A Case Study from the Overexpression of OsTZF5, Encoding a CCCH Tandem Zinc Finger Protein, in Rice Plants Across Nineteen Yield Trials

BACKGROUND

Development of transgenic rice overexpressing transcription factors involved in drought response has been previously reported to confer drought tolerance and therefore represents a means of crop improvement. We transformed lowland rice IR64 with OsTZF5, encoding a CCCH-tandem zinc finger protein, under the control of the rice LIP9 stress-inducible promoter and compared the drought response of transgenic lines and nulls to IR64 in successive screenhouse paddy and field trials up to the T6 generation.

RESULTS

Compared to the well-watered conditions, the level of drought stress across experiments varied from a minimum of - 25 to - 75 kPa at a soil depth of 30 cm which reduced biomass by 30-55% and grain yield by 1-92%, presenting a range of drought severities. OsTZF5 transgenic lines showed high yield advantage under drought over IR64 in early generations, which was related to shorter time to flowering, lower shoot biomass and higher harvest index. However, the increases in values for yield and related traits in the transgenics became smaller over successive generations despite continued detection of drought-induced transgene expression as conferred by the LIP9 promoter. The decreased advantage of the transgenics over generations tended to coincide with increased levels of homozygosity. Background cleaning of the transgenic lines as well as introgression of the transgene into an IR64 line containing major-effect drought yield QTLs, which were evaluated starting at the BC3F1 and BC2F3 generation, respectively, did not result in consistently increased yield under drought as compared to the respective checks.

CONCLUSIONS

Although we cannot conclusively explain the genetic factors behind the loss of yield advantage of the transgenics under drought across generations, our results help in distinguishing among potential drought tolerance mechanisms related to effectiveness of the transgenics, since early flowering and harvest index most closely reflected the levels of yield advantage in the transgenics across generations while reduced biomass did not.

Relationship of dietary intake between children aged 12-59 months and their mothers in rural Kenya: a cross-sectional study in two seasons

OBJECTIVE

The aim of the study was to investigate the quantitative association between the dietary intakes of children and their caregivers.

METHOD

In this cross-sectional study, a non-consecutive 2-day 24-h dietary recall was conducted in two seasons. Participants comprised 142 pairs of 12-59-month-old children and their female caregivers from rural areas of Kenya. Energy and micronutrient adequacy, food group intakes and food allocation were assessed. Differences and correlations between caregiver and child diets were examined, and multiple regression analysis was used to investigate the relationship between the children's and caregivers' dietary intakes.

RESULTS

The child's diet was significantly lower in energy and higher in micronutrient adequacy than was the caregiver's diet (p < 0.001). Specifically, the child's diet contained more fruits, dairy products, sugar and confectionaries per 4184 kj. Children were allocated relatively more dishes containing nutrient-rich foods than staple foods. The correlation coefficients between the dietary intake of caregivers and children were stronger among 24-59-month-old children. After controlling with covariates, caregiver energy intake was significantly associated with child energy intake (standardised beta [β] = 0.512, p < 0.001), and caregiver micronutrient adequacy was associated with child micronutrient adequacy (β = 0.679 and β = 0.262 after energy adjustment, p < 0.001).

CONCLUSIONS

The dietary intakes of caregivers and children were closely related. The children had a more nutrient-rich diet compared to that of their caregivers. Differences in food group intakes and food allocation may contribute to the higher nutrient adequacy of children. There is a need to improve the diet of caregivers, which would contribute to improving the diet of children.

Urinary Biomarkers in Screening for the Usual Intake of Fruit and Vegetables, and Sodium, Potassium, and the Sodium-to-Potassium Ratio: Required Number and Accuracy of Measurements

Because of within-individual variation, surveys to estimate an individual's usual food intake must be conducted over many days, in general. Here, using non-invasive biomarkers, we examined the number of measurements required to screen for the usual intake of fruit and vegetables, in addition to sodium, potassium, and the sodium-to-potassium (Na/K) ratio. Participants were 202 subjects aged 40-74 years from five areas of Japan who completed weighed food records (WFR) and five 24-hour urinary collections (24-h UCs) between 2012 and 2013. The number of 24-h UCs required to screen for intake that deviated from guidelines estimated by the WFR and their accuracies were assessed by the area under the curve (AUC) in a receiver-operating characteristics (ROC) analysis. The single urinary excretion of sodium, potassium, and the Na/K ratio showed moderate performance (AUC value: >0.7) in discriminating deviations from their criteria by respective intake based on the WFR. Urinary potassium excretion also showed moderate performance (AUC value: >0.7) in estimating the intake of vegetables but could not be used to estimate fruit intake even after five collections. The non-invasive measurement of biomarkers in a single 24-h UC showed moderate performance in screening the usual intake of vegetables, as measured based on the 12-day WFR, as well as of sodium, potassium, and the Na/K ratio.

Novel Soybean Variety Lacking Raffinose Synthase 2 Activity

Variation in the raffinose family oligosaccharide (RFO) content in soybean is advantageous for livestock farming and health science. In this study, a soybean variety (GmJMC172) with a significantly low stachyose content in its seeds was identified in the NARO Genebank core collection. The results of the single-nucleotide polymorphism (SNP) analysis suggested that this phenomenon was related to a single-base deletion, inducing a frameshift mutation in raffinose synthase 2 (RS2), rather than the polymorphisms in the RS3, RS4, and stachyose synthase (STS) sequences. Differences in the enzymatic properties between the native RS2 and truncated RS2 were examined by using a three-dimensional model predicted using Alphafold2. In addition to revealing the missing active pocket in truncated RS2, the modeled structure explained the catalytic role of W331* and suggested a sufficient space to bind both sucrose and raffinose in the ligand-binding pocket. The soybean line, with seeds available from the NARO Genebank, could serve as breeding materials for manipulating the RFO content.

LsMybW-encoding R2R3-MYB transcription factor is responsible for a shift from black to white in lettuce seed

KEY MESSAGE

We identified LsMybW as the allele responsible for the shift in color from black to white seeds in wild ancestors of lettuce to modern cultivars. Successfully selected white seeds are a key agronomic trait for lettuce cultivation and breeding; however, the mechanism underlying the shift from black-in its wild ancestor-to white seeds remains uncertain. We aimed to identify the gene/s responsible for white seed trait in lettuce. White seeds accumulated less proanthocyanidins than black seeds, similar to the phenotype observed in Arabidopsis TT2 mutants. Genetic mapping of a candidate gene was performed with double-digest RAD sequencing using an F2 population derived from a cross between "ShinanoPower" (white) and "Escort" (black). The white seed trait was controlled by a single recessive locus (48.055-50.197 Mbp) in linkage group 7. Using five PCR-based markers and numerous cultivars, eight candidate genes were mapped in the locus. Only the LG7_v8_49.251Mbp_HinfI marker, employing a single-nucleotide mutation in the stop codon of Lsat_1_v5_gn_7_35020.1, was completely linked to seed color phenotype. In addition, the coding region sequences for other candidate genes were identical in the resequence analysis of "ShinanoPower" and "Escort." Therefore, we proposed Lsat_1_v5_gn_7_35020.1 as the candidate gene and designated it as LsMybW (Lactuca sativa Myb White seeds), an ortholog encoding the R2R3-MYB transcription factor in Arabidopsis. When we validated the role of LsMybW through genome editing, LsMybW knockout mutants harboring an early termination codon showed a change in seed color from black to white. Therefore, LsMybW was the allele responsible for the shift in seed color. The development of a robust marker for marker-assisted selection and identification of the gene responsible for white seeds have implications for future breeding technology and physiological analysis.

