Assessing genetic diversity and geographical differentiation in a global collection of wild soybean (Glycine soja Sieb. et Zucc.) and assigning a mini-core collection.

Wild soybean (Glycine soja), the ancestor of the cultivated soybean (G. max), is a crucial resource for capturing the genetic diversity of soybean species. In this study, we used a set of 78 genome-wide microsatellite markers to analyse the genetic diversity and geographic differentiation patterns in a global collection of 2,050 G. soja accessions and a mini-core collection of G. max stored in two public seed banks. We observed a notable reduction in the genetic diversity of G. max compared with G. soja and identified a close phylogenetic relationship between G. max and a G. soja subpopulation located in central China. Furthermore, we revealed substantial genetic divergence between northern and southern subpopulations, accompanied by diminished genetic diversity in the northern subpopulations. Two clusters were discovered among the accessions from north-eastern China-one genetically close to those from South Korea and Southern Japan, and another close to those from Amur Oblast, Russia. Finally, 192 accessions were assigned to a mini-core collection of G. soja, retaining 73.8% of the alleles detected in the entire collection. This mini-core collection is accessible to those who need it, facilitating efficient evaluation and utilization of G. soja genetic resources in soybean breeding initiatives.

CRISPR/Cas9-mediated knockout of NYC1 gene enhances chlorophyll retention and reduces tillering in Zoysia matrella (L.) Merrill.

KEY MESSAGE: Genome editing by CRISPR/Cas9 can be applied to Z. matrella 'Wakaba', and knockout mutants of ZmNYC1 gene exhibited stay-green phenotype and reduced tillering. Zoysia matrella is a widely used C4 warm-season turfgrass for landscaping, golf courses, and sports fields. Here, we used the CRISPR/Cas9 system to target the Non-Yellow Coloring1 (ZmNYC1) gene in the highly heterozygous allotetraploid Z. matrella 'Wakaba', aiming to generate a novel stay-green variety. Of 441 Agrobacterium-infected calli, 22 (5.0%) were transformed, and 14 of these (63.6%) showed targeted mutations through cleaved amplified polymorphic sequences analysis. Sequencing analysis revealed mutations mostly consisting of 1 or 2 bp indels, occurring 2 to 4 bp upstream of the PAM sequence. Regenerated plants exhibited five ZmNYC1 target locus genotypes, including homozygous mutants with a complete knockout of all four alleles in the T0 generation. Under dark treatment, ZmNYC1-mutated plants displayed suppressed chlorophyll b (Chl b) degradation, leading to higher chlorophyll content and Chl b, with a lower chlorophyll a/chlorophyll b ratio compared to the wild type (WT). However, the ZmNYC1 mutation also inhibited plant growth in homozygous mutant genotypes, exhibiting reduced tillering compared to WT. Additionally, during winter simulation, mutant with a complete knockout retained greenness longer than the WT. This is the first successful use of CRISPR/Cas9 genome editing in zoysiagrass. The mutants of the ZmNYC1 gene would serve as valuable breeding material for developing improved zoysiagrass varieties that can maintain their green color for longer periods, even during winter dormancy.

Construction of prediction models for growth traits of soybean cultivars based on phenotyping in diverse genotype and environment combinations.

As soybean cultivars are adapted to a relatively narrow range of latitude, the effects of climate changes are estimated to be severe. To address this issue, it is important to improve our understanding of the effects of climate change by applying the simulation model including both genetic and environmental factors with their interactions (G×E). To achieve this goal, we conducted the field experiments for soybean core collections using multiple sowing times in multi-latitudinal fields. Sowing time shifts altered the flowering time (FT) and growth phenotypes, and resulted in increasing the combinations of genotypes and environments. Genome-wide association studies for the obtained phenotypes revealed the effects of field and sowing time to the significance of detected alleles, indicating the presence of G×E. By using accumulated phenotypic and environmental data in 2018 and 2019, we constructed multiple regression models for FT and growth pattern. Applicability of the constructed models was evaluated by the field experiments in 2020 including a novel field, and high correlation between the predicted and measured values was observed, suggesting the robustness of the models. The models presented here would allow us to predict the phenotype of the core collections in a given environment.

