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Mean and standard errors (× 10 3 ) of flavonol contents by HPLC analysis of flower petals from soybean cv, Clark and five G. soja accessions in 2006 at Tsukuba, Japan.
Source publication
Glycine soja is a wild relative of soybean that has purple flowers. No flower color variant of Glycine soja has been found in the natural habitat.
B09121, an accession with light purple flowers, was discovered in southern Japan. Genetic analysis revealed that the gene responsible for the light purple flowers was allelic to the W1 locus encoding fla...
Context in source publication
Context 1
... peak (F9) corresponding to dihydroflavonol (aro- madendrin 3-O-glucoside) was found by HPLC analysis in Clark and all of the G. soja lines. The amount of aro- madendrin 3-O-glucoside estimated by peak area in HPLC analysis is presented in Table 5. The G. soja lines had 33 to 155% more aromadendrin 3-O-glucoside than Clark. ...
Citations
... To determine whether the genetic maps constructed in this study were capable of QTL mapping, the flower color quality trait was also mapped in the RIL population ( Figure 3). Here, the primary QTL for flower color was identified with an LOD value of 13.25 and a PVE value of 30% on chromosome 13 near the physical location of 16,983,990 bp, where the W gene responsible for flower color has previously been reported [46]. Taken together, these results indicate that the genetic linkage map constructed here would be useful for further QTL mapping of seed quality and nutrient translocation efficiency traits. ...
... this study were capable of QTL mapping, the flower color quality trait was also mapped in the RIL population ( Figure 3). Here, the primary QTL for flower color was identified with an LOD value of 13.25 and a PVE value of 30% on chromosome 13 near the physical location of 16,983,990 bp, where the W gene responsible for flower color has previously been reported [46]. Taken together, these results indicate that the genetic linkage map constructed here would be useful for further QTL mapping of seed quality and nutrient translocation efficiency traits. ...
Soybean (Glycine max (L.) Merr.) is an important nutritional crop with high seed protein content. Production of high protein concentrations relies on sufficient nutrient supplies, especially of nitrogen (N) and phosphorus (P). Although the genetic basis for seed quality traits has been well studied, little information exists on any genetic connections between seed quality and nutrient supplies in soybean. Here, a recombinant inbred line (RIL) population of 179 progeny was generated using HC6 and JD17 as parents contrasting in seed quality and N and P translocation efficiencies. Seed protein and N and P translocation efficiencies were higher in HC6 than in JD17. Meanwhile, positive correlations were observed between seed protein content and translocation efficiency of N and P in RILs, implying that high N and P translocation efficiencies might facilitate seed protein accumulation. A genetic map was constructed using 5250 SNP markers covering a genetic distance of 3154.83 cM. A total of 6 loci for quality and 13 loci for N and P translocation efficiency were detected. Among them, two fragments on chromosome 6 and chromosome 20 contained multiple significant markers for both quality and N and P translocation efficiencies, with the respective observed LOD values ranging from 2.98 to 5.61, and 3.01 to 11.91, while the respective PVE values ranged from 8.2% to 13.9%, and 8.3% to 28.0%. Interestingly, one significant locus on chromosome 20 appears to be the product of a transposable element (TE) InDel in Glyma.20G085100, with progeny lacking the TE also exhibiting higher N and P translocation efficiencies, along with higher seed protein contents. Taken together, these results provide genetic evidence that increasing N and P translocation efficiencies may lead to increasing protein contents in soybean seeds. Furthermore, a TE InDel may be used as a genetic marker for breeding elite soybean cultivars with high protein content and N and P translocation efficiencies.
... If it is inhibited, the total flavonoid level will be reduced [32]. The mutation of F3 5 H leads to a decrease in delphinid levels and an increase in anthocyanin levels [33]. Ectopic expression of FLS promotes the accumulation of kaempferol and a decrease in the anthocyanin content in flowers [34]. ...