Variation among individual beef cattle in methane-to-carbon dioxide ratio measured under on-farm conditions using the sniffer method

This study proposed a method for measuring the methane (CH4 )/carbon dioxide (CO2 ) ratio from individual beef cattle under on-farm conditions and estimated the variance components of the CH4 /CO2 ratio. Gas measurements were conducted using 166 Japanese Black cattle group-housed in pens equipped with individual feed bins. The gas containing the animal's breath was measured individually after concentrate feeding by covering the feed bin with a sheet with sampling inlets. Measurements were performed six times (three consecutive days, twice daily) per individual. Most of the sampled gas contained more than 1000 ppm of the mean background-corrected CO2 , suggesting that the method proposed in this study successfully collected sufficient breath concentration to accurately measure the CH4 /CO2 ratio. The between-animal variance accounted for 31.7% of the total variance in the CH4 /CO2 ratio. The results showed that the gas collection method proposed in this study could be a useful tool for measuring the CH4 /CO2 ratio under on-farm conditions. The variance component obtained from this study will help to establish protocols for generating data for genetic evaluation and performing dietary experiments with sufficient statistical power.

Assessing population structure and migration patterns of wild boar (Sus scrofa) in Japan

Geographical wildlife patterns reflect historical range expansion and connectivity and provide insights into wildlife population management. In our large-scale phylogeographic population analysis of wild boars (Sus scrofa leucomystax) in Japan, we identified 15 clusters using 29 microsatellite markers, each structured within a range of approximately 200 km. This suggests that evolution was essentially driven by isolation by distance, and that the range of gene flow was limited. One cluster contained subpopulations located approximately 900 km apart, indicating the occurrence of past anthropogenic introductions. Moreover, we estimated effective migration to visualize the geographic genetic population diversity. This analysis identified six potential barriers, one of which involved large plains and mountainous areas in the Kanto region of eastern Japan. This barrier likely persisted in the two eastern clusters for an extended period, restricting migration to the neighboring areas. Overall, our study sheds light on the demographic history of wild boar in Japan, provides evidence of past anthropogenic introductions from distant areas, and highlights the importance of geographic barriers in shaping genetic diversity and population dynamics. This knowledge will be beneficial for forming informed wildlife management strategies toward the conservation of genetic integrity and ecological balance of wild boar populations in Japan.

Rapid determination of domoic acid in seafood by fluorescence polarization immunoassay using a portable analyzer

Monitoring phycotoxin accumulation in marine products such as edible shellfish is a regulatory requirement in many countries. Therefore, a simple and rapid onsite quantification method is sought. Herein, we present a fluorescence polarization immunoassay (FPIA), a well-known one-step immunoassay, using a portable fluorescence polarization analyzer for domoic acid (DA), widely referred to as the primary toxin of amnesic shellfish poisoning (ASP). To establish FPIA for DA, the matrix effect of methanol, which is widely used to extract DA from shellfish, on FPIA was investigated. To validate this method, we performed a spike recovery test using oysters containing DA at a concentration equivalent to the regulatory limits of North America and the European Union (20 mg/kg). The recovery rate was found to be 79.4-114.7%, which is equivalent to that of the commercially available enzyme-linked immunosorbent assay (ELISA). We expect that this FPIA system will enable the quantitative onsite analysis of DA and significantly contribute to the safety of marine products.

Production of yellow-flowered gentian plants by genetic engineering of betaxanthin pigments

Genetic engineering of flower color provides biotechnological products such as blue carnations or roses by accumulating delphinidin-based anthocyanins not naturally existing in these plant species. Betalains are another class of pigments that in plants are only synthesized in the order Caryophyllales. Although they have been engineered in several plant species, especially red-violet betacyanins, the yellow betaxanthins have yet to be engineered in ornamental plants. We attempted to produce yellow-flowered gentians by genetic engineering of betaxanthin pigments. First, white-flowered gentian lines were produced by knocking out the dihydroflavonol 4-reductase (DFR) gene using CRISPR/Cas9-mediated genome editing. Beta vulgaris BvCYP76AD6 and Mirabilis jalapa MjDOD, driven by gentian petal-specific promoters, flavonoid 3',5'-hydroxylase (F3'5'H) and anthocyanin 5,3'-aromatic acyltransferase (AT), respectively, were transformed into the above DFR-knockout white-flowered line; the resultant gentian plants had vivid yellow flowers. Expression analysis and pigment analysis revealed petal-specific expression and accumulation of seven known betaxanthins in their petals to c. 0.06-0.08 μmol g FW-1 . Genetic engineering of vivid yellow-flowered plants can be achieved by combining genome editing and a suitable expression of betaxanthin-biosynthetic genes in ornamental plants.

Evaluation of ammonia emission reducing effect by adding waste cooking oil in pilot-scale composting of dairy cattle manure

OBJECTIVE

In our previous study, we observed that the addition of waste cooking oil (WCO) reduced ammonia (NH3) emissions during laboratory-scale composting of dairy cattle manure under low-aeration condition. Therefore, this study aimed to evaluate the effect of addition of WCO on NH3 emissions reduction during pilot-scale composting of dairy cattle manure, which is close to the conditions of practical composting treatment.

METHODS

Composting tests were conducted using pilot-scale composting facilities (1.8 m3 of capacity). The composting mixtures were prepared from manure, sawdust, and WCO. Two treatments were set: without WCO (Control) and with WCO added to 3 wt% of manure (WCO3). Composting was conducted under continuous aeration at 40 L/min, corresponding to 22.2 L/(min‧m3) of the mixture at the start of composting. The changes in temperatures, NH3 concentrations in the exhaust gases, and contents of the composted mixtures were analyzed. Based on these analysis results, the effect of WCO addition on NH3 emissions and nitrogen loss during composting was evaluated.

RESULTS

During composting, the temperature increase of the composting mixture became higher, and the decreases of weight and water content of the mixture became larger in WCO3 than in Control. In the decrease of weight, and the residual weight and water content of the mixture, significant differences (p<0.05) were detected between the two treatments at the end of composting. The NH3 concentrations in the exhaust gases tended to be lower in WCO3 than in Control. Nitrogen loss was 21.5% lower in WCO3 than in Control.

CONCLUSION

Reduction of NH3 emissions by the addition of WCO under low aeration condition was observed in pilot-scale composting, as well as in laboratory-scale composting. This result suggests that this method is effective in reducing NH3 emissions in practicalscale composting.

