Mapping quantitative trait loci for root development under hypoxia conditions in soybean (Glycine max L. Merr.).

KEY MESSAGE: Greatest potential, QTLs for hypoxia and waterlogging tolerance in soybean roots were detected using a new phenotypic evaluation method. Waterlogging is a major environmental stress limiting soybean yield in wet parts of the world. Root development is an important indicator of hypoxia tolerance in soybean. However, little is known about the genetic control of root development under hypoxia. This study was conducted to identify quantitative trait loci (QTLs) responsible for root development under hypoxia. Recombinant inbred lines (RILs) developed from a cross between a hypoxia-sensitive cultivar, Tachinagaha, and a tolerant landrace, Iyodaizu, were used. Seedlings were subjected to hypoxia, and root development was evaluated with the value change in root traits between after and before treatments. We found 230 polymorphic markers spanning 2519.2 cM distributed on all 20 chromosomes (Chrs.). Using these, we found 11 QTLs for root length (RL), root length development (RLD), root surface area (RSA), root surface area development (RSAD), root diameter (RD), and change in average root diameter (CARD) on Chrs. 11, 12, 13 and 14, and 7 QTLs for hypoxia tolerance of these root traits. These included QTLs for RLD and RSAD between markers Satt052 and Satt302 on Chr. 12, which are important markers of hypoxia tolerance in soybean; those QTLs were stable between 2 years. To validate the QTLs, we developed a near-isogenic line with the QTL region derived from Iyodaizu. The line performed well under both hypoxia and waterlogging, suggesting that the region contains one or more genes with large effects on root development. These findings may be useful for fine mapping and positional cloning of gene responsible for root development under hypoxia.

Controlling the formation process and atomic structures of single pyrazine molecular junction by tuning the strength of the metal-molecule interaction.

The formation process and atomic structures were investigated for single pyrazine molecular junctions sandwiched by three different Au, Ag, and Cu electrodes using a mechanically controllable break junction technique in ultrahigh vacuum conditions at 300 K. We demonstrated that the formation process of the single-molecule junction crucially depended on the choice of the metal electrodes. While single-molecule junction showing two distinct conductance states were found for the Au electrodes, only the single conductance state was evident for the Ag electrodes, and there was no junction formation for the Cu electrodes. These results suggested that metal-molecule interaction dominates the formation process and probability of the single-molecule junction. In addition to the metal-molecule interaction, temperature affected the formation process of the single-molecule junction. The single pyrazine molecular junction formed between Au electrodes exhibited significant temperature dependence where the junction-formation probability was about 8% at 300 K, while there was no junction-formation at 100 K. Instead of the junction formation, an Au atomic wire was formed at the low temperature. This study provides insight into the tuning of the junction-forming process for single-molecule junctions, which is needed to construct device structures on a single molecule scale.

Cloning and characterization of soybean gene Fg1 encoding flavonol 3-O-glucoside/galactoside (1→6) glucosyltransferase.

KEY MESSAGE: Flavonoids are important secondary metabolites in plants. Sugar-sugar glycosyltransferases are involved in the final step of flavonoid biosynthesis and contribute to the structural diversity of flavonoids. This manuscript describes the first cloning of a sugar-sugar glucosyltransferase gene in the UGT family that attaches glucose to the 6″-position of sugar bound to a flavonol. The results provide a glimpse on the possible evolution of sugar-sugar glycosyltransferase genes and identify putative amino acids responsible for the recognition of the hydroxyl group of the sugar moiety and specification of sugar. A scheme for the genetic control of flavonol glycoside biosynthesis is proposed. Flavonol glycosides (FGs) are predominant in soybean leaves and they show substantial differences among genotypes. In previous studies, we identified two flavonoid glycoside glycosyltransferase genes that segregated in recombinant inbred lines developed from a cross between cultivars Nezumisaya and Harosoy; one was responsible for the attachment of glucose to the 2″-position of glucose or galactose that is bound to the 3-position of kaempferol and the other was involved in the attachment of glucose to the 6″-position. This study was conducted to clone and characterize the 6″-glucosyltransferase gene. Linkage mapping indicated that the gene was located in the molecular linkage group I (chromosome 20). Based on the genome sequence, we cloned a candidate cDNA, GmF3G6"Gt from Harosoy but the corresponding cDNA could not be amplified by PCR from Nezumisaya. The coding region of GmF3G6″Gt in Harosoy is 1386 bp long encoding 462 amino acids. This gene was not expressed in leaves of Nezumisaya. The GmF3G6″Gt recombinant protein converted UDP-glucose and kaempferol 3-O-glucoside or kaempferol 3-O-galactoside to kaempferol 3-O-glucosyl-(1→6)-glucoside or kaempferol 3-O-glucosyl-(1→6)-galactoside, respectively. These results indicate that GmF3G6″Gt encodes a flavonol 3-O-glucoside/galactoside (1→6) glucosyltransferase and corresponds to the Fg1 gene. GmF3G6″Gt had an amino acid similarity of 82 % with GmF3G6″Rt encoding flavonol 3-O-glucoside/galactoside (1→6) rhamnosyltransferase, suggesting a recent evolutionary divergence of the two genes. This may be the first cloning of a sugar-sugar glucosyltransferase gene in the UGT family that attaches glucose to the 6″-position of sugar bound to a flavonol. A scheme for the control of FG biosynthesis is proposed.

