughout Bragg's case, but expression level decreased with each developmental stage in PUSA 40. In quantitative terms, an overall 9.34-fold enhancement in the expression of IFS2 was observed in Bragg at 55 DAF compared to its expression at 35 DAF. In comparison, the expression reduced to about 6% of the value at 35 DAF in PUSA 40. These results align with the study by Dhaubhadel et al (2003), who observed the accumulation of IFS2 transcripts in later stages of seed development, but IFS1 expression stayed constant throughout. Gutierrez‑Gonzalez et al (2010) also observed a more significant increase in IFS2 expression of up to 20-fold at 70 days after pollination compared to 30 days after pollination during seed development. IFS1, in contrast, only increased 4-fold in the same period. The corresponding levels of the total isoflavone contents at each stage were also determined using HPLC. Total isoflavone content in Bragg remained higher than PUSA 40 at all three stages of seed development.
Further, the total isoflavone content in Bragg showed an increase from 14.07 µg/gm to 78.4 µg/gm at 55 DAF, but in the case of PUSA 40, this increase observed was only about 2.19-fold from 35 DAF to 55 DAF. The expression of IFS2 matched the pattern of isoflavone accumulation in developing soybean seeds. However, no such correlation could be observed with expression levels of IFS1, as the two contrasting cultivars, despite having similar expression levels of IFS1, differed significantly in the isoflavone levels at all the stages of seed development, the difference in the isoflavone being more pronounced at 55 DAF. Thus, IFS2 may directly affect the isoflavone accumulation during the grain filling stage.
3.4 Cloning and in-silico analysis of IFS1 and IFS2
The results of qRT PCR analysis suggested a putative role of isoflavone synthase in the accumulation of isoflavones in soybean seeds, which encouraged us to delve deeper into the analysis of isoforms. Based on the sequence information available on NCBI, specific primers were designed for PCR amplification of IFS cDNA genes. The PCR products were run on an agarose gel, and the approximate size of the amplicon was 1566bp. (Fig. 5a & b) for both IFS1 and IFS2. The amplicon obtained was then gel eluted and cloned into the pENTR/D-TOPO vector. The cloning of IFS1 & IFS2 was confirmed using plasmid PCR and restriction digestion (PvuII). PvuII restriction enzyme has two cut positions (174, 812) in the TOPO entry vector. We found a linear band of 2204bp (1566bp insert + 638bp vector) and 1942bp vector backbone in the case of both IFS1 and IFS2 (Fig. 5c). The released inserts were then sequenced commercially by the Sanger sequencing method (Chromus Pvt. ltd.). After that, the gene sequences were submitted to the National Center for Biotechnology Information (NCBI) GenBank (Accession no. KP843618.1 & KT581120.1). The 1566bp long IFS1 and IFS2 coding sequences showed 92.98% identity to each other with 110 nucleotides difference (S2). The amino acid sequence of IFS1 and IFS2 was also aligned, which showed 97.12 % identity to each other with 12 amino acid differences out of 521 amino acid residues (S3). The 3D models prepared for both IFS1 and IFS2 using RoseTTAFold showed over 94.8% and 96.5% of the residues in the most favoured region (Fig. 6 & 7). The IFS isoforms showed minor differences in their tertiary structures, but their predicted interactions with other proteins differed significantly. In the interaction study done using STRING, IFS2 intriguingly showed a maximum interaction with chalcone isomerase (CHI) with a score of 0.933 (Fig. 8 & S4), which was not the case for IFS1. Dastmalchi et al (2016) studied the interactions and subcellular localisation of major enzymes involved in isoflavone biosynthesis. This study's interesting finding was the interaction of Chalcone reductase (GmCHR14) with GmIFS2, but not with GmIFS1. We also got a similar result in the in-silico analysis. GmCHR14 is present upstream of the isoflavone synthase in the phenylpropanoid pathway responsible for the biosynthesis of isoflavones. A recent study conducted CRISPR mediated knockdown of IFS1 in which the mutants had nearly all the physiological processes intact, indicating a role of IFS2 (Dinkins et al. 2021). However, a peculiar finding of this study was more effect of IFS1 knockdown on genistein rather than daidzein accumulation, which could explain the more content of daidzein in the Bragg than genistein. It, therefore, appears that IFS2 is more suited for the formation of metabolon (a multi-enzyme complex), which may help in efficient and effective substrate channelling leading to a higher accumulation of isoflavone through this pathway. Thus, over-expression of IFS2 can enhance isoflavone levels.