Wind tunnel and field assessment of pollen dispersal in Soybean [<Emphasis Type="Italic">Glycine max</Emphasis> (L.) Merr.]

Although genetically modified (GM) soybean has never been cultivated commercially in Japan, it is essential to set up the isolation distance required to prevent out-crossing between GM and conventional soybean in preparation for any future possibility of pollen transfer. The airborne soybean pollen was sampled using some Durham pollen samplers located in the range of 20 m from the field edge. In addition, the dispersal distance was assessed in a wind tunnel under constant air flow and then it was compared with the anticipated distances based on the pollen diameter. In the field, the maximum pollen density per day observed was 1.235 grains cm⁻² day⁻¹ at three observation points within 2.5 m from the field and inside the field the mean density did not reach the rate of 1 grain cm⁻² day⁻¹ during 19 flowering days. The results of the wind tunnel experiment also showed that the plants had almost no airborne release of pollen and the dispersal distance was shorter than theoretical value due to clustered dispersal. This study showed little airborne pollen in and around the soybean field and the dispersal is restricted to a small area. Therefore, wind-mediated pollination appears to be negligible.     

Polygenic inheritance of canopy wilting in soybean [<Emphasis Type="Italic">Glycine max</Emphasis> (L.) Merr.]

As water demand for agriculture exceeds water availability, cropping systems need to become more efficient in water usage, such as deployment of cultivars that sustain yield under drought conditions. Soybean cultivars differ in how quickly they wilt during water-deficit stress, and this trait may lead to yield improvement during drought. The objective of this study was to determine the genetic mechanism of canopy wilting in soybean using a mapping population of recombinant inbred lines (RILs) derived from a cross between KS4895 and Jackson. Canopy wilting was rated in three environments using a rating scale of 0 (no wilting) to 100 (severe wilting and plant death). Transgressive segregation was observed for the RIL population with the parents expressing intermediate wilting scores. Using multiple-loci analysis, four quantitative trait loci (QTLs) on molecular linkage groups (MLGs) A2, B2, D2, and F were detected (P ≤ 0.05), which collectively accounted for 47% of the phenotypic variation of genotypic means over all three environments. An analysis of the data by state revealed that 44% of the observed phenotypic variation in the Arkansas environments could be accounted for by these QTLs. Only the QTL on MLG F was detected at North Carolina where it accounted for 16% of the phenotypic variation. These results demonstrate that the genetic mechanism controlling canopy wilting was polygenic and environmentally sensitive and provide a foundation for future research to examine the importance of canopy wilting in drought tolerance of soybean.     

Cloning and functional analysis of two <Emphasis Type="Italic">GmDeg</Emphasis> genes in soybean [<Emphasis Type="Italic">Glycine max</Emphasis> (L.) Merr.]

Although light is the ultimate substrate in photosynthesis, strong light can also be harmful and lead to photoinhibition. The DEG proteases play important roles in the degradation of misfolded and damaged proteins. In this study, two photoinhibition-related genes from soybean [Glycine max (L.) Merr.], GmDeg1 and GmDeg2, were cloned. Bioinformatics analysis indicated that these two proteases both contain a PDZ domain and are serine proteases. The expression levels of GmDeg1 and GmDeg2 increased significantly after 12 h of photooxidation treatment, indicating that GmDeg1 and GmDeg2 might play protective roles under strong light conditions. In in vitro proteolytic degradation assays, recombinant GmDeg1 and GmDeg2 demonstrated biological activities at temperatures ranging from 20°C to 60°C and at pH 5.0 to 8.0. By contrast, the proteases showed no proteolytic effect in the presence of a serine protease inhibitor. Taken together, these results provided strong evidence that GmDeg1 and GmDeg2 are serine proteases that could degrade the model substrate in vitro, indicating that they might degrade damaged D1 protein and other mis-folded proteins in vivo. Furthermore, GmDeg1 and GmDeg2 were transformed into Arabidopsis thaliana to obtain transgenic plants. Leaves from the transgenic and wild-type plants were subjected to strong light conditions in vitro, and the PSII photochemical efficiency (Fv/Fm) was measured. The Fv/Fm of the transgenic plants was significantly higher than that of the wild-type plants at most time points. These results imply that GmDeg1 and GmDeg2 would have similar functions to Arabidopsis AtDeg1, thus accelerating the recovery of PSII photochemical efficiency.     