Rhododendron liliiflorum H. Lév., with white outer edges and yellow inner edges of petals, is an ornamental flower that originated in China. In this study, we analysed the white (W) and yellow (Y) parts of R. liliiflorum flowers by RNA sequencing. Then, unigene assembly, unigene annotation, and classification of Eukaryotic Orthologous Groups (KOGs) were performed. Gene ontology (GO) classification and pathway enrichment analysis for unigenes were also conducted. A total of 219,221 transcripts and 180,677 unigenes of R. liliiflorum were obtained from 48.52 Gb of clean reads. Differentially expressed gene (DEG) analysis indicated that 2310 unigenes were upregulated and 3062 were downregulated in W vs. Y. Thirty-six of these DEGs were involved in the flavonoid biosynthesis pathway. Pathway enrichment analysis showed that DEGs were significantly enriched in phenylpropanoid, flavonoid, and isoflavone biosynthesis. The expression of dihydroflavonol-4-reductase (DFR) and chalcone synthase (CHS) may affect differences in R. liliiflorum flower colour. The findings on flavonoid biosynthesis and other related genes in this study will provide guidance for exploring the mechanism of flower colour formation in Rhododendron.
... Through the 180K Axiom SoyaSNP assay, the high-density genetic map was constructed for the Daepung × Danbaek RIL population. In the population, the colors of flower and pubescence, which had been reported to be controlled by single genes previously 19,20 , were divided into purple (70) and white (43), gray (76), and brown (37), respectively. The responsive genes, T and W1, for the colors of pubescence and flower could be identified using the constructed genetic map. ...
... Flower color and pubescence color were also scored in two RIL populations for detecting W1 and T genes, respectively, previously reported 19,20 . Three qualitative phenotypic data (sensitivity of PE, flower color, and pubescence color) were recorded by two types, reference allele or alternative allele. ...
Phytotoxicity is caused by the interaction between plants and a chemical substance, which can cause critical damage to plants. Understanding the molecular mechanism underlying plant-chemical interactions is important for managing pests in crop fields and avoiding plant phytotoxicity by insecticides. The genomic region responsible for sensitivity to phytotoxicity of etofenprox (PE), controlled by a single dominant gene, was detected by constructing high density genetic map using recombination inbred lines (RILs) in soybean. The genomic region of ~ 80 kbp containing nine genes was identified on chromosome 16 using a high-throughput single nucleotide polymorphism (SNP) genotyping system using two different RIL populations. Through resequencing data of 31 genotypes, nonsynonymous SNPs were identified in Glyma.16g181900 , Glyma.16g182200 , and Glyma.16g182300 . The genetic variation in Glyma.16g182200 , encoding glycosylphosphatidylinositol-anchored protein (GPI-AP), caused a critical structure disruption on the active site of the protein. This structural variation of GPI-AP may change various properties of the ion channels which are the targets of pyrethroid insecticide including etofenprox. This is the first study that identifies the candidate gene and develops SNP markers associated with PE. This study would provide genomic information to understand the mechanism of phytotoxicity in soybean and functionally characterize the responsive gene.
... The expression of the two alternatively-spliced DFR transcripts, DFRa and DFRb, varied between the colored varieties ( Fig. 8) and was lower in Shepody, the control. DFRa expression was greater than DFRb expression in RedR3 but less than that in PurpleR2, consistent with the Fig. 8 Differential expression proposition composed of differentially expressed genes and differential metabolites in RedR3 and PurpleR2 potato leaves differences in cyanidin and delphinidin content between these varieties [40]: at the higher DFRa-type transcript spliceosomes content, cyanidin 3-O-galactoside, pelargonin, and pelargonidin 3-O-glucoside accumulated, producing the red color [41], and at the higher DFRb-type content, petunidin 3-O-glucoside, malvidin 3-O-glucoside, delphinidin 3-O-glucoside, and cyanidin 3-O-glucoside accumulated, producing the purple color [42]. In tobacco, AN1 overexpression caused anthocyanin accumulation, leading to purple leaves. ...