Development of a high-affinity anti-bovine PD-1 rabbit-bovine chimeric antibody using an efficient selection and large production system

Immune checkpoint molecules PD-1/PD-L1 cause T-cell exhaustion and contribute to disease progression in chronic infections of cattle. We established monoclonal antibodies (mAbs) that specifically inhibit the binding of bovine PD-1/PD-L1; however, conventional anti-PD-1 mAbs are not suitable as therapeutic agents because of their low binding affinity to antigen. In addition, their sensitivity for the detection of bovine PD-1 is low and their use for immunostaining PD-1 is limited. To address these issues, we established two anti-bovine PD-1 rabbit mAbs (1F10F1 and 4F5F2) and its chimeric form using bovine IgG1 (Boch1D10F1), which exhibit high binding affinity. One of the rabbit mAb 1D10F1 binds more strongly to bovine PD-1 compared with a conventional anti-PD-1 mAb (5D2) and exhibits marked inhibitory activity on the PD-1/PD-L1 interaction. In addition, PD-1 expression in bovine T cells could be detected with higher sensitivity by flow cytometry using 1D10F1. Furthermore, we established higher-producing cells of Boch1D10F1 and succeeded in the mass production of Boch1D10F1. Boch1D10F1 exhibited a similar binding affinity to bovine PD-1 and the inhibitory activity on PD-1/PD-L1 binding compared with 1D10F1. The immune activation by Boch1D10F1 was also confirmed by the enhancement of IFN-γ production. Finally, Boch1D10F1 was administered to bovine leukemia virus-infected cows to determine its antiviral effect. In conclusion, the high-affinity anti-PD-1 antibody developed in this study represents a powerful tool for detecting and inhibiting bovine PD-1 and is a candidate for PD-1-targeted immunotherapy in cattle.

Brassica rapa L. prevents Western diet-induced obesity in C57BL/6 mice through its binding capacity of cholesterol and fat

Obesity, a chronic disorder caused by excessive energy intake leading to fat accumulation in adipose tissue, increases the risk of severe diseases. Brassica rapa L. is known as a traditional vegetable in the Nagano area of Japan. C57BL/6 mice were randomly assigned to three groups, with different diets as follows: a normal diet, a Western diet (WD), and a WD plus B. rapa L. powder (BP) in a 56-day experiment. Brassica rapa L. supplementation reduced the body weight gain and lipid accumulation of mice significantly. The BP group also had higher fecal bile acid, total cholesterol, and triglyceride excretion levels compared with those in the other groups. The antiobesity effects of B. rapa L. were due to its binding with cholesterol and fat, and possibly enhancing the bile acid excretion and modulating gut microbiota, suggesting that B. rapa L. could be a functional vegetable with potential uses in targeting obesity.

Complete genome sequences of epizootic hemorrhagic disease virus serotypes 5 and 6 isolated in Japan

Here, we report the complete genome sequences of epizootic hemorrhagic disease (EHD) virus serotypes 5 (EHDV-5) and 6 (EHDV-6) isolated in the Yaeyama Islands of Okinawa Prefecture, Japan. The EHDV-5 strain, ON-11/E/16, which was isolated in 2016, is, to our knowledge, the second EHDV-5 strain to be isolated after the first was isolated in Australia in 1977. In each of the genome segments, ON-11/E/16 was most closely related to EHDV strains of different serotypes isolated in Australia and Japan. Our results support the idea that various serotypes of EHDV have been circulating while causing reassortment in the Asia-Pacific region. In all genome segments, the EHDV-6 strain, ON-3/E/14, which was isolated in 2014, was highly similar to EHDV-6 strain HG-1/E/15, which was detected in affected cattle during the EHD epidemic in Hyogo prefecture in 2015. Therefore, these two EHDV-6 strains, ON-3/E/14 and HG-1/E/15, may have the same origin. However, it is unclear whether EHDV-6 was transmitted directly between the locations where those strains were isolated/detected (approx. 1,500 km apart) or whether EHDV-6 strains of the same origin entered each location at different times. In addition, we cannot rule out the possibility that EHDV-6 infection has spread unnoticed through asymptomatic cattle in other areas of Japan. Therefore, further investigation into EHDV infection in cattle is necessary for a more detailed understanding of the ecology of EHDV in Japan.

The probability distributions of the movement of dairy and beef cattle in Japan: a data note

OBJECTIVES

Animal movement is an important factor in the transmission of infectious diseases among livestock. A better understanding of animal movement characteristics provides a more reliable estimation of disease spread and promotes modeling studies. In Japan, all the cattle movement information is recorded in a national database called the Individual Cattle Identification Register (ICIR)." Our previous studies using this information demonstrated heterogeneity in the movement of dairy and beef cows according to location, season, and age. The present study describes the probability distributions of the movement of Japanese dairy and beef cows in the following month on a regional basis.

DATA DESCRIPTION

This publication contains four probability distribution datasets for the predicted locations of dairy and beef cows in Japan in the following month, which were developed using individual cattle movement information obtained from the ICIR. These datasets provide information on cattle movement in the following month on a regional basis, given properties such as birth region, location, time, and age.

Generation and Efficacy of Two Chimeric Viruses Derived from GPE- Vaccine Strain as Classical Swine Fever Vaccine Candidates

A previous study proved that vGPE^- mainly maintains the properties of classical swine fever (CSF) virus, which is comparable to the GPE^- vaccine seed and is a potentially valuable backbone for developing a CSF marker vaccine. Chimeric viruses were constructed based on an infectious cDNA clone derived from the live attenuated GPE^- vaccine strain as novel CSF vaccine candidates that potentially meet the concept of differentiating infected from vaccinated animals (DIVA) by substituting the glycoprotein E^rns of the GPE^- vaccine strain with the corresponding region of non-CSF pestiviruses, either pronghorn antelope pestivirus (PAPeV) or Phocoena pestivirus (PhoPeV). High viral growth and genetic stability after serial passages of the chimeric viruses, namely vGPE^-/PAPeV E^rns and vGPE^-/PhoPeV E^rns, were confirmed in vitro. In vivo investigation revealed that two chimeric viruses had comparable immunogenicity and safety profiles to the vGPE^- vaccine strain. Vaccination at a dose of 10^4.0 TCID₅₀ with either vGPE^-/PAPeV E^rns or vGPE^-/PhoPeV E^rns conferred complete protection for pigs against the CSF virus challenge in the early stage of immunization. In conclusion, the characteristics of vGPE^-/PAPeV E^rns and vGPE^-/PhoPeV E^rns affirmed their properties, as the vGPE^- vaccine strain, positioning them as ideal candidates for future development of a CSF marker vaccine.

Sex-based differences in the distribution of Aujeszky's disease-seropositive Japanese wild boar

BACKGROUND

Aujeszky's disease virus (ADV) primarily infects domestic pigs and wild boars, causing the abortion and death of young piglets due to central nervous system disorders. In Japan, the national eradication program for ADV in domestic pigs has been successful in most prefectures; however, concern has been raised regarding ADV-infected wild boars as a source of transmission to domestic pigs.

RESULTS

We assessed the nationwide seroprevalence of ADV among wild boars (Sus scrofa) in Japan. Moreover, we determined the sex-based differences in the spatial clustering of seropositive animals. Serum samples were obtained from a total of 1383 wild boars acquired by hunting in 41 prefectures in three fiscal years (April-March in 2014, 2015, and 2017). Seropositivity tests for ADV using enzyme-linked immunosorbent assay, the latex agglutination and neutralization tests showed 29 boars seropositive for ADV (29/1383, 2.1% [95% confidence interval, CI: 1.4-3.0%]), with 28 of these boars originating from three prefectures in the Kii Peninsula (28/121, 23.1% [95% CI: 16.0-31.7%]). The degree of spatial clustering of these ADV-seropositive adult boars in the Kii Peninsula was evaluated using the K-function and data from sera samples of 46 (14 seropositive) male and 54 (12 seropositive) female boars. The degree of clustering among females was significantly higher in seropositive animals than in tested animals; however, such a difference was not observed for seropositive males.