Determination of the number of atoms present in nano contact based on shot noise measurements with highly stable nano-fabricated electrodes.

A highly stable experimental setup was developed for the measurement of shot noise in atomic contacts and molecular junctions to determine the number of atoms or molecules present. The use of a nano-fabricated mechanically controllable break junction (MCBJ) electrode improved the overall stability of the experimental setup. The improved stability of the system and optimization of measurement system enabled us to comprehensively investigate the shot noise as well as charge transport properties in Au atomic contacts and molecular junctions. We present a solid proof that the number of atoms (cross sectional atom) in the Au atomic contacts was exactly one. In the atomic contacts, contribution from the additional channels was under the detection limit. Furthermore, the effect of molecular adsorption on the charge transport in the Au atomic contact was investigated. Additional transport channels were opened by exposing pyrazine molecules to the Au contacts, which gave rise to an increase in the Fano factor in the shot noise.

Quantitative trait locus mapping of soybean maturity gene E5.

Time to flowering and maturity in soybean is controlled by loci E1 to E5, and E7 to E9. These loci were assigned to molecular linkage groups (MLGs) except for E5. This study was conducted to map the E5 locus using F2 populations expected to segregate for E5. F2 populations were subjected to quantitative trait locus (QTL) analysis for days to flowering (DF) and maturity (DM). In Harosoy-E5 × Clark-e2 population, QTLs for DF and DM were found at a similar position with E2. In Harosoy × Clark-e2E5 population, QTLs for DF and DM were found in MLG D1a and B1, respectively. In Harosoy-E5Dt2 × Clark-e2 population, a QTL for DF was found in MLG B1. Thus, results from these populations were not fully consistent, and no candidate QTL for E5 was found. In Harosoy × PI 80837 population, from which E5 was originally identified, QTLs corresponding to E1 and E3 were found, but none for E5 existed. Harosoy and PI 80837 had the e2-ns allele whereas Harosoy-E5 had the E2-dl allele. The E2-dl allele of Harosoy-E5 may have been generated by outcrossing and may be responsible for the lateness of Harosoy-E5. We conclude that a unique E5 gene may not exist.

Linkage mapping, molecular cloning and functional analysis of soybean gene Fg3 encoding flavonol 3-O-glucoside/galactoside (1 → 2) glucosyltransferase.