Background
Anthocyanins, which account for color variation and remove reactive oxygen species, are widely synthesized in plant tissues and organs. Using targeted metabolomics and nanopore full-length transcriptomics, including differential gene expression analysis, we aimed to reveal potato leaf anthocyanin biosynthetic pathways in different colored potato varieties.
Results
Metabolomics analysis revealed 17 anthocyanins. Their levels varied significantly between the different colored varieties, explaining the leaf color differences. The leaves of the Purple Rose2 (PurpleR2) variety contained more petunidin 3-O-glucoside and malvidin 3-O-glucoside than the leaves of other varieties, whereas leaves of Red Rose3 (RedR3) contained more pelargonidin 3-O-glucoside than the leaves of other varieties. In total, 114 genes with significantly different expression were identified in the leaves of the three potato varieties. These included structural anthocyanin synthesis–regulating genes such as F3H , CHS , CHI , DFR , and anthocyanidin synthase and transcription factors belonging to multiple families such as C3H, MYB, ERF, NAC, bHLH, and WRKY. We selected an MYB family transcription factor to construct overexpression tobacco plants; overexpression of this factor promoted anthocyanin accumulation, turning the leaves purple and increasing their malvidin 3-o-glucoside and petunidin 3-o-glucoside content.
Conclusions
This study elucidates the effects of anthocyanin-related metabolites on potato leaves and identifies anthocyanin metabolic network candidate genes.
... The white flower w1 allele contains a tandem repeat that introduces an early stop codon that eliminates the critical C-terminal SRS6 domain. The light purple flowers of the G. soja w1-lp allele have greatly reduced levels of dihydromyricetin-derived flavonoid glucosides (Takahashi et al., 2010). A V210M substitution in the third amino acid of SRS2 in the w1-lp protein occurs in a residue that is invariant among all legume F3′5′H proteins that produce purple flowers. ...
The classic V (violet, purple) gene of common bean (Phaseolus vulgaris) functions in a complex genetic network that controls seed coat and flower color and flavonoid content. V was cloned to understand its role in the network and the evolution of its orthologs in the Viridiplantae. V mapped genetically to a narrow interval on chromosome Pv06. A candidate gene was selected based on flavonoid analysis and confirmed by recombinational mapping. Protein and domain modeling determined V encodes flavonoid 3′5′ hydroxylase (F3′5′H), a P450 enzyme required for the expression of dihydromyricetin-derived flavonoids in the flavonoid pathway. Eight recessive haplotypes, defined by mutations of key functional domains required for P450 activities, evolved independently in the two bean gene pools from a common ancestral gene. V homologs were identified in Viridiplantae orders by functional domain searches. A phylogenetic analysis determined F3′5′H first appeared in the Streptophyta and is present in only 41% of Angiosperm reference genomes. The evolutionarily related flavonoid pathway gene flavonoid 3′ hydroxylase (F3′H) is found nearly universally in all Angiosperms. F3′H may be conserved because of its role in abiotic stress, while F3′5′H evolved as a major target gene for the evolution of flower and seed coat color in plants.
... The ectopic expression of apple F3 H genes increases the levels of quercetin and cyanidin in Arabidopsis and tobacco [105]. Meanwhile, delphinidin levels are decreased while those of cyanidin are increased in a natural Glycine soja f3 5 h mutant [106]. ...