CONCLUSIONS

The spatial dynamics of ADV among adult wild boars may be characterized based on sex, and is likely due to sex-based differences in behavioral patterns including dispersal among wild boars.

Targeted deletion of grape retrotransposon associated with fruit skin color via CRISPR/Cas9 in Vitis labrascana 'Shine Muscat'

Transposition of transposable elements affect expression levels, splicing and epigenetic status, and function of genes located in, or near, the inserted/excised locus. For example, in grape, presence of the Gret1 retrotransposon in the promoter region of the VvMYBA1a allele at the VvMYBA1 locus suppress the expression of the VvMYBA1 transcription factor gene for the anthocyanin biosynthesis and this transposon insertion is responsible for the green berry skin color of Vitis labrascana, 'Shine Muscat', a major grape cultivar in Japan. To prove that transposons in grape genome can be removed by genome editing, we focused on Gret1 in the VvMYBA1a allele as a target of CRISPR/Cas9 mediated transposon removal. PCR amplification and sequencing detected Gret1 eliminated cells in 19 of 45 transgenic plants. Although we have not yet confirmed any effects on grape berry skin color, we were successful in demonstrating that cleaving the long terminal repeat (LTR) present at both ends of Gret1 can efficiently eliminate the transposon.

Natural variations of wheat EARLY FLOWERING 3 highlight their contributions to local adaptation through fine-tuning of heading time

KEY MESSAGE

We identified a large chromosomal deletion containing TaELF-B3 that confers early flowering in wheat. This allele has been preferred in recent wheat breeding in Japan to adapt to the environment. Heading at the appropriate time in each cultivation region can greatly contribute to stabilizing and maximizing yield. Vrn-1 and Ppd-1 are known as the major genes for vernalization requirement and photoperiod sensitivity in wheat. Genotype combinations of Vrn-1 and Ppd-1 can explain the variation in heading time. However, the genes that can explain the remaining variations in heading time are largely unknown. In this study, we aimed to identify the genes conferring early heading using doubled haploid lines derived from Japanese wheat varieties. Quantitative trait locus (QTL) analysis revealed a significant QTL on the long arm of chromosome 1B in multiple growing seasons. Genome sequencing using Illumina short reads and Pacbio HiFi reads revealed a large deletion of a ~ 500 kb region containing TaELF-B3, an orthologue of Arabidopsis clock gene EARLY FLOWERING 3 (ELF3). Plants with the deleted allele of TaELF-B3 (ΔTaELF-B3 allele) headed earlier only under short-day vernalization conditions. Higher expression levels of clock- and clock-output genes, such as Ppd-1 and TaGI, were observed in plants with the ΔTaELF-B3 allele. These results suggest that the deletion of TaELF-B3 causes early heading. Of the TaELF-3 homoeoalleles conferring early heading, the ΔTaELF-B3 allele showed the greatest effect on the early heading phenotype in Japan. The higher allele frequency of the ΔTaELF-B3 allele in western Japan suggests that the ΔTaELF-B3 allele was preferred during recent breeding to adapt to the environment. TaELF-3 homoeologs will help to expand the cultivated area by fine-tuning the optimal timing of heading in each environment.

MORE PANICLES 3, a natural allele of OsTB1/FC1, impacts rice yield in paddy fields at elevated CO2 levels

Improving crop yield potential through an enhanced response to rising atmospheric CO₂ levels is an effective strategy for sustainable crop production in the face of climate change. Large-sized panicles (containing many spikelets per panicle) have been a recent ideal plant architecture (IPA) for high-yield rice breeding. However, few breeding programs have proposed an IPA under the projected climate change. Here, we demonstrate through the cloning of the rice (Oryza sativa) quantitative trait locus for MORE PANICLES 3 (MP3) that the improvement in panicle number increases grain yield at elevated atmospheric CO₂ levels. MP3 is a natural allele of OsTB1/FC1, previously reported as a negative regulator of tiller bud outgrowth. The temperate japonica allele advanced the developmental process in axillary buds, moderately promoted tillering, and increased the panicle number without negative effects on the panicle size or culm thickness in a high-yielding indica cultivar with large-sized panicles. The MP3 allele, containing three exonic polymorphisms, was observed in most accessions in the temperate japonica subgroups but was rarely observed in the indica subgroup. No selective sweep at MP3 in either the temperate japonica or indica subgroups suggested that MP3 has not been involved and utilized in artificial selection during domestication or breeding. A free-air CO₂ enrichment experiment revealed a clear increase of grain yield associated with the temperate japonica allele at elevated atmospheric CO₂ levels. Our findings show that the moderately increased panicle number combined with large-sized panicles using MP3 could be a novel IPA and contribute to an increase in rice production under climate change with rising atmospheric CO₂ levels.

Nationwide analysis of antimicrobial resistance in pathogenic Escherichia coli strains isolated from diseased swine over 29 years in Japan

Pathogenic Escherichia coli strains are important causes of several swine diseases that result in significant economic losses worldwide. In Japan, the use of antimicrobials in swine is much higher than that in other farm animals every year. Antimicrobial resistance in pathogenic E. coli strains also heavily impacts the swine industry due to the limited treatment options and an increase in the potential risk of the One Health crisis. In 2016, we investigated 684 Japanese isolates of swine pathogenic E. coli belonging to four major serogroups and reported the emergence and increase in the highly multidrug-resistant serogroups O116 and OSB9 and the appearance of colistin-resistant strains. In the present study, by expanding our previous analysis, we determined the serotypes and antimicrobial resistance of 1,708 E. coli strains isolated from diseased swine between 1991 and 2019 in Japan and found recent increases in the prevalences of multidrug-resistant strains and minor serogroup strains. Among the antimicrobials examined in this study that have been approved for animal use, a third-generation cephalosporin was found to be effective against the most isolates (resistance rate: 1.2%) but not against highly multidrug-resistant strains. We also analyzed the susceptibilities of the 1,708 isolates to apramycin and bicozamycin, both which are available for treating swine in Japan, and found that the rates of resistance to apramycin and bicozamycin were low (6.7% and 5.8%, respectively), and both antimicrobials are more effective (resistance rates: 2.7% and 5.4%, respectively) than third-generation cephalosporins (resistance rate: 16.2%) against highly multidrug-resistant strains.

A Pilot Study to Assess Glucose, Insulin, and Incretin Responses Following Novel High Resistant Starch Rice Ingestion in Healthy Men

INTRODUCTION

A newly developed resistant starch (RS) rice line with double mutation of starch synthase IIIa and branching enzyme IIb (ss3a/be2b) exhibits a tenfold greater percentage RS value than the wild-type rice line. Currently, the effects of cooked rice with such high RS content on secretion and action of glucagon-like peptide-1 (GLP-1) and glucose-dependent insulinotropic polypeptide (GIP) are unclear. Therefore, we conducted a pilot study to assess postprandial responses of GLP-1 and GIP along with glucose and insulin and also gastric emptying after ingestion of the high-RS cooked rice with ss3a/be2b in healthy subjects.

METHODS

In a non-randomized crossover design, five healthy men ingested two test foods, control (low-RS) and high-RS cooked rice, with at least 1-week washout period between testing days. Plasma glucose, serum insulin, plasma total GLP-1, plasma total GIP, and also gastric emptying rate were measured after ingestion of each test food, and the incremental area under the curves (iAUC) was calculated for each biochemical parameter using the values from 0 to 180 min after ingestion.