BACKGROUND: Flavonol glycosides (FGs) are major components of soybean leaves and there are substantial differences in FG composition among genotypes. The first objective of this study was to identify genes responsible for FG biosynthesis and to locate them in the soybean genome. The second objective was to clone the candidate genes and to verify their function. Recombinant inbred lines (RILs) were developed from a cross between cultivars Nezumisaya and Harosoy. RESULTS: HPLC comparison with authentic samples suggested that FGs having glucose at the 2″-position of glucose or galactose that is bound to the 3-position of kaempferol were present in Nezumisaya, whereas FGs of Harosoy were devoid of 2″-glucose. Conversely, FGs having glucose at the 6″-position of glucose or galactose that is bound to the 3-position of kaempferol were present in Harosoy, whereas these FGs were absent in Nezumisaya. Genetic analysis suggested that two genes control the pattern of attachment of these sugar moieties in FGs. One of the genes may be responsible for attachment of glucose to the 2″-position, probably encoding for a flavonol 3-O-glucoside/galactoside (1 → 2) glucosyltransferase. Nezumisaya may have a dominant whereas Harosoy may have a recessive allele of the gene. Based on SSR analysis, linkage mapping and genome database survey, we cloned a candidate gene designated as GmF3G2″Gt in the molecular linkage group C2 (chromosome 6). The open reading frame of GmF3G2″Gt is 1380 bp long encoding 459 amino acids with four amino acid substitutions among the cultivars. The GmF3G2″Gt recombinant protein converted kaempferol 3-O-glucoside to kaempferol 3-O-sophoroside. GmF3G2″Gt of Nezumisaya showed a broad activity for kaempferol/quercetin 3-O-glucoside/galactoside derivatives but it did not glucosylate kaempferol 3-O-rhamnosyl-(1 → 4)-[rhamnosyl-(1 → 6)-glucoside] and 3-O-rhamnosyl-(1 → 4)-[glucosyl-(1 → 6)-glucoside]. CONCLUSION: GmF3G2″Gt encodes a flavonol 3-O-glucoside/galactoside (1 → 2) glucosyltransferase and corresponds to the Fg3 gene. GmF3G2″Gt was designated as UGT79B30 by the UGT Nomenclature Committee. Based on substrate specificity of GmF3G2″Gt, 2″-glucosylation of flavonol 3-O-glycoside may be irreconcilable with 4″-glycosylation in soybean leaves.

CACTA-superfamily transposable element is inserted in MYB transcription factor gene of soybean line producing variegated seeds.

The R gene of soybean, presumably encoding a MYB transcription factor, controls seed coat color. The gene consists of multiple alleles, R (black), r-m (black spots and (or) concentric streaks on brown seed), and r (brown seed). This study was conducted to determine the structure of the MYB transcription factor gene in a near-isogenic line (NIL) having r-m allele. PCR amplification of a fragment of the candidate gene Glyma.09G235100 generated a fragment of about 1 kb in the soybean cultivar Clark, whereas a fragment of about 14 kb in addition to fragments of 1 and 1.4 kb were produced in L72-2040, a Clark 63 NIL with the r-m allele. Clark 63 is a NIL of Clark with the rxp and Rps1 alleles. A DNA fragment of 13 060 bp was inserted in the intron of Glyma.09G235100 in L72-2040. The fragment had the CACTA motif at both ends, imperfect terminal inverted repeats (TIR), inverse repetition of short sequence motifs close to the 5' and 3' ends, and a duplication of three nucleotides at the site of integration, indicating that it belongs to a CACTA-superfamily transposable element. We designated the element as Tgm11. Overall nucleotide sequence, motifs of TIR, and subterminal repeats were similar to those of Tgm1 and Tgs1, suggesting that these elements comprise a family.

Atomic level rendering of DNA-drug encounter.

Computer simulations have been demonstrated to be important for unraveling atomic mechanisms in biological systems. In this study, we show how combining unbiased molecular dynamic simulations with appropriate analysis tools can successfully describe metal-based drug interactions with DNA. To elucidate the noncovalent affinity of cisplatin's family to DNA, we performed extensive all-atom molecular dynamics simulations (3.7 µs total simulation length). The results show that the parent drug, cisplatin, has less affinity to form noncovalent adducts in the major groove than its aquo complexes. Furthermore, the relative position in which the drugs enter the major groove is dependent on the compound's net charge. Based on the simulations, we estimated noncovalent binding free energies through the use of Markov state models. In addition, and to overcome the lack of experimental information, we employed two additional methods: Molecular Mechanics Poisson-Boltzmann Surface Area (MMPB-SA) and steered molecular dynamics with the Jarzynski estimator, with an overall good agreement between the three methods. All complexes show interaction energies below 3 kcal/mol with DNA but the charged hydrolysis products have slightly more favorable binding free energies than the parent drug. Moreover, this study sets the precedent for future unbiased DNA-ligand simulations of more complex binders.

Linkage mapping, molecular cloning and functional analysis of soybean gene Fg2 encoding flavonol 3-O-glucoside (1 → 6) rhamnosyltransferase.