Isolation and Functional Characterization of a SERK Gene from Soybean (<Emphasis Type="Italic">Glycine max</Emphasis> (L.) Merr.)

It is well accepted that somatic embryogenesis serves a primary role in plant regeneration. However, it is also a model system to explore the regulatory and morphogenetic events in the life of a plant. To date, a suite of genes that serve important roles in somatic embryogenesis have been isolated and identified. In the present study, a novel gene designated as GmSERK1 was isolated from soybean (Glycine max (L.) Merr). Sequence and structural analysis determined that the GmSERK1 protein, which encodes 624 amino acids, belongs to the somatic embryogenesis receptor-like kinase (SERK) gene family. GmSERK1 shared all the characteristic domains of the SERK family, including five leucine-rich repeats, one proline-rich region motif, transmembrane domain, and kinase domains. DNA gel blot analysis indicated that a single copy of the GmSERK1 gene resides in the soybean genome. The GmSERK1 tissue-specific and induced expression patterns were explored using quantitative real-time PCR. Dissimilar expression levels in various tissues under different treatments were found. In addition, transient expression experiments in onion epidermal cells indicated that the GmSERK1 protein was located on the plasma membrane. The results from this study suggested that GmSERK1, a member of the SERK gene family, exhibits a broader role in various aspects of plant development and function, in addition to its basic functions in somatic embryogenesis.     

Improved <Emphasis Type="Italic">Agrobacterium tumefaciens-</Emphasis>mediated transformation of soybean [<Emphasis Type="Italic">Glycine max</Emphasis> (L.) Merr.] following optimization of culture conditions and mechanical techniques

In the present study, Agrobacterium tumefaciens-mediated transformation of Glycine max (L.) Merr. (soybean) cv. DS-9712 using half-seed explants was optimized for eight different parameters, including seed imbibition, medium pH, infection mode (sonication and vacuum infiltration), co-cultivation conditions, concentrations of supplementary compounds, and selection. Using this improved protocol, maximum transformation of 14% and regeneration efficiencies of 45% were achieved by using explants prepared from mature seeds imbibed for 36 h, infected with A. tumefaciens strain EHA105 at an optical density (OD₆₀₀) of 0.8, suspended in pH 5.4 medium containing 0.2 mM acetosyringone and 450 mg L^?1 L-cysteine, followed by sonication for 10 s, vacuum infiltration for 2 min, and co-cultivated for 3 d on 35 mg L^?1 kanamycin-containing medium. Independent transgenic lines were confirmed to be transgenic after ß-glucuronidase histochemical assays, polymerase chain reaction, and southern hybridization analysis. The protocol developed in the present study showed high regeneration efficiency within a relatively short time of 76 d. This rapid and efficient protocol might overcome some hurdles associated with the genetic manipulation of soybean.     

<Emphasis Type="Italic">Organogenic callus</Emphasis> as the target for plant regeneration and transformation via <Emphasis Type="Italic">Agrobacterium</Emphasis> in soybean (<Emphasis Type="Italic">Glycine max</Emphasis> (L.) Merr.)