Tissue Culture and Somatic Embryogenesis in Warm-Season Grasses-Current Status and Its Applications: A Review.

Warm-season grasses are C4 plants and have a high capacity for biomass productivity. These grasses are utilized in many agricultural production systems with their greatest value as feeds for livestock, bioethanol, and turf. However, many important warm-season perennial grasses multiply either by vegetative propagation or form their seeds by an asexual mode of reproduction called apomixis. Therefore, the improvement of these grasses by conventional breeding is difficult and is dependent on the availability of natural genetic variation and its manipulation through breeding and selection. Recent studies have indicated that plant tissue culture system through somatic embryogenesis complements and could further develop conventional breeding programs by micropropagation, somaclonal variation, somatic hybridization, genetic transformation, and genome editing. This review summarizes the tissue culture and somatic embryogenesis in warm-season grasses and focus on current status and above applications including the author's progress.

Rhamnogalacturonan-I as a nematode chemoattractant from Lotus corniculatus L. super-growing root culture.

Introduction: The soil houses a tremendous amount of micro-organisms, many of which are plant parasites and pathogens by feeding off plant roots for sustenance. Such root pathogens and parasites often rely on plant-secreted signaling molecules in the rhizosphere as host guidance cues. Here we describe the isolation and characterization of a chemoattractant of plant-parasitic root-knot nematodes (Meloidogyne incognita, RKN). Methods: The Super-growing Root (SR) culture, consisting of excised roots from the legume species Lotus corniculatus L., was found to strongly attract infective RKN juveniles and actively secrete chemoattractants into the liquid culture media. The chemo-attractant in the culture media supernatant was purified using hydrophobicity and anion exchange chromatography, and found to be enriched in carbohydrates. Results: Monosaccharide analyses suggest the chemo-attractant contains a wide array of sugars, but is enriched in arabinose, galactose and galacturonic acid. This purified chemoattractant was shown to contain pectin, specifically anti-rhamnogalacturonan-I and anti-arabinogalactan protein epitopes but not anti-homogalacturonan epitopes. More importantly, the arabinose and galactose sidechain groups were found to be essential for RKN-attracting activities. This chemo-attractant appears to be specific to M. incognita, as it wasn't effective in attracting other Meloidogyne species nor Caenorhabditis elegans. Discussion: This is the first report to identify the nematode attractant purified from root exudate of L corniculatus L. Our findings re-enforce pectic carbohydrates as important chemicals mediating micro-organism chemotaxis in the soil, and also highlight the unexpected utilities of the SR culture system in root pathogen research.

A review of okara (soybean curd residue) utilization as animal feed: Nutritive value and animal performance aspects.

Year by year, huge quantities of by-products are generated during the manufacturing process of soybean-based products. Okara is one of the by-products, and it is an insoluble portion of the soybean. It consists of high moisture (8.4-22.9%); on dry matter basis, it contains high metabolizable energy (9.0-14.2 MJ/kg) and other components that include crude protein (20.9-39.1%), crude fiber (12.2-61.3%), crude fat (4.9-21.5%), and ash (3.4-5.3%). Fermentation of okara improves its nutritional quality and reduces its anti-nutrient contents. Due to animals' palatability, okara can be used to replace the soybean meal/concentrate feed partially or completely in ruminant's diet and partially in nonruminant's diet. Okara feeding does not depress the intake, digestibility, growth, milk production, blood metabolic profiles, and meat quality of animals. However, this by-product decays quickly due to its high moisture content, and its heavy weight and sticky nature make it difficult to process and expensive to dry using conventional methods. This paper thoroughly summarizes the utilization of okara as animal feed in the cause of developing a general guideline with favorable levels of inclusion in the diets of animals for its exploitation and valorization. This review will encourage further research to develop eco-friendly and value added feed for animals.

Mesorhizobium sp. J8 can establish symbiosis with Glycyrrhiza uralensis, increasing glycyrrhizin production.