There are substantial genotypic differences in the levels of flavonol glycosides (FGs) in soybean leaves. The first objective of this study was to identify and locate genes responsible for FG biosynthesis in the soybean genome. The second objective was to clone and verify the function of these candidate genes. Recombinant inbred lines (RILs) were developed by crossing the Kitakomachi and Koganejiro cultivars. The FGs were separated by high performance liquid chromatography (HPLC) and identified. The FGs of Koganejiro had rhamnose at the 6″-position of the glucose or galactose bound to the 3-position of kaempferol, whereas FGs of Kitakomachi were devoid of rhamnose. Among the 94 RILs, 53 RILs had HPLC peaks classified as Koganejiro type, and 41 RILs had peaks classified as Kitakomachi type. The segregation fitted a 1:1 ratio, suggesting that a single gene controls FG composition. SSR analysis, linkage mapping and genome database survey revealed a candidate gene in the molecular linkage group O (chromosome 10). The coding region of the gene from Koganejiro, designated as GmF3G6″Rt-a, is 1,392 bp long and encodes 464 amino acids, whereas the gene of Kitakomachi, GmF3G6″Rt-b, has a two-base deletion resulting in a truncated polypeptide consisting of 314 amino acids. The recombinant GmF3G6″Rt-a protein converted kaempferol 3-O-glucoside to kaempferol 3-O-rutinoside and utilized 3-O-glucosylated/galactosylated flavonols and UDP-rhamnose as substrates. GmF3G6″Rt-b protein had no activity. These results indicate that GmF3G6″Rt encodes a flavonol 3-O-glucoside (1 â†’ 6) rhamnosyltransferase and it probably corresponds to the Fg2 gene. GmF3G6″Rt was designated as UGT79A6 by the UGT Nomenclature Committee.

Allelic variation of soybean flower color gene W4 encoding dihydroflavonol 4-reductase 2.

BACKGROUND: Flower color of soybean is primarily controlled by six genes, viz., W1, W2, W3, W4, Wm and Wp. This study was conducted to investigate the genetic and chemical basis of newly-identified flower color variants including two soybean mutant lines, 222-A-3 (near white flower) and E30-D-1 (light purple flower), a near-isogenic line (Clark-w4), flower color variants (T321 and T369) descended from the w4-mutable line and kw4 (near white flower, Glycine soja). RESULTS: Complementation tests revealed that the flower color of 222-A-3 and kw4 was controlled by the recessive allele (w4) of the W4 locus encoding dihydroflavonol 4-reductase 2 (DFR2). In 222-A-3, a single base was deleted in the first exon resulting in a truncated polypeptide consisting of 24 amino acids. In Clark-w4, base substitution of the first nucleotide of the fourth intron abolished the 5' splice site, resulting in the retention of the intron. The DFR2 gene of kw4 was not expressed. The above results suggest that complete loss-of-function of DFR2 gene leads to near white flowers. Light purple flower of E30-D-1 was controlled by a new allele at the W4 locus, w4-lp. The gene symbol was approved by the Soybean Genetics Committee. In E30-D-1, a single-base substitution changed an amino acid at position 39 from arginine to histidine. Pale flowers of T369 had higher expression levels of the DFR2 gene. These flower petals contained unique dihydroflavonols that have not yet been reported to occur in soybean and G. soja. CONCLUSIONS: Complete loss-of-function of DFR2 gene leads to near white flowers. A new allele of the W4 locus, w4-lp regulates light purple flowers. Single amino acid substitution was associated with light purple flowers. Flower petals of T369 had higher levels of DFR2 gene expression and contained unique dihydroflavonols that are absent in soybean and G. soja. Thus, mutants of the DFR2 gene have unique flavonoid compositions and display a wide variety of flower color patterns in soybean, from near white, light purple, dilute purple to pale.

High-pressure synthesis, crystal structure, and unusual valence state of novel perovskite oxide CaCu3Rh4O12.

A novel perovskite oxide, CaCu3Rh4O12, has been synthesized under high-pressure and high-temperature conditions (15 GPa and 1273 K). Rietveld refinement of synchrotron X-ray powder diffraction data indicates that this compound crystallizes in a cubic AA'3B4O12-type perovskite structure. Synchrotron X-ray absorption and photoemission spectroscopy measurements reveal that the Cu and Rh valences are nearly trivalent. The spectroscopic analysis based on calculations suggests that the appropriate ionic model of this compound is Ca(2+)Cu(∼2.8+)3Rh(∼3.4+)4O12, as opposed to the conventional Ca(2+)Cu(2+)3Rh(4+)4O12. The uncommon valence state of this compound is attributed to the relative energy levels of the Cu 3d and Rh 4d orbitals, in which the large crystal-field splitting energy of the Rh 4d orbitals is substantial.