Flavonoids are an important class of secondary metabolites widely found in plants, contributing to plant growth and development and having prominent applications in food and medicine. The biosynthesis of flavonoids has long been the focus of intense research in plant biology. Flavonoids are derived from the phenylpropanoid metabolic pathway, and have a basic structure that comprises a C15 benzene ring structure of C6-C3-C6. Over recent decades, a considerable number of studies have been directed at elucidating the mechanisms involved in flavonoid biosynthesis in plants. In this review, we systematically summarize the flavonoid biosynthetic pathway. We further assemble an exhaustive map of flavonoid biosynthesis in plants comprising eight branches (stilbene, aurone, flavone, isoflavone, flavonol, phlobaphene, proanthocyanidin, and anthocyanin biosynthesis) and four important intermediate metabolites (chalcone, flavanone, dihydroflavonol, and leucoanthocyanidin). This review affords a comprehensive overview of the current knowledge regarding flavonoid biosynthesis, and provides the theoretical basis for further elucidating the pathways involved in the biosynthesis of flavonoids, which will aid in better understanding their functions and potential uses.
... The ectopic expression of apple F3 H genes increases the levels of quercetin and cyanidin in Arabidopsis and tobacco [105]. Meanwhile, delphinidin levels are decreased while those of cyanidin are increased in a natural Glycine soja f3 5 h mutant [106]. ...
Flavonoids are an important class of secondary metabolites widely found in plants, contributing to plant growth and development and having prominent applications in food and medicine.
The biosynthesis of flavonoids has long been the focus of intense research in plant biology. Flavonoids
are derived from the phenylpropanoid metabolic pathway, and have a basic structure that comprises
a C15 benzene ring structure of C6-C3-C6. Over recent decades, a considerable number of studies
have been directed at elucidating the mechanisms involved in flavonoid biosynthesis in plants. In
this review, we systematically summarize the flavonoid biosynthetic pathway. We further assemble
an exhaustive map of flavonoid biosynthesis in plants comprising eight branches (stilbene, aurone,
flavone, isoflavone, flavonol, phlobaphene, proanthocyanidin, and anthocyanin biosynthesis) and
four important intermediate metabolites (chalcone, flavanone, dihydroflavonol, and leucoanthocyanidin). This review affords a comprehensive overview of the current knowledge regarding flavonoid
biosynthesis, and provides the theoretical basis for further elucidating the pathways involved in the
biosynthesis of flavonoids, which will aid in better understanding their functions and potential uses.
... Taken together, the loss of function of F3 5 H in soybean always halts anthocyanin production, consequently resulting in white color flowers [16]. Apart from the aforementioned white color variants, a light-purplecolored G. soja variant (B09121) has been reported with a new w1-lp allele [18]. A unique single-base substitution in the nucleotide position 653 of w1-lp mutant led to a noteworthy amino acid change (V 210 M). ...
... However, there was no difference in the transcription level between the alleles of w1-lp and W1. On the basis of their results, the authors suggested that an SNP mutation in the F3 5 H gene may lead to reduced F3 5 H enzymatic activity [18]. ...
... Scores above the threshold indicate that the variant has a "neutral" effect [21]. We used the mutants IT261811 (w1-s3) and PE1837 (w1-p1) for predicting the amino acid substitution's effect on F3 5 H protein function, along with the previously reported lightpurple flower-bearing wild soybean mutant B09121 (w1-lp), whose F3 5 H protein was described as hypofunctional due to an alteration in one of its amino acid residue [18]. The results showed that the F3 5 H proteins of all the three w1-s3, w1-p1, and w1-lp mutants had deleterious effects, with −2.692, −3.550, and −2673 PROVEAN scores, respectively. ...
The enzyme flavonoid 3′,5′-hydroxylase (F3′5′H) plays an important role in producing anthocyanin pigments in soybean. Loss of function of the W1 locus encoding F3′5′H always produces white flowers. However, few color variations have been reported in wild soybean. In the present study, we isolated a new color variant of wild soybean accession (IT261811) with pinkish-white flowers. We found that the flower’s pinkish-white color is caused by w1-s3, a single recessive allele of W1. The SNP detected in the mutant caused amino acid substitution (A304S) in a highly conserved SRS4 domain of F3′5′H proteins. On the basis of the results of the protein variation effect analyzer (PROVEAN) tool, we suggest that this mutation may lead to hypofunctional F3′5′H activity rather than non-functional activity, which thereby results in its pinkish-white color.