Licorice (Glycyrrhiza uralensis) is a medicinal plant that contains glycyrrhizin (GL), which has various pharmacological activities. Because licorice is a legume, it can establish a symbiotic relationship with nitrogen-fixing rhizobial bacteria. However, the effect of this symbiosis on GL production is unknown. Rhizobia were isolated from root nodules of Glycyrrhiza glabra, and a rhizobium that can form root nodules in G. uralensis was selected. Whole-genome analysis revealed a single circular chromosome of 6.7 Mbp. This rhizobium was classified as Mesorhizobium by phylogenetic analysis and was designated Mesorhizobium sp. J8. When G. uralensis plants grown from cuttings were inoculated with J8, root nodules formed. Shoot biomass and SPAD values of inoculated plants were significantly higher than those of uninoculated controls, and the GL content of the roots was 3.2 times that of controls. Because uninoculated plants from cuttings showed slight nodule formation, we grew plants from seeds in plant boxes filled with sterilized vermiculite, inoculated half of the seedlings with J8, and grew them with or without 100 µM KNO3. The SPAD values of inoculated plants were significantly higher than those of uninoculated plants. Furthermore, the expression level of the CYP88D6 gene, which is a marker of GL synthesis, was 2.5 times higher than in inoculated plants. These results indicate that rhizobial symbiosis promotes both biomass and GL production in G. uralensis.

Quantitative analysis of seven plant hormones in Lotus japonicus using standard addition method.

Plant hormones have been identified to be versatile signaling molecules essential for plant growth, development, and stress response. Their content levels vary depending on the species, and they also change in response to any external stimuli. Thus, simultaneous quantification of multiple plant hormones is required to understand plant physiology. Sensitive and quantitative analysis using liquid chromatography-linked mass spectrometry (LC-MS/MS) has been used in detecting plant hormones; however, quantification without stable isotopes is yet to be established. In this study, we quantified seven representative plant hormones of Lotus japonicus, which is a model legume for standard addition method. Accurate masses for monoisotopic ions of seven phytohormones were determined for high-resolution mass spectrometry (HR-MS). Selected ion monitoring (SIM) mode based on accurate masses was used in detecting phytohormones in the roots, stems, and leaves. Evaluation of matrix effects showed ion suppression ranging from 10.2% to 87.3%. Both stable isotope dilution and standard addition methods were able to detect plant hormones in the roots, stems, and leaves, with no significant differences in using both approaches and thus a standard addition method can be used to quantify phytohormones in L. japonicus. The method will be effective, especially when stable isotopes are not available to correct for matrix effects.

Varietal differences in flavonoid and antioxidant activity in Japanese soybean accessions.

Soybean seeds contain many antioxidants, including flavonoids and other phytochemicals. Isoflavone is a phytoestrogen that mimics estrogenic effects on target tissues and also exerts antioxidant activity by sequestering free radicals. Despite many cultivars developed to date, varietal differences in flavonoid content and antioxidant activity in Japanese soybean accessions remain less well characterized. Here, we evaluated the seed content of isoflavones, total flavonoids, and total phenolics in 26 soybean accessions. Next, the antioxidant activity of each accession was examined using antioxidant responsive element (ARE) linked to a luciferase reporter in human HepG2 stable cells. The relative ARE luciferase activity rate of all soybean accessions varied up to 4-fold which ranged from 1.00 to 4.02; and 22 accessions exhibited significant antioxidant activities. Correlation analysis indicated that the level of total isoflavone moderately correlated with antioxidant activity.

Whole-genome sequence diversity and association analysis of 198 soybean accessions in mini-core collections.

We performed whole-genome Illumina resequencing of 198 accessions to examine the genetic diversity and facilitate the use of soybean genetic resources and identified 10 million single nucleotide polymorphisms and 2.8 million small indels. Furthermore, PacBio resequencing of 10 accessions was performed, and a total of 2,033 structure variants were identified. Genetic diversity and structure analysis congregated the 198 accessions into three subgroups (Primitive, World, and Japan) and showed the possibility of a long and relatively isolated history of cultivated soybean in Japan. Additionally, the skewed regional distribution of variants in the genome, such as higher structural variations on the R gene clusters in the Japan group, suggested the possibility of selective sweeps during domestication or breeding. A genome-wide association study identified both known and novel causal variants on the genes controlling the flowering period. Novel candidate causal variants were also found on genes related to the seed coat colour by aligning together with Illumina and PacBio reads. The genomic sequences and variants obtained in this study have immense potential to provide information for soybean breeding and genetic studies that may uncover novel alleles or genes involved in agronomically important traits.