Charge-order melting in charge-disproportionated perovskite CeCu3Fe4O12.

A novel quadruple perovskite oxide CeCu3Fe4O12 has been synthesized under high-pressure and high-temperature conditions of 15 GPa and 1473 K. (57)Fe Mössbauer spectroscopy displays a charge disproportionation transition of 4Fe(3.5+) → 3Fe(3+) + Fe(5+) below ∼270 K, whereas hard X-ray photoemission and soft X-ray absorption spectroscopy measurements confirm that the Ce and Cu valences are retained at approximately +4 and +2, respectively, over the entire temperature range measured. Electron and X-ray diffraction studies reveal that the body-centered cubic symmetry (space group Im3̅, No. 204) is retained at temperatures as low as 100 K, indicating the absence of any types of charge-ordering in the charge-disproportionated CeCu3Fe4O12 phase. The magnetic susceptibility and neutron powder diffraction data illustrate that the antiferromagnetic ordering of Fe ions is predominant in the charge-disproportionated CeCu3Fe4O12 phase. These findings suggest that CeCu3Fe4O12 undergoes a new type of electronic phase in the ACu3Fe4O12 series and that the melting of the charge-ordering in CeCu3Fe4O12 is caused by the substantial decrease in the Fe valence and the resulting large deviation from the ideal abundance ratio of Fe(3+):Fe(5+) = 1:1 for rock-salt-type charge-ordering.

Suppression of intersite charge transfer in charge-disproportionated perovskite YCu3Fe4O12.

A novel iron perovskite YCu3Fe4O12 was synthesized under high pressure and high temperature of 15 GPa and 1273 K. Synchrotron X-ray and electron diffraction measurements have demonstrated that this compound crystallizes in the cubic AA'3B4O12-type perovskite structure (space group Im3, No. 204) with a lattice constant of a = 7.30764(10) Šat room temperature. YCu3Fe4O12 exhibits a charge disproportionation of 8Fe(3.75+) → 3Fe(5+) + 5Fe(3+), a ferrimagnetic ordering, and a metal-semiconductor-like transition simultaneously at 250 K, unlike the known isoelectronic compound LaCu3Fe4O12 that currently shows an intersite charge transfer of 3Cu(2+) + 4Fe(3.75+) → 3Cu(3+) + 4Fe(3+), an antiferromagnetic ordering, and a metal-insulator transition at 393 K. This finding suggests that intersite charge transfer is not the only way of relieving the instability of the Fe(3.75+) state in the A(3+)Cu(2+)3Fe(3.75+)4O12 perovskites. Crystal structure analysis reveals that bond strain, rather than the charge account of the A-site alone, which is enhanced by large A(3+) ions, play an important role in determining which of intersite charge transfer or charge disproportionation is practical.

B-site deficiencies in A-site-ordered perovskite LaCu3Pt(3.75)O12.

An A-site-ordered perovskite LaCu3Pt(3.75)O12 was synthesized by replacing Ca(2+) with La(3+) in a cubic quadruple AA'3B4O12-type perovskite CaCu3Pt4O12 under high-pressure and high-temperature of 15 GPa and 1100 °C. In LaCu3Pt(3.75)O12, 1/16 of B-site cations are vacant to achieve charge balance. The B-site deficiencies were evidenced by crystal structure refinement using synchrotron X-ray powder diffraction, hard X-ray photoemission spectroscopy, and soft X-ray absorption spectroscopy, leading to the ionic model La(3+)Cu(2+)3Pt(4+)(3.75)O(2-)12. Magnetic susceptibility data for this compound indicated a spin-glass-like behavior below T(g) = 3.7 K, which is attributed to disturbance of the antiferromagnetic superexchange interaction by the B-site deficiencies.

Pd(2+)-incorporated perovskite CaPd3B4O12 (B = Ti, V).