A regeneration and transformation system has been developed using organogenic calluses derived from soybean axillary nodes as the starting explants. Leaf-node or cotyledonary-node explants were prepared from 7 to 8-d-old seedlings. Callus was induced on medium containing either Murashige and Skoog (MS) salts or modified Finer and Nagasawa (FNL) salts and B5 vitamins with various concentrations of benzylamino purine (BA) and thidiazuron (TDZ). The combination of BA and TDZ had a synergistic effect on callus induction. Shoot differentiation from the callus occurred once the callus was transferred to medium containing a low concentration of BA. Subsequently, shoots were elongated on medium containing indole-3-acetic acid (IAA), zeatin riboside, and gibberellic acid (GA). Plant regeneration from callus occurred 90 ∼ 120 d after the callus was cultured on shoot induction medium. Both the primary callus and the proliferated callus were used as explants for Agrobacterium-mediated transformation. The calluses were inoculated with A. tumefaciens harboring a binary vector with the bar gene as the selectable marker gene and the gusINT gene for GUS expression. Usually 60–100% of the callus showed transient GUS expression 5 d after inoculation. Infected calluses were then selected on media amended with various concentrations of glufosinate. Transgenic soybean plants have been regenerated and established in the greenhouse. GUS expression was exhibited in various tissues and plant organs, including leaf, stem, and roots. Southern and T₁ plant segregation analysis of transgenic events showed that transgenes were integrated into the soybean genome with a copy number ranging from 1–5 copies.     

Induction of pathogenesis-related proteins during biocontrol of <Emphasis Type="Italic">Rhizoctonia solani</Emphasis> with <Emphasis Type="Italic">Pseudomonas aureofaciens</Emphasis> in soybean (<Emphasis Type="Italic">Glycine max</Emphasis> L. Merr.) plants

To investigate the biocontrol effectiveness of the antibiotic producing bacterium, Pseudomonas aureofaciens 63–28 against the phytopathogen Rhizoctonia solani AG-4 on Petri plates and in soybean roots, growth response and induction of PR-proteins were estimated after inoculation with P. aureofaciens 63–28 (P), with R. solani AG-4 (R), or with P. aureofaciens 63–28 + R. solani AG-4 (P + R). P. aureofaciens 63–28 showed strong antifungal activity against R. solani AG-4 pathogens in Petri plates. Treatment with P. aureofaciens 63–28 alone increased the emergence rate, shoot fresh weight, shoot dry weight and root fresh weight at 7 days after inoculation, when compared to R. solani AG-4; P + R treatment showed similar effects. Peroxidase (POD) and β-1,3-glucanase activity of P. aureofaciens 63–28 treated roots increased by 41.1 and 49.9%, respectively, compared to control roots. POD was 26% greater in P + R treated roots than R. solani treated roots. Two POD isozymes (59 and 27 kDa) were strongly induced in P + R treated roots. The apparent molecular weight of chitinase from treated roots, as determined through SDS-PAGE separation and comparison with standards, was about 29 kDa. Five β-1,3-glucanase isozymes (80, 70, 50, 46 and 19 kDa) were observed in all treatments. These results suggest that inoculation of soybean plants with P. aureofaciens 63–28 elevates plant growth inhibition by R. solani AG-4 and activates PR-proteins, potentially through induction of systemic resistance mechanisms.     

Genetic variability in <Emphasis Type="Italic">Bradyrhizobium japonicum</Emphasis> strains nodulating soybean [<Emphasis Type="Italic">Glycine max</Emphasis> (L.) Merrill]

Brazil has succeeded in sustaining production of soybean [Glycine max (L.) Merrill] by relying mainly on symbiotic N₂ fixation, thanks to the selection and use in inoculants of very effective strains of Bradyrhizobium japonicum and Bradyrhizobium elkanii. It is desirable that rhizobial strains used in inoculants have stable genetic and physiological traits, but experience confirms that rhizobial strains nodulating soybean often lose competitiveness in the field. In this study, soybean cultivar BR 16 was single-inoculated with four B. japonicum strains (CIAT 88, CIAT 89, CIAT 104 and CIAT 105) under aseptic conditions. Forty colonies were isolated from nodules produced by each strain. The progenitor strains, the isolates and four other commercially recommended strains were applied separately to the same cultivar under controlled greenhouse conditions. We observed significant variability in nodulation, shoot dry weight, shoot total N, nodule efficiency (total N mass over nodule mass) and BOX-PCR fingerprinting profiles between variant and progenitor strains. Some variant strains resulted in significantly larger responses in terms of shoot total N, dry weight and nodule efficiency, when compared to their progenitor strain. These results highlight the need for intermittent evaluation of stock bacterial cultures to guarantee effective symbiosis after inoculation. Most importantly, it indicates that it is possible to improve symbiotic effectiveness by screening rhizobial strains for higher N₂ fixation capacity within the natural variability that can be found within each progenitor strain.     