RESULTS

The high-RS cooked rice ingestion tended to reduce iAUC-glucose (p = 0.06) and significantly reduced iAUC-insulin (p < 0.01) and iAUC-GLP-1 (p < 0.05) but not iAUC-GIP (p = 0.21) relative to control cooked rice ingestion. In addition, the high-RS cooked rice ingestion did not affect gastric emptying.

CONCLUSIONS

The present results indicate that the suppressive effects of the high-RS cooked rice ingestion on postprandial responses of glucose and insulin may be provided through attenuation in GLP-1 secretion along with its low digestibility into glucose. We suggest that the high-RS rice with ss3a/be2b may serve as a better carbohydrate source and also as a novel functional food for dietary interventions to improve postprandial hyperglycemia and hyperinsulinemia without both enhancing GLP-1 secretion and affecting gastric emptying in patients with diabetes.

Bacteria Community Inhabiting Heterobasidion Fruiting Body and Associated Wood of Different Decay Classes

The microbiome of Heterobasidion-induced wood decay of living trees has been previously studied; however, less is known about the bacteria biota of its perennial fruiting body and the adhering wood tissue. In this study, we investigated the bacteria biota of the Heterobasidion fruiting body and its adhering deadwood. Out of 7,462 operational taxonomic units (OTUs), about 5,918 OTUs were obtained from the fruiting body and 5,469 OTUs were obtained from the associated dead wood. Interestingly, an average of 52.6% of bacteria biota in the fruiting body was shared with the associated dead wood. The overall and unique OTUs had trends of decreasing from decay classes 1 to 3 but increasing in decay class 4. The fruiting body had the highest overall and unique OTUs number in the fourth decay class, whereas wood had the highest OTU in decay class 1. Sphingomonas spp. was significantly higher in the fruiting body, and phylum Firmicutes was more dominant in wood tissue. The FAPROTAX functional structure analysis revealed nutrition, energy, degradation, and plant-pathogen-related functions of the communities. Our results also showed that bacteria communities in both substrates experienced a process of a new community reconstruction through the various decay stages. The process was not synchronic in the two substrates, but the community structures and functions were well-differentiated in the final decay class. The bacteria community was highly dynamic; the microbiota activeness, community stability, and functions changed with the decay process. The third decay class was an important turning point for community restructuring. Host properties, environmental factors, and microbial interactions jointly influenced the final community structure. Bacteria community in the fruiting body attached to the living standing tree was suppressed compared with those associated with dead wood. Bacteria appear to spread from wood tissue of the standing living tree to the fruiting body, but after the tree is killed, bacteria moved from fruiting body to wood. It is most likely that some of the resident endophytic bacteria within the fruiting body are either parasitic, depending on it for their nutrition, or are mutualistic symbionts.

Laser microdissection transcriptome data derived gene regulatory networks of developing rice endosperm revealed tissue- and stage-specific regulators modulating starch metabolism

Laser microdissection applied on the developing rice endosperm revealed tissue- and stage-specific regulators modulating programmed cell death and desiccation tolerance mechanisms in the central starchy endosperm following starch metabolism. Rice (Oryza sativa L.) filial seed tissues are heterozygous in its function, which accumulate distinct storage compounds spatially in starchy endosperm and aleurone. In this study, we identified the 18 tissue- and stage-specific gene co-regulons in the developing endosperm by isolating four fine tissues dorsal aleurone layer (AL), central starchy endosperm (CSE), dorsal starchy endosperm (DSE), and lateral starchy endosperm (LSE) at two developmental stages (7 days after flowering, DAF and 12DAF) using laser microdissection (LM) coupled with gene expression analysis of a 44 K microarray. The derived co-expression regulatory networks depict that distinct set of starch biosynthesis genes expressed preferentially at first in CSE at 7 DAF and extend its spatial expression to LSE and DSE by 12 DAF. Interestingly, along with the peak of starch metabolism we noticed accumulation of transcripts related to phospholipid and glycolipid metabolism in CSE during 12 DAF. The spatial distribution of starch accumulation in distinct zones of starchy endosperm contains specific transcriptional factors and hormonal-regulated genes. Genes related to programmed cell death (PCD) were specifically expressed in CSE at 12DAF, when starch accumulation was already completed in that tissue. The aleurone layer present in the outermost endosperm accumulates transcripts of lipid, tricarboxylic acid metabolism, several transporters, while starch metabolism and PCD is not pronounced. These regulatory cascades are likely to play a critical role in determining the positional fate of cells and offer novel insights into the molecular physiological mechanisms of endosperm development from early to middle storage phase.

Estimation of the Lethality Rate, Recovery Rate, and Case Fatality Ratio of Classical Swine Fever in Japanese Wild Boar: An Analysis of the Epidemics From September 2018 to March 2019

Understanding the morbidity and lethality of diseases is necessary to evaluate the effectiveness of countermeasure against the epidemics (e.g., vaccination). To estimate them, detailed data on host population dynamics are required; however, estimating the population size for wildlife is often difficult. We aimed to elucidate the morbidity and lethality of classical swine fever (CSF) currently highly prevalent in the wild boar population in Japan. To this end, we estimated lethality rate, recovery rate, and case fatality ratio (CFR) of CSF without detailed data on the population estimates of wild boar. A mathematical model was constructed to describe the CSF dynamics and population dynamics of wild boar. We fitted the model to the (i) results of the reverse transcription polymerase chain reaction (RT-PCR) test for the CSFV gene and the (ii) results of the enzyme-linked immunosorbent assay (ELISA) test for the antibody against CSFV in sampled wild boar. In the 280 wild boar sampled from September 2018 to March 2019 in the major CSF-affected area in Japan, the lethality rate and recovery rate of CSF per week were estimated as 0.165 (95% confidence interval: 0.081–0.250) and 0.004 (0–0.009), respectively. While the estimate of lethality rate of CSF was similar with the estimates in previous studies, the recovery rate was lower than those reported previously. CFR was estimated as 0.959 (0.904–0.981) using our estimate of recovery rate. This study is the first to estimate lethality rate of CSF from the dynamics of CSF epidemics in the wild boar population. Since the value of CFR is sensitive to the value of recovery rate, the accuracy in the estimate of recovery rate is a key for the accurate estimation of CFR. A long-term transmission experiment of moderately virulent strains may lead to more accurate estimation of the recovery rate and CFR of CSF.