Novel A-site ordered perovskites CaPd(3)Ti(4)O(12) and CaPd(3)V(4)O(12) were synthesized under high-pressure and high-temperature of 15 GPa and 1000 °C. These compounds are the first example in which a crystallographic site in a perovskite-type structure is occupied by Pd(2+) ions with a 4d(8) low spin configuration. The ionic models for these compounds were determined to be Ca(2+)Pd(2+)(3)Ti(4+)(4)O(12) and Ca(2+)Pd(2+)(3)V(4+)(4)O(12) by structural refinement using synchrotron X-ray powder diffraction, hard X-ray photoemission, and soft X-ray absorption spectroscopy. Magnetic susceptibility, electrical resistivity, and specific heat measurements demonstrated diamagnetic insulating behavior for CaPd(3)Ti(4)O(12) in contrast to the Pauli-paramagnetic metallic nature of CaPd(3)V(4)O(12).

Control of bond-strain-induced electronic phase transitions in iron perovskites.

Unusual electronic phase transitions in the A-site ordered perovskites LnCu3Fe4O12 (Ln: trivalent lanthanide ion) are investigated. All LnCu3Fe4O12 compounds are in identical valence states of Ln(3+)Cu(2+)3Fe(3.75+)4O12 at high temperature. LnCu3Fe4O12 with larger Ln ions (Ln = La, Pr, Nd, Sm, Eu, Gd, Tb) show an intersite charge transfer transition (3Cu(2+) + 4Fe(3.75+) → 3Cu(3+) + 4Fe(3+)) in which the transition temperature decreases from 360 to 240 K with decreasing Ln ion size. In contrast, LnCu3Fe4O12 with smaller Ln ions (Ln = Dy, Ho, Er, Tm Yb, Lu) transform into a charge-disproportionated (8Fe(3.75+) → 5Fe(3+) + 3Fe(5+)) and charge-ordered phase below ∼250-260 K. The former series exhibits metal-to-insulator, antiferromagnetic, and isostructural volume expansion transitions simultaneously with intersite charge transfer. The latter shows metal-to-semiconductor, ferrimagnetic, and structural phase transitions simultaneously with charge disproportionation. Bond valence calculation reveals that the metal-oxygen bond strains in these compounds are classified into two types: overbonding or compression stress (underbonding or tensile stress) in the Ln-O (Fe-O) bond is dominant in the former series, while the opposite stresses or bond strains are found in the latter. Intersite charge transfer transition temperatures are strongly dependent upon the global instability indices that represent the structural instability calculated from the bond valence sum, whereas the charge disproportionation occurs at almost identical temperatures, regardless of the magnitude of structural instability. These findings provide a new aspect of the structure-property relationship in transition metal oxides and enable precise control of electronic states by bond strains.

A MYB transcription factor controls flower color in soybean.

Purple-blue flower of soybean (Glycine max [L.] Merr.) is controlled by the W2 locus. Previous studies revealed that a MYB transcription factor gene GmMYB-G20-1 was located at a position similar to the W2 gene and that a base substitution generated a stop codon in the MYB domains of 2 soybean lines with purple-blue flowers. This study was conducted to confirm the relationship between GmMYB-G20-1 and the W2 gene. Cleaved amplified polymorphic sequence analysis to detect the base substitution suggested that a similar mutation occurred in 2 other soybean lines having purple-blue flowers, 037-E-8, and Yogetsu 1-blue. Thus, all genotypes having purple-blue flowers had identical base substitutions. To verify the function of GmMYB-G20-1, apple latent spherical virus (ALSV) vectors were constructed to perform virus-induced gene silencing of GmMYB-G20-1. A cultivar Harosoy with purple flowers (W2W2) was infected by the empty ALSV vector (wtALSV) or the GmMYB-G20-1-ALSV vector containing a fragment (nucleotide position 685-885) of GmMYB-G20-1. Plants infected by empty vectors had only purple flowers. In contrast, most flowers of plants infected with GmMYB-G20-1-ALSV had irregular gray/blue sectors in flower petals and some of the flowers had almost gray/blue petals. These results strongly suggest that silencing of GmMYB-G20-1 can alter flower color and that it may correspond to the W2 gene.

The soybean F3'H protein is localized to the tonoplast in the seed coat hilum.

