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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. Local adaptation contributes to plant colonization across extreme environmental gradients. Here, the authors reconstruct the colonization history of Lotus japonicus in Japan and identify extreme genetic signatures of local adaptation to a cold climate using genome resequencing and common garden experiments.

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.

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.

Aim “Super-Root” (SR) is a fast-growing root culture established in the legume forage species Lotus corniculatus that displays vigorous growth and high embryogenic capacity, uniquely allowing for continuous root cloning, direct somatic embryogenesis, and mass regeneration of plants under hormone-free culture conditions . This study’s primary aim was to verify the possibility of introducing the SR trait to another legume species as a means of enhancing root traits. Our previous research produced a F 1 -generation hybrid between the colchicine-doubled form of the diploid Lotus japonicus ‘Miyakojima’ MG-20 and SR-derived Lotus corniculatus . The current study’s focus was to evaluate the root phenotype of the F 2 -generation to confirm the introduction of SR characteristics to Lotus japonicus . Methods We assessed 242 rooted F 2 -hybrid progeny using cluster analysis, concentrating on four morphological root traits: root fresh weight, total root length, maximum root length, and root diameter. Principal Component Analysis (PCA) was used to determine the correlations among eight traits of the F 2 -progeny of the WinRhizo root morphological measurement data and to identify what traits contributed most to their root variation. Results The 242-hybrid progeny and both parents were grouped into eight different clusters using a similarity phenogram. One cluster consisted of lines 36, 82, 86 and 184 that considerably exceeded the RFW, TRL, and MRL values of the L. japonicus and SR parents. Conclusion The results confirmed the introduction of SR traits to the F 2 -hybrid progeny and identified potential candidates for breeding and gene isolation that will be conducted to expand the scope of this research.

Commensal bacteria affect host health by producing various metabolites from dietary carbohydrates via bacterial glycometabolism; however, the underlying mechanism of action remains unclear. Here, we identified Streptococcus salivarius as a unique anti-obesity commensal bacterium. We found that S. salivarius may prevent host obesity caused by excess sucrose intake via the exopolysaccharide (EPS) –short-chain fatty acid (SCFA) –carbohydrate metabolic axis in male mice. Healthy human donor-derived S. salivarius produced high EPS levels from sucrose but not from other sugars. S. salivarius abundance was significantly decreased in human donors with obesity compared with that in healthy donors, and the EPS–SCFA bacterial carbohydrate metabolic process was attenuated. Our findings reveal an important mechanism by which host–commensal interactions in glycometabolism affect energy regulation, suggesting an approach for preventing lifestyle-related diseases via prebiotics and probiotics by targeting bacteria and EPS metabolites. While diet is essential for daily nutrient acquisition, excessive intake of sugar-rich foods drives obesity and related health issues like diabetes. Here, the authors show that commensal bacterium S. salivarius curbs obesity by transforming dietary sugars into beneficial compounds.

The rate of gas exchange in plants is regulated mainly by stomatal size and density. Generally, higher densities of smaller stomata are advantageous for gas exchange; however, it is unclear what the effect of an extraordinary change in stomatal size might have on a plant's gas-exchange capacity. We investigated the stomatal responses to CO₂ concentration changes among 374 Arabidopsis (Arabidopsis thaliana) ecotypes and discovered that Mechtshausen (Me-0), a natural tetraploid ecotype, has significantly larger stomata and can achieve a high stomatal conductance. We surmised that the cause of the increased stomatal conductance is tetraploidization; however, the stomatal conductance of another tetraploid accession, tetraploid Columbia (Col), was not as high as that in Me-0. One difference between these two accessions was the size of their stomatal apertures. Analyses of abscisic acid sensitivity, ion balance, and gene expression profiles suggested that physiological or genetic factors restrict the stomatal opening in tetraploid Col but not in Me-0. Our results show that Me-0 overcomes the handicap of stomatal opening that is typical for tetraploids and achieves higher stomatal conductance compared with the closely related tetraploid Col on account of larger stomatal apertures. This study provides evidence for whether larger stomatal size in tetraploids of higher plants can improve stomatal conductance.

Wild soybean (Glycine soja) is a valuable genetic resource for soybean improvement. Seed composition profiles provide beneficial information for the effective conservation and utilization of wild soybeans. Therefore, this study aimed to assess the variation in free amino acid abundance in the seeds of wild soybean germplasm collected in Japan. The free amino acid content in the seeds from 316 accessions of wild soybean ranged from 0.965 to 5.987 mg/g seed dry weight (DW), representing a 6.2-fold difference. Three amino acids had the highest coefficient of variation (CV): asparagine (1.15), histidine (0.95) and glutamine (0.94). Arginine (0.775 mg/g DW) was the predominant amino acid in wild soybean seeds, whereas the least abundant seed amino acid was glutamine (0.008 mg/g DW). A correlation network revealed significant positive relationships among most amino acids. Wild soybean seeds from different regions of origin had significantly different levels of several amino acids. In addition, a significant correlation between latitude and longitude of the collection sites and the total free amino acid content of seeds was observed. Our study reports diverse phenotypic data on the free amino acid content in seeds of wild soybean resources collected from throughout Japan. This information will be useful in conservation programmes for Japanese wild soybean and for the selection of accessions with favourable characteristics in future legume crop improvement efforts.

Light is critical for supplying carbon to the energetically expensive, nitrogen-fixing symbiosis between legumes and rhizobia. Here, we show that phytochrome B (phyB) is part of the monitoring system to detect suboptimal light conditions, which normally suppress Lotus japonicus nodule development after Mesorhizobium loti inoculation. We found that the number of nodules produced by L. japonicus phyB mutants is significantly reduced compared with the number produced of WT Miyakojima MG20. To explore causes other than photoassimilate production, the possibility that local control by the root genotype occurred was investigated by grafting experiments. The results showed that the shoot and not the root genotype is responsible for root nodule formation. To explore systemic control mechanisms exclusive of photoassimilation, we moved WT MG20 plants from white light to conditions that differed in their ratios of low or high red/far red (R/FR) light. In low R/FR light, the number of MG20 root nodules dramatically decreased compared with plants grown in high R/FR, although photoassimilate content was higher for plants grown under low R/FR. Also, the expression of jasmonic acid (JA) -responsive genes decreased in both low R/FR light-grown WT and white light-grown phyB mutant plants, and it correlated with decreased jasmonoyl-isoleucine content in the phyB mutant. Moreover, both infection thread formation and root nodule formation were positively influenced by JA treatment of WT plants grown in low R/FR light and white lightgrown phyB mutants. Together, these results indicate that root nodule formation is phötomorphogenetically controlled by sensing the R/FR ratio through JA signaling.

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.

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.