Verification of our empirical understanding of the physiology and ecology of two contrasting plantation species using a trait database

The effects of climate change on forest ecosystems take on increasing importance more than ever. Information on plant traits is a powerful predictor of ecosystem dynamics and functioning. We reviewed the major ecological traits, such as foliar gas exchange and nutrients, xylem morphology and drought tolerance, of Cryptomeria japonica and Chamaecyparis obtusa, which are major timber species in East Asia, especially in Japan, by using a recently developed functional trait database for both species (SugiHinokiDB). Empirically, C. obtusa has been planted under drier conditions, whereas C. japonica, which grows faster but thought to be less drought tolerant, has been planted under wetter conditions. Our analysis generally support the empirical knowledge: The maximum photosynthetic rate, stomatal conductance, foliar nutrient content and soil-to-foliage hydraulic conductance were higher in C. japonica than in C. obtusa. In contrast, the foliar turgor loss point and xylem pressure corresponding to 50% conductivity, which indicate drought tolerance, were lower in C. obtusa and are consistent with the drier habitat of C. obtusa. Ontogenetic shifts were also observed; as the age and height of the trees increased, foliar nutrient concentrations, foliar minimum midday water potential and specific leaf area decreased in C. japonica, suggesting that nutrient and water limitation occurs with the growth. In C. obtusa, the ontogenetic shits of these foliar traits were less pronounced. Among the Cupressaceae worldwide, the drought tolerance of C. obtusa, as well as C. japonica, was not as high. This may be related to the fact that the Japanese archipelago has historically not been subjected to strong dryness. The maximum photosynthetic rate showed intermediate values within the family, indicating that C. japonica and C. obtusa exhibit relatively high growth rates in the Cupressaceae family, and this is thought to be the reason why they have been selected as economically suitable timber species in Japanese forestry. This study clearly demonstrated that the plant trait database provides us a promising opportunity to verify out empirical knowledge of plantation management and helps us to understand effect of climate change on plantation forests by using trait-based modelling.

Cas9-mediated genome editing reveals a significant contribution of calcium signaling pathways to anhydrobiosis in Pv11 cells

Pv11 is an insect cell line established from the midge Polypedilum vanderplanki, whose larval form exhibits an extreme desiccation tolerance known as anhydrobiosis. Pv11 itself is also capable of anhydrobiosis, which is induced by trehalose treatment. Here we report the successful construction of a genome editing system for Pv11 cells and its application to the identification of signaling pathways involved in anhydrobiosis. Using the Cas9-mediated gene knock-in system, we established Pv11 cells that stably expressed GCaMP3 to monitor intracellular Ca2+ mobilization. Intriguingly, trehalose treatment evoked a transient increase in cytosolic Ca2+ concentration, and further experiments revealed that the calmodulin-calcineurin-NFAT pathway contributes to tolerance of trehalose treatment as well as desiccation tolerance, while the calmodulin-calmodulin kinase-CREB pathway conferred only desiccation tolerance on Pv11 cells. Thus, our results show a critical contribution of the trehalose-induced Ca2+ surge to anhydrobiosis and demonstrate temporally different roles for each signaling pathway.

Complete root specimen of plants grown in soil-filled root box: sampling, measuring, and staining method

BACKGROUND

Detailed datasets containing root system and its architecture in soil are required to improve understanding of resource capture by roots. However, most of the root study methods have paid little attention to make and preserve whole root specimens. This study introduces root system sampling equipment that makes the entire root specimen with minimum impairment and without displacement of the spatial arrangement of the root system in root boxes. The objectives are to assess: whether the equipment can rapidly sample the entire root system; whether root surface area is measurable from a scanned digital image of the root specimen; and whether staining of the entire root specimens would provide multidimensional visual information on the interaction between soil and physiological function of root system architecture (RSA). For validation, we examined the root response of two soybean cultivars to arbuscular mycorrhizal (AM) inoculation and the effect of waterlogging stress on the physiological activity of buckwheat RSA.

RESULTS

The root boxes allowed soybean and buckwheat plants to grow uniformly across the replications. Both species showed significant differences between cultivars and/or among treatments in shoot and root traits. The equipment enabled to sample the whole-root specimens of soybean and buckwheat, where the tips of the fine roots were alive (diameter < 0.2 mm). Also, the whole root specimens of soybean were made in about 7 min. The root surface area calculated from the scanned soybean specimens showed a significant correlation with that calculated from the roots spread out in water (a common method). Staining of the soybean root specimens enabled us to observe the localized root proliferation induced by AM colonization. Moreover, staining of the buckwheat root specimens made it possible to examine the respiratory activity of each root at different depths.

CONCLUSIONS

The present method realized: fast and accurate production of the whole root specimen and precise calculation of the specimens' root surface area. Moreover, staining of the root specimens enabled analyzing the interaction between soil and physiological function of RSA. The evaluation of root traits, using our methods, will contribute to developing agronomic management and breeding program for sustainable food production.

Comprehensive Proteomic Analysis Revealed a Large Number of Newly Identified Proteins in the Small Extracellular Vesicles of Milk from Late-Stage Lactating Cows

Bovine milk contains small extracellular vesicles (sEVs) that provide proteins, miRNAs, mRNAs, DNAs, and lipids to target cells and play a role in intracellular communications. Previous studies have characterized proteins in milk sEVs from early- and mid-stage lactation. However, the proteins in milk sEVs from late-stage lactation are mostly unexplored. The aim of this study was to determine the proteomic profile of milk sEVs from late-stage lactating cows. A comprehensive nanoliquid chromatography-tandem mass spectrometry (nanoLC-MS/MS) approach was carried out to reveal the proteins in milk sEVs. Additionally, bioinformatics analysis was carried out to interpret the molecular signatures of newly identified proteins in milk sEVs from three late-stage lactating cows. NanoLC-MS/MS analysis revealed a total of 2225 proteins in milk sEVs from cows. Notably, after comparing these identified proteins with previously deposited datasets of proteins in bovine milk sEVs, 429 proteins were detected as newly identified. Bioinformatic analysis indicated that these newly identified proteins in milk sEVs were engaged in a diverse range of molecular phenomena relevant to mammary gland physiology, milk production, immunity, and immune response. These findings suggest that the newly identified proteins could expand the inventory application of molecular cargos, nutritional status, and immune modulation of sEVs in milk during the late-stage lactation.

Antimicrobial use on 74 Japanese pig farms in 2019: A comparison of Japanese and European defined daily doses in the field

Defined daily doses (DDD) have been established in human medicine to standardize the measurement of treatment in a population. In veterinary medicine, the European Medicine Agency published defined daily dose (DDDvet) values for antimicrobial agents used in food-producing animals in 2016. National defined doses (DDDjp) for antimicrobials used for pigs in Japan have recently been determined. The aim of this study was to compare the results of calculated antimicrobial use in the field using the DDDjp and DDDvet values. Data from 74 pig farms in Japan relative to antimicrobial use in 2019 was collected. The numbers of DDDs (the weight of biomass treated in kg-days) using DDDjp and DDDvet values for each farm and for different antimicrobial classes were compared. Associations between calculated numbers of DDDjp and DDDvet on farm level were investigated. In addition, differences in antimicrobial use were investigated between different production types of farms (farrowing, finishing and farrow-to-finish farms). Using DDDjp and DDDvet values, the aggregated number of DDDs for 74 farms were 4,099,188 and 2,217,085 respectively, with the former being larger by 1.85 times than the latter. The most frequently used antimicrobial class was penicillin regardless of whether DDDjp or DDDvet was used. The absence of DDDvet values for certain antimicrobial agents used in Japan and the differences in the number of DDDjps/PCU and DDDvets/PCU indicated the need for Japanese DDDs. The number of DDDs per kg population correction unit (PCU) per farm tended to be higher in farrowing farms than in farrow-to-finish farms and finishing farms, with no significant difference (P = 0.19).