We previously isolated a soybean (Glycine max (L.) Merr.) flavonoid 3'-hydroxylase (F3'H) gene (sf3'h1) corresponding to the T locus, which controls pubescence and seed coat color, from two near-isogenic lines (NILs), To7B (TT) and To7G (tt). The T allele is also associated with chilling tolerance. Here, Western-blot analysis shows that the sf3'h1 protein was predominantly detected in the hilum and funiculus of the immature seed coat in To7B, whereas sf3'h1 was not detected in To7G. A truncated sf3'h1 protein isolated from To7G was detected only upon enrichment by immunoprecipitation. An analysis using diphenylboric acid 2-aminoethyl ester (DBPA) staining revealed that flavonoids accumulated in the hilum and the funiculus in both To7B and To7G. Further, the scavenging activity of the 1,1-diphenyl-2-picrylhydrazyl (DPPH) radical in methanol extracts from the funiculus and hilum of To7B was higher than that of To7G. Moreover, the enzymatic activity of F3'H was detected using microsomal fractions from yeast transformed with sf3'h1 from To7B, but not from To7G. These results indicate that sf3'h1 is involved in flavonoid biosynthesis in the seed coat and affects the antioxidant properties of those tissues. As shown by immunofluorescence microscopy, the sf3'h1 protein was detected primarily around the vacuole in the parenchymatic cells of the hilum in To7B. Further immunoelectron microscopy detected sf3'h1 protein on the membranous structure of the vacuole. Based on these observations, we conclude that F3'H, which is a cytochrome P450 monooxygenase and has been found to be localized to the ER in other plant systems, is localized in the tonoplast in soybean.

Single-base substitution in P1B-ATPase gene is associated with a major QTL for seed cadmium concentration in soybean.

Cadmium (Cd) is a pollutant metal present in soils and toxic to biologic organisms. Previous studies using recombinant inbred lines derived from a cross between soybean (Glycine max [L.] Merr.) cultivars Harosoy and Fukuyutaka revealed a major quantitative trait loci for seed Cd concentration (cd1) in chromosome 9. The genome sequence of Williams 82 suggested that a P(1B)-ATPase gene involved in the transport of metals was located in the vicinity of cd1. cDNA sequencing suggested existence of two types of transcripts: one (GmHMA1a) consisting of 9 exons and 8 introns and the other (GmHMA1b) consisting of 8 exons and 7 introns. The putative polypeptide, GmHMA1a, consisted of 885 amino acids, whereas premature termination of translation of GmHMA1b generated a putative polypeptide with 559 amino acids. GmHMA1a had a 49.8% similarity with AtHMA3, a P(1B)-ATPase of Arabidopsis. GmHMA1a of Fukuyutaka differed from that of Harosoy by a single-base substitution that led to an amino acid substitution from E to G at amino acid position 608. A derived cleaved amplified polymorphic sequence (dCAPS) marker was developed to detect the base substitution, and this dCAPS marker was successfully associated with seed Cd concentration. Transgenic experiments may be necessary to verify that GmHMA1 actually corresponds to cd1.

Nonsense mutation of an MYB transcription factor is associated with purple-blue flower color in soybean.

Previous studies revealed that the recessive allele of the W2 locus generated purple-blue color and high vacuolar pH of flower petals in soybean. The location of W2 gene was reportedly close to simple sequence repeat marker Satt318 in molecular linkage group B2. We used information from the soybean genome to clone a candidate gene for W2. An MYB transcription factor gene belonging to G20 group was found in the vicinity of Satt318. Full-length cDNAs were cloned from purple-flowered cultivar Harosoy (W2 allele) and purple-blue flowered cultivars, Nezumisaya and w2-20 (w2 allele), by reverse transcription-PCR and designated as GmMYB-G20-1. Its open reading frame was 1083 bp long that encoded 361 amino acids in Harosoy. GmMYB-G20-1 had 53.7% similarity in amino acid sequence with the PH4 gene of petunia controlling blueness and vacuolar pH of flower petals. GmMYB-G20-1 of Nezumisaya and w2-20 had 3 base substitutions compared with that of Harosoy. The first substitution generated a stop codon in the MYB domain, resulting in truncated polypeptides. Cleaved amplified polymorphic sequence (CAPS) marker was developed to detect the base substitution. The polymorphic CAPS marker co-segregated with alleles at the W2 locus in the F(2) population. These results suggest that GmMYB-G20-1 might correspond to the W2 gene.