Replacement of soybean meal with levels of inclusion of soya waste in the diet of growing goats.

An experiment was conducted to investigate the effect of replacing soybean meal with soya waste at different levels on intake, digestibility and growth in goats. Eighteen male goat kids with initial body weight (BW) of 13.0 kg were distributed equally to three dietary groups. They were fed Napier grass (Pennisetum purpureum) and concentrate mixture, and each goat was assigned to an individual pen. Soybean meal in the concentrate mixture was replaced with soya waste at 0% (T1), 50% (T2) and 100% (T3) levels in respective dietary groups. These diets were isocaloric and isonitrogenous. Results showed that animals fed T3 diet exhibited higher Napier grass intake than those fed T1 or T2 diet. There was no influence on total intakes of dry matter (DM), organic matter (OM), crude protein (CP), metabolic BW, per cent BW and metabolisable energy by the dietary groups. However, there was an increasing trend on intake and digestibility of neutral detergent fibre (NDF) with increasing levels of soya waste in the diets. Animals fed T3 diet showed higher intake and digestibility of NDF than those fed T1 diet. There was no influence of the dietary groups on digestibilities of DM, OM and CP. Similarly, there was no effect of them on the final BW, total BW gain, daily BW gain, feed conversion ratio and feed cost. Soya waste can replace 100% soybean meal in diets for growing goats, because no change was observed in nutrient intake, digestibility and growth performance; inclusion of soya waste enhanced the intake and digestibility of NDF.

Extreme genetic signatures of local adaptation during Lotus japonicus colonization of Japan.

Colonization of new habitats is expected to require genetic adaptations to overcome environmental challenges. Here, we use full genome re-sequencing and extensive common garden experiments to investigate demographic and selective processes associated with colonization of Japan by Lotus japonicus over the past ~20,000 years. Based on patterns of genomic variation, we infer the details of the colonization process where L. japonicus gradually spread from subtropical conditions to much colder climates in northern Japan. We identify genomic regions with extreme genetic differentiation between northern and southern subpopulations and perform population structure-corrected association mapping of phenotypic traits measured in a common garden. Comparing the results of these analyses, we find that signatures of extreme subpopulation differentiation overlap strongly with phenotype association signals for overwintering and flowering time traits. Our results provide evidence that these traits were direct targets of selection during colonization and point to associated candidate genes.

Highly Efficient and Selective Oxidation of Ethanol to Acetaldehyde by a Hybrid Photocatalyst Consisting of SnO2 Nanorod and Rutile TiO2 with Heteroepitaxial Junction.

Single-crystal SnO2 nanorods were grown on rutile TiO2 with a heteroepitaxial relation of SnO2 {001}/TiO2 {001} (SnO2 -NR#TiO2 ) by a hydrothermal reaction. Resulting compressive lattice strain in the SnO2 -NR near the interface induces a continuous increase in the a-axis length extending over 60 nm to relax towards the [001] direction from the root to the tip. UV-light irradiation of the robust SnO2 -NR#TiO2 stably progresses the selective oxidation of ethanol to acetaldehyde with an external quantum yield of 25.6 % at excitation wavelength (λex )=365 nm under ambient temperature and pressure. Spectroscopic analyses and density functional theory simulation results suggested that the extremely high photocatalytic activity stems from the smooth interfacial electron transfer from TiO2 to SnO2 -NR through the high-quality junction and subsequent efficient charge separation due to the lattice strain-induced unidirectional potential gradient of the conduction band minimum in the SnO2 -NR.

Asparaginyl-tRNA synthetase gene (SYNC1) characterized by Lotus corniculatus FOX-superroot lines has effects on plant morphology and amino acid contents of seed in soybean.