Ethanol treatment for sterilization, concentration, and stabilization of a biodegradable plastic-degrading enzyme from Pseudozyma antarctica culture supernatant

Biodegradable plastics must be sufficiently stable to maintain functionality during use but need to be able to degrade rapidly after use. We previously reported that treatment with an enzyme named PaE, secreted by the basidiomycete yeast Pseudozyma antarctica can speed up this degradation. To facilitate the production of large quantities of PaE, here, we aimed to elucidate the optimal conditions of ethanol treatment for sterilization of the culture supernatant and for concentration and stabilization of PaE. The results showed that Pseudozyma antarctica completely lost its proliferating ability when incubated in ≥20% (v/v) ethanol. When the ethanol concentration was raised to 90% (v/v), PaE formed a precipitate; however, its activity was restored completely when the precipitate was dissolved in water. To reduce ethanol use, PaE was successfully concentrated and recovered by sequential ammonium sulfate precipitation and ethanol precipitation steps. Over 90% of the activity in the original culture supernatant was recovered and the specific activity was increased 3.4-fold. By preparing the enzyme solution at a final concentration of 20% (v/v) ethanol, about 60% of the initial activity was maintained at ambient temperature for over 6 months without growth of microbes. We conclude that ethanol treatment is effective for sterilization, concentration, and stabilization of PaE, and that concentrating PaE by sequential ammonium sulfate precipitation and ethanol precipitation substantially increases the PaE purity and decreases ethanol use.

Establishing defined daily doses (DDDs) for antimicrobial agents used in pigs, cattle and poultry in Japan and comparing them with European DDD values

Monitoring of antimicrobial use is essential in the management of the development and selection of antimicrobial resistance. A variety of indicators has become available to monitor antimicrobial use in human and animal medicine. One of them is an indicator based on defined daily dose (DDD). By using the number of DDDs administered and normalising it by the population at risk of being treated over a defined period, one can estimate the number of treatment days with antimicrobial agents in a population. For veterinary medicine, the European Medicines Agency (EMA) has published the European values of DDD (DDDvet) for food-producing animals. In this study, we defined Japanese defined daily doses for antimicrobial agents (DDDjp) using DDD values that we previously assigned for antimicrobial products approved for use in pigs, cattle and poultry in Japan and compared them with DDDvet values. For the comparison, the quotient of Japanese and European values (QDDD) was calculated and the effect of the administration route and the number of active substances contained in the preparation was investigated. A total of 59 DDDjp values were defined for 43 antimicrobial agents using the data of 276 products approved for use in pigs. Likewise, a total of 55 DDDjp values were defined for 32 antimicrobial agents using the data of 196 products for use in cattle, and a total of 27 DDDjps values were defined for 25 antimicrobial agents using the data of 131 products approved for use in poultry. A comparison was made for 42, 28 and 17 pairs of DDDjp and DDDvet values for antimicrobial agents used for pigs, cattle and poultry respectively. The comparison showed median QDDD value of 0.61 and 0.66 for antimicrobial agents used for pigs and cattle respectively (p<0.01), indicating that the Japanese daily doses are significantly lower than the corresponding EMA values in these species. For the antimicrobial agents used for poultry, no significant difference was observed between DDDjp and DDDvet values with a median QDDD value of 1.15. The difference between DDDvet and DDDjp values and absence of DDDvet values for some antimicrobial agents marketed in Japan indicate that DDDjp rather than DDDvet should be used as the basis for the calculation of antimicrobial use monitoring in farm animals in Japan.

Haplotype analysis from unmanned aerial vehicle imagery of rice MAGIC population for the trait dissection of biomass and plant architecture

Unmanned aerial vehicles (UAVs) are popular tools for high-throughput phenotyping of crops in the field. However, their use for evaluation of individual lines is limited in crop breeding because research on what the UAV image data represent is still developing. Here, we investigated the connection between shoot biomass of rice plants and the vegetation fraction (VF) estimated from high-resolution orthomosaic images taken by a UAV 10 m above a field during the vegetative stage. Haplotype-based genome-wide association studies of multi-parental advanced generation inter-cross (MAGIC) lines revealed four quantitative trait loci (QTLs) for VF. VF was correlated with shoot biomass, but the haplotype effect on VF was better correlated with that on shoot biomass at these QTLs. Further genetic characterization revealed the relationships between these QTLs and plant spreading habit, final shoot biomass and panicle weight. Thus, genetic analysis using high-throughput phenotyping data derived from low-altitude, high-resolution UAV images during early stages of rice growing in the field provides insights into plant growth, architecture, final biomass, and yield.

Estimations and projections of Avena fatua dynamics under multiple management scenarios in crop fields using simplified longitudinal monitoring

Integrated weed management (IWM) is currently the most appropriate and effective method of agricultural weed control. To determine the most effective strategy, it is necessary to compare the effects of different control options and their rotation. Avena fatua (common wild oat) is one of the most common and economically threatening grass weed species of cereal crops worldwide. To examine the effects of non-chemical weed management options (farmland use, delayed sowing, and summer irrigation) on control of A. fatua, we recorded coverage levels and field conditions in 41 sites during the spring growing season of winter wheat for about 10 years. A transition matrix model was then constructed to project coverage levels of A. fatua under each management option using ordinal logistic regression. The results showed that farmland use had a remarkable effect on coverage; notably, planting of paddy rice and vegetables, which respectively eliminated the effect of coverage in the previous year and facilitated rapid convergence of coverage to 0%. Thus, although 90% of fields under continuous wheat cultivation were found to be at risk of A. fatua colonization, the risk was reduced to almost 0% with rotation of effective farmland use. As summer irrigation was also effective, more than 50% of wheat fields with the option continuously converged to no risk for A. fatua colonization. When the different management cycles were repeated, the effects were observed within 3 years, with a steady state reached in less than 10 years. Overall, these results suggest that simplified monitoring data could help decision-making on IWM, thereby helping to improve the efficiency of agricultural production.

Development of a Tet-On Inducible Expression System for the Anhydrobiotic Cell Line, Pv11

The Pv11 cell line established from an African chironomid, Polypedilum vanderplanki, is the only cell line tolerant to complete desiccation. In Pv11 cells, a constitutive expression system for Pv11 cells was previously exploited and several reporter genes were successfully expressed. Here we report the identification of an effective minimal promoter for Pv11 cells and its application to the Tet-On inducible expression system. First, using a luciferase reporter assay, we showed that a 202 bp deletion fragment derived from the constitutively active 121-promoter functions in Pv11 cells as an appropriate minimal promoter with the Tet-On inducible expression system. The AcGFP1 (Aequorea coerulescens green fluorescent protein) was also successfully expressed in Pv11 cells using the inducible system. In addition to these reporter genes, the avian myeloblastosis virus reverse transcriptase α subunit (AMV RTα), which is one of the most widely commercially available RNA-dependent DNA polymerases, was successfully expressed through the inducible expression system and its catalytic activity was verified. These results demonstrate the establishment of an inducible expression system in cells that can be preserved in the dry state and highlight a possible application to the production of large and complex proteins.

Evaluation of the antimicrobial use in pigs in Japan using dosage-based indicators

The use of antimicrobial agents in food-producing animals may lead to the emergence and spread of antimicrobial resistance in bacteria of animal origin. The use of antimicrobial agents in pigs in 2018 in Japan was evaluated in terms of the weight of active ingredient and number of defined daily doses (DDD), using annual sales data of veterinary antimicrobials sold for use in pigs. In addition, the use of antimicrobial agents in the Japanese pig sector in 2008 to 2017 was evaluated to determine whether or not there were any differences in temporal change pattern by use of different metrics. In 2018, 447 metric tons of active ingredient, corresponding to 77,379 × 106 kg-days (Japanese DDD) and 34,903 × 106 kg-days (European DDD) were sold. The proportion of the sales amount of sulfonamides, trimethoprim and lincosamides to the total sales amount was significantly different depending on the metric used. For most antimicrobial classes, the number of Japanese DDDs was greater than the number of European DDDs. These results indicate that the DDD-based metric, which is more reflective of the selective pressure of antimicrobials, is recommended for use in monitoring the antimicrobial use in pigs in Japan. The differences in the number of Japanese DDDs and European DDDs appear to confirm the need for Japanese DDDs.