... Six of them control and regulate soybean ower color, including W1, W2, W3, W4, Wm and Wp [20]. Cloning results showed that these six locus were F3'5'H [21], MYB [22], DFR1 [23],DFR2 [24] FLS1/gm s1 [25] and F3H [26], respectively (Fig. 1). The ower color of soybeans with dominant W1W3W4 genotype is dark purple, the ower color of W1W3w4 genotype is light purple, the ower color of W1w3W4 genotype is purple, and W1w3w4 has nearly white owers [27]. ...
... Subsequent research showed that w1w3W4 has white owers [23]. The F3'5'H gene was cloned in Clark and B09121 strains [21]. The ower colors of the two soybean lines are purple (W1) and light purple (w1-lp). ...
Background
Cultivated soybean (Glycine max) is an important source for protein and oil. Each soybean strain has its own genetic diversity, and the availability of more soybean genomes may enhance comparative genomic analysis of soybean.ResultsIn this study, we constructed a high-quality de novo assembly of an elite soybean cultivar Jidou 17 (JD17) with high contiguity, completeness, and accuracy. We annotated 59,629 gene models and reconstructed 235,109 high-quality full-length transcripts. We have molecularly characterized the genotypes of some important agronomic traits of JD17 by taking advantage of these newly established genomic resources.Conclusions
We reported a high-quality genome and annotations of a wide range of cultivars, and used them to analyze the genotypes of genes related to important agronomic traits of soybean in JD17. We have demonstrated that high-quality genome assembly can serve as a valuable reference for soybean genomics and breeding research community.
... A sharp deviation from the expected P-value distribution in the tail area would indicate that a model appropriately controlled both false positives and false negatives. Models were also compared using qualitative traits in soybean, which have known published genes for flower color (Takahashi et al., 2010), stem termination (Bernard, 1972), seedcoat luster (Gijzen et al., 2003), seed-coat color , hilum color (Carpentieri-Pipolo et al., 2015), and pubescence color (Toda et al., 2002;Zabala and Vodkin, 2003). Models were also compared using simulated data in which there were a known number of QTLs in the simulated data. ...
Association mapping (AM) is a powerful tool for fine mapping complex trait variation down to nucleotide sequences by exploiting historical recombination events. A major problem in AM is controlling false positives that can arise from population structure and family relatedness. False positives are often controlled by incorporating covariates for structure and kinship in mixed linear models (MLM). These MLM-based methods are single locus models and can introduce false negatives due to over fitting of the model. In this study, eight different statistical models, ranging from single-locus to multilocus, were compared for AM for three traits differing in heritability in two crop species: soybean (Glycine max L.) and maize (Zea mays L.). Soybean and maize were chosen, in part, due to their highly differentiated rate of linkage disequilibrium (LD) decay, which can influence false positive and false negative rates. The fixed and random model circulating probability unification (FarmCPU) performed better than other models based on an analysis of Q-Q plots and on the identification of the known number of quantitative trait loci (QTLs) in a simulated data set. These results indicate that the FarmCPU controls both false positives and false negatives. Six qualitative traits in soybean with known published genomic positions were also used to compare these models, and results indicated that the FarmCPU consistently identified a single highly significant SNP closest to these known published genes. Multiple comparison adjustments (Bonferroni, false discovery rate, and positive false discovery rate) were compared for these models using a simulated trait having 60% heritability and 20 QTLs. Multiple comparison adjustments were overly conservative for MLM, CMLM, ECMLM, and MLMM and did not find any significant markers; in contrast, ANOVA, GLM, and SUPER models found an excessive number of markers, far more than 20 QTLs. The FarmCPU model, using less conservative methods (false discovery rate, and positive false discovery rate) identified 10 QTLs, which was closer to the simulated number of QTLs than the number found by other models.