The application of useful genes from model plants to crops is an important step to verify its agricultural usefulness. SYNC1, an asparaginyl-tRNA synthetase gene, was previously identified through the Full-length cDNA Over-eXpressor gene (FOX gene-hunting system) of Arabidopsis cDNA by using super-growing root (SR) culture of Lotus corniculatus, and was suggested to have a potential in increasing some amino acid contents and plant biomass. To identify the functionality of SYNC1 gene in a typical legume crop soybean, the effects of its overexpression in transgenic plants to agricultural traits and free amino acid contents were evaluated. The transgenic soybean plants were produced from infected half-seed explants of 1 day old seedlings with the suspension of Agrobacterium tumefaciens harboring expression vector pB7WG2D-SYNC1. The transgenic plants that overexpressed SYNC1 gene had increased asparagine and lysine contents in matured seeds, and increased aspartate, lysine, alanine and histidine contents in germinated seeds. The changes in those free amino acid contents affected plant morphology and led to significant increase in plant length, number of branches and number of branch nodes as yield components of soybean. The transgenic plants also showed a tendency of higher number of pods, seeds and total seed weight per plant. These results showed that the overexpression of SYNC1 gene contributes on the increase of plant free amino acid contents and biomass, and this approach is expected to be applicable in other legumes, grain and forage crops.

Longitudinal Optical Phonons Modified by Organic Molecular Cation Motions in Organic-Inorganic Hybrid Perovskites.

We performed terahertz time-domain spectroscopy for methylammonium (MA) lead halide perovskite single crystals and characterized the longitudinal optical (LO) phonons directly. We found that the effective LO phonon wave number does not change in the wide temperature range between 10 and 300 K. However, the coupling between MA cation modes and the LO phonon mode derived from lead halide cages induces a mode splitting at low temperatures and a damping of the LO phonon mode at high temperatures. These results influence the interpretation of electron-LO phonon interactions in perovskite semiconductors, as well as the interpretations of mobility, carrier diffusion, and polaron formation.

Lotus japonicus Genetic, Mutant, and Germplasm Resources.

A quarter of a century has passed since Lotus japonicus was proposed as a model legume because of its suitability for molecular genetic studies. Since then, a comprehensive set of genetic resources and tools has been developed, including recombinant inbred lines, a collection of wild accessions, published mutant lines, a large collection of mutant lines tagged with LORE1 insertions, cDNA clones with expressed sequence tag (EST) information, genomic clones with end-sequence information, and a reference genome sequence. Resource centers in Japan and Denmark ensure easy access to data and materials, and the resources have greatly facilitated L. japonicus research, thereby contributing to the molecular understanding of characteristic legume features such as endosymbiosis. Here, we provide detailed instructions for L. japonicus cultivation and describe how to order materials and access data using the resource center websites. The comprehensive overview presented here will make L. japonicus more easily accessible as a model system, especially for research groups new to L. japonicus research. © 2018 by John Wiley & Sons, Inc.

Red-Light-Driven Water Splitting by Au(Core)-CdS(Shell) Half-Cut Nanoegg with Heteroepitaxial Junction.

A key material for artificial photosynthesis including water splitting is heteronanostructured (HNS) photocatalysts. The photocatalytic activity depends on the geometry and dimension, and the quality of junctions between the components. Here we present a half-cut Au(core)-CdS(shell) (HC-Au@CdS) nanoegg as a new HNS plasmonic photocatalyst for water splitting. UV-light irradiation of Au nanoparticle (NP)-loaded ZnO (Au/ZnO) at 50 °C induces the selective deposition of hexagonal CdS on the Au surface of Au/ZnO with an epitaxial (EPI) relation of CdS{0001}/Au{111}. The subsequent selective dissolution of the ZnO support at room temperature yields HC-Au@CdS with the Au NP size and EPI junction (#) retained. Red-light irradiation (λex = 640 nm) of HC-Au@#CdS gives rise to continuous stoichiometric water splitting with an unprecedentedly high external quantum yield of 0.24%.