Genome-wide analysis of the PHB gene family in <Emphasis Type="Italic">Glycine max</Emphasis> (L.) Merr.

Prohibitins (PHBs) have one SPFH domain in common and present in species ranging from prokaryotes to eukaryotes. Although a number of researches on PHBs were performed in different plant species, a systematic analysis of the PHB family in soybean is still remains uncharacterized. In the present study, 24 putative PHB genes have been first systemically identified in soybean. According to phylogenetic analysis, these GmPHBs could be classified into four groups. Gene structures and motif patterns showed high levels of conservation within the phylogenetic subgroups. Several members of this family have undergone purifying selection based on Ka/Ks analysis on duplicated PHB genes in soybean. We performed microsynteny analysis across four legume species based on the comparisons among the specific regions contained in PHB genes. As a result, numerous microsyntenic gene pairs among soybean, Medicago, Lotus and Phaseolus were identified. Most soybean PHB genes exhibited different expression levels in various tissues and developmental stages through expression analysis using publicly available RNA-seq datasets. The 11 GmPHB genes from III_B subgroup were examined by qPCR for their expression in two soybean cultivar after infection by Phytophthora sojae. Besides three GmPHB genes previous reported by us, here other four genes also were rapidly induced by P. sojae infection in the resistant genotype, while induction was very weak in the susceptible genotype. The comprehensive overview of the PHB gene family in soybean genome will provide useful information for further functional analysis of the PHB gene family in soybean.     

Enhancing the frequency of somatic embryogenesis following <Emphasis Type="Italic">Agrobacterium</Emphasis>-mediated transformation of immature cotyledons of soybean [<Emphasis Type="Italic">Glycine max</Emphasis> (L.) Merrill.]

Summary A characteristic phenotype of highly embryogenic explants along with the location of embryogenesis- and transformation-competent cells/tissues on immature cotyledons of soybean [Glycine max (L.) Merrill.] under hygromycin selection was identified. This highly embryogenic immature cotyledon was characterized with emergence of somatic embryos and incidence of browning/necrotic tissues along the margins and collapsed tissues in the mid-region of an explant incubated upwards on the selection medium. The influences of various parameters on induction of somatic embryogenesis on immature cotyledons following Agrobacterium tumefaciens-mediated transformation and selection were investigated. Using cotyledon explants derived from immature embryos of 5–8 mm in length, a 1∶1 (v/v; bacterial cells to liquid D40 medium) concentration of bacterial suspension and 4-wk cocultivation period significantly increased the frequency of transgenic somatic embryos. Whereas, increasing the infection period of explants or subjecting explants to either wounding or acetosyringone treatments did not increase the frequency of transformation. An optimal selection regime was identified when inoculated immature cotyledons were incubated on either 10 or 25 mgl⁻¹ hygromycin for a 2-wk period, and then maintained on selection media containing 25 mgl⁻¹ hygromycin in subsequent selection periods. However, somatic embryogenesis was completely inhibited when inoculated immature cotyledons were incubated on a kanamycin selection medium. These findings clearly demonstrated that the tissue culture protocols for transformation of soybean should be established under both Agrobacterium and selection conditions.     

Fine mapping of a <Emphasis Type="Italic">Phytophthora</Emphasis>-resistance gene <Emphasis Type="Italic">RpsWY</Emphasis> in soybean (<Emphasis Type="Italic">Glycine max</Emphasis> L.) by high-throughput genome-wide sequencing

Key message

Using a combination of phenotypic screening, genetic and statistical analyses, and high-throughput genome-wide sequencing, we have finely mapped a dominant Phytophthora resistance gene in soybean cultivar Wayao.

Abstract

Phytophthora root rot (PRR) caused by Phytophthora sojae is one of the most important soil-borne diseases in many soybean-production regions in the world. Identification of resistant gene(s) and incorporating them into elite varieties are an effective way for breeding to prevent soybean from being harmed by this disease. Two soybean populations of 191 F₂ individuals and 196 F_7:8 recombinant inbred lines (RILs) were developed to map Rps gene by crossing a susceptible cultivar Huachun 2 with the resistant cultivar Wayao. Genetic analysis of the F₂ population indicated that PRR resistance in Wayao was controlled by a single dominant gene, temporarily named RpsWY, which was mapped on chromosome 3. A high-density genetic linkage bin map was constructed using 3469 recombination bins of the RILs to explore the candidate genes by the high-throughput genome-wide sequencing. The results of genotypic analysis showed that the RpsWY gene was located in bin 401 between 4466230 and 4502773 bp on chromosome 3 through line 71 and 100 of the RILs. Four predicted genes (Glyma03g04350, Glyma03g04360, Glyma03g04370, and Glyma03g04380) were found at the narrowed region of 36.5 kb in bin 401. These results suggest that the high-throughput genome-wide resequencing is an effective method to fine map PRR candidate genes.

     

Refined glufosinate selection in<Emphasis Type="Italic"> Agrobacterium</Emphasis>-mediated transformation of soybean [<Emphasis Type="Italic">Glycine max</Emphasis> (L.) Merrill]

Modern genetic analysis and manipulation of soybean (Glycine max) depend heavily on an efficient and dependable transformation process, especially in public genotypes from which expressed sequence tag (EST), bacterial artificial chromosome and microarray data have been derived. Williams 82 is the subject of EST and functional genomics analyses. However, it has not previously been transformed successfully using either somatic embryogenesis-based or cotyledonary-node transformation methods, the two predominant soybean transformation systems. An advance has recently been made in using antioxidants to enhance Agrobacterium infection of soybean. Nonetheless, an undesirable effect of using these antioxidants is the compromised recovery of transgenic soybean when combined with the use of the herbicide glufosinate as a selective agent. Therefore, we optimized both Agrobacterium infection and glufosinate selection in the presence of l-cysteine for Williams 82. We have recovered transgenic lines of this genotype with an enhanced transformation efficiency using this herbicide selection system.Abbreviations DTT Dithiothreitol - EST Expressed sequence tag - GUS -Glucuronidase Communicated by P. Ozias-Akins     

Identification of new QTLs for seed mineral,cysteine, and methionine concentrations in soybean [<Emphasis Type="Italic">Glycine max</Emphasis> (L.) Merr.]

Increased concentrations of important nutrients in edible parts of plants could result in biofortified foods. Soybean [Glycine max (L.) Merr.] is a major legume crop and an important source of certain nutrients, including protein and minerals, in human and animal diets. Understanding the underlying genetic basis of seed composition is crucial to improving seed nutrient composition. In this study we used three soybean recombinant inbred line mapping populations derived from the crosses Williams 82 × DSR-173, Williams 82 × NKS19-90 and Williams 82 × Vinton 81, and constructed a joint linkage map from these populations. Forty quantitative trait loci (QTLs) were detected for 18 traits: seed weight, seed magnesium, sulfur, calcium, manganese, potassium, iron, cobalt, nickel, copper, zinc, selenium, molybdenum, cadmium and arsenic concentrations, total nitrogen:total sulfur (N:S) ratio, cysteine and methionine concentrations. Using the joint linkage map, we detected nine QTLs that were not identified in the individual populations. We identified several candidate genes that might contribute to these traits, including transporters and genes involved in nitrogen and amino acid metabolism. Some strong QTLs had no obvious candidate genes, offering the possibility that subsequent confirmation of these QTLs may result in identification of new genes affecting seed nutrients in soybean. Seed weight and seed mineral concentrations were not highly correlated, suggesting the possibility of improving seed mineral concentrations without significant changes in seed weight. An inverse relationship between N:S ratio and most other minerals suggests the possibility of using N:S ratio as an indirect measure of seed mineral concentration in soybean breeding programs.