In Situ Shape Change of Au Nanoparticles on TiO2 by CdS Photodeposition: Its Near-Field Enhancement Effect on Photoinduced Electron Injection from CdS to TiO2.

Hemisphere-like gold nanoparticles (NPs) were loaded on TiO2 (Au/TiO2) by the deposition-precipitation method. Subsequent photodeposition of CdS on the Au surface of Au/TiO2 at 50 °C yields Au(core)-CdS(shell) hybrid quantum dots with a heteroepitaxial (HEPI) junction on TiO2 (Au@#CdS/TiO2), whereas nonHEPI Au@CdS/TiO2 was formed by CdS photodeposition at 25 °C. In the HEPI system, the shape of the Au core changes to an angular shape, whereas it remains in a hemisphere-like shape in the nonHEPI system. The hot photodeposition technique was applied to the Au NP-loaded mesoporous TiO2 nanocrystalline film (Au/mp-TiO2). Using Au@CdS/mp-TiO2 and Au@#CdS/mp-TiO2 as the photoanodes, two-electrode quantum dot-sensitized photoelectrochemical cells were fabricated for hydrogen (H2) generation from water, and the performances of the cells were evaluated under illumination of simulated sunlight. In the photocurrent and the rate of H2 evolution, the Au@#CdS/mp-TiO2 photoanode cell surpasses the CdS/mp-TiO2 and Au@CdS/mp-TiO2 ones. Three-dimensional finite-difference time-domain calculations for the model systems indicated that the angular shape Au core generates an intense electric field at the corners and edges, extending the electric field distribution over the Au core-CdS shell interface. The striking shape effect on the cell performances can originate from the promotion of the CdS excitation and charge separation due to the near-field enhancement by the deformed Au core.

Short-term grazing behavior of cattle under indoor housing for a new-bred tetraploid ruzigrass (Brachiaria ruziziensis Germain et Everard).

OBJECTIVE: The preference evaluation of cattle is an important factor for estimation and improvement of the grazing amounts of newly introduced or bred grasses or cultivars in barn. This study was performed to assess the grazing behavior (the amount of grazing and/or the grazing speed) of cattle as indirect method using newly bred Brachiaria ruziziensis tetraploid strain 'OKI-1'(BR) hay as treatment group and Cloris gayana 'Callide' (CG) hay as control group. It also compared the feasibility of using behavioral differences between two groups as one criteria for evaluating preference by Japanese black cattle in barn. METHODS: Three experiments were carried out using 12 growing Japanese Black cattle including 6 males and 6 females. In each experiment, the four Japanese Black cattle (2 males and 2 females) were placed in separated stall and allowed to graze BR and CG in manger that was separated into two portions for about 30 min. The position and behavior of the cattle were recorded, and weighed the residual of each gay at 15 and 30 minutes after experiment start. RESULTS: The BR was superior to CG in chemical composition such as protein, fibers and non-fibrous carbohydrate. The cattle, over all, tended to prefer BR over CG in the first half 15 minutes in terms of the time spent and amount of grazing. Additionally, growing cattle exhibited neophilia for BR bred newly. CONCLUSION: These findings indicated the current approach could be applied for one of criteria to evaluate the preference of hay by Japanese black cattle under indoor housing environment.

Impact of Chemical Doping on Optical Responses in Bismuth-Doped CH3NH3PbBr3 Single Crystals: Carrier Lifetime and Photon Recycling.

We studied the optical responses of organic-inorganic halide perovskite CH3NH3PbBr3 single crystals doped with heterovalent Bi3+ ions (electron densities up to 2.3 × 1012 cm-3). The Bi doping causes no significant changes in the band gap energy but leads to an enhanced Urbach tail and photoluminescence blue shift. On the basis of the time-resolved photoluminescence measurements, we attribute the PL response to a shorter carrier lifetime induced by Bi doping, which results in a reduced photon recycling effect (i.e., the repeated emission and reabsorption of photons inside the crystal). We discuss the physical relation between Bi concentration and the optical and electric properties of Bi-doped CH3NH3PbBr3 and reveal the unique nature of the Bi3+ ion as a dopant in halide perovskites.