Evaluation of sampling methods for effective detection of infected pig farms during a disease outbreak

Emergency surveillance following an outbreak of transboundary animal diseases such as classical swine fever (CSF), is conducted to find another new infection as early as possible. Although larger sample sizes can help achieve higher disease surveillance sensitivity, the sample size is limited by the availability of resources in an emergency situation. Moreover, the recent CSF outbreak reported in Japan was associated with fewer clinical signs; this emphasizes the importance of detecting infected farms by surveillance. In this study, we aimed to identify effective and labor-efficient sampling methods showing high probabilities of detecting infection, by simulating infection and sampling in pigsties. We found that impartial sampling, which involves selection of pigs to be sampled from the four corners and the center of the pigsty, and random sampling showed comparable probabilities of detection. Impartial sampling involves sample collection without pig identification and random selection. Owing to its simplicity, impartial sampling is labor-efficient and thus a possible substitute for random sampling. In a group-housing pigsty, testing five pigs from five pens showed a higher detection probability than testing five pigs from one pen. These results suggest preferable surveillance methods for conducting emergency surveillance of infectious diseases.

Molecular characterization of an anthocyanin-related glutathione S-transferase gene in Japanese gentian with the CRISPR/Cas9 system

BACKGROUND

The blue pigmentation of Japanese gentian flowers is due to a polyacylated anthocyanin, gentiodelphin, and all associated biosynthesis genes and several regulatory genes have been cloned and characterized. However, the final step involving the accumulation of anthocyanins in petal vacuoles remains unclear. We cloned and analyzed the glutathione S-transferases (GSTs) in Japanese gentian that are known to be involved in anthocyanin transport in other plant species.

RESULTS

We cloned GST1, which is expressed in gentian flower petals. Additionally, this gene belongs to the Phi-type GST clade related to anthocyanin biosynthesis. We used the CRISPR/Cas9-mediated genome editing system to generate loss-of-function GST1 alleles. The edited alleles were confirmed by Sanger and next-generation sequencing analyses. The GST1 genome-edited lines exhibited two types of mutant flower phenotypes, severe (almost white) and mild (pale blue). The phenotypes were associated with decreased anthocyanin accumulation in flower petals. In the GST1 genome-edited lines, sugar-induced stress conditions inhibited the accumulation of anthocyanins in stems and leaves, suggestvhing that GST1 is necessary for stress-related anthocyanin accumulation in organs other than flowers. These observations clearly demonstrate that GST1 is the gene responsible for anthocyanin transport in Japanese gentian, and is necessary for the accumulation of gentiodelphin in flowers.

CONCLUSIONS

In this study, an anthocyanin-related GST gene in Japanese gentian was functionally characterized. Unlike other biosynthesis genes, the functions of GST genes are difficult to examine in in vitro studies. Thus, the genome-editing strategy described herein may be useful for in vivo investigations of the roles of transport-related genes in gentian plants.

Introgression of chromosomal segments conferring early heading date from wheat diploid progenitor, Aegilops tauschii Coss., into Japanese elite wheat cultivars

The breeding of agriculturally useful genes from wild crop relatives must take into account recent and future climate change. In Japan, the development of early heading wheat cultivars without the use of any major gene controlling the heading date is desired to avoid overlap of the harvesting time before the rainy season. Here, we backcrossed two early heading lines of a synthetic hexaploid wheat, derived from a crossing between durum wheat and the wild wheat progenitor Aegilops tauschii, with four Japanese elite cultivars to develop early heading lines of bread wheat. In total, nine early heading lines that showed a heading date two to eight days earlier than their parental cultivars in field conditions were selected and established from the selfed progenies of the two- or three-times backcrossed populations. The whole appearance and spike shape of the selected early heading lines looked like their parental wheat cultivars. The mature grains of the selected lines had the parental cultivars’ characteristics, although the grains exhibited longer and narrower shapes. RNA sequencing-based genotyping was performed to detect single nucleotide polymorphisms between the selected lines and their parental wheat cultivars, which revealed the chromosomal regions transmitted from the parental synthetic wheat to the selected lines. The introgression regions could shorten wheat heading date, and their chromosomal positions were dependent on the backcrossed wheat cultivars. Therefore, early heading synthetic hexaploid wheat is useful for fine-tuning of the heading date through introgression of Ae. tauschii chromosomal regions.

Genetic diversity and population structure of feral rapeseed (Brassica napus L.) in Japan

Rapeseed (Brassica napus L.) is one of the most economically important oilseed crops worldwide. In Japan, it has been cultivated for more than a century and has formed many feral populations. The aim of this study was to elucidate the genetic diversity of feral rapeseeds by genotyping 537 individuals (among which 130 were determined to be genetically modified) sampled from various regions in Japan. Analysis of 30 microsatellite markers amplified 334 alleles and indicated moderate genetic diversity and high inbreeding (expected heterozygosity, 0.50; observed heterozygosity, 0.16; inbreeding coefficient within individuals, 0.68) within the feral populations. The Mantel test showed only an insignificant weak positive correlation between geographic distance and genetic distance. Analysis of molecular variance showed a greater genetic diversity among individuals than between populations. These results are in accordance with population structure assessed by using principal coordinate analysis and the program STRUCTURE, which showed that the 537 individuals could be assigned to 8 genetic clusters with very large genetic differences among individuals within the same geographic population, and that among feral individuals, many are closely related to rapeseed accessions in the NARO Genebank but some have unknown origins. These unique feral rapeseeds are likely to be affected by strong selection pressure. The results for genetically modified individuals also suggest that they have two different sources and have a considerable degree of diversity, which might be explained by hybridization with nearby individuals and separation of hybrid cultivars. The information obtained in this study could help improve the management of feral rapeseed plants in Japan.

Development of the Timed Re-Insemination (TRI-synch) program re-inseminating 24 days after the initial service in dairy cows

For the timed re-insemination at the minimal interbreeding interval, cows were treated with a progesterone (P4 )-releasing intravaginal device from Days 13-15 to 21 post-insemination (Day 0 = estrus), followed by plasma P4 assay on Day 23 and then subjected to the Experiments 1 and 2. In Experiment 1, of 18 cows, 6 cows were determined as luteolysis with low (<1 ng/ml) plasma P4 concentrations on Day 23 and ovulated on Days 24 (3 cows), 25 (1 cow), and 26 (1 cow) except a cow affected by ovarian quiescence. In Experiment 2, all cows were treated with GnRH on Day 23. Cows with low (<1 ng/ml) plasma P4 concentrations on Day 23 were diagnosed as non-pregnant and subjected to the re-insemination in the morning of Day 24 irrespective of estrous signs. Of 36 cows, 15 cows were diagnosed as being non-pregnant on Day 23. Fourteen cows of the non-pregnant animals were re-inseminated in the morning of Day 24 irrespective of estrous signs and the pregnancy rate of re-insemination was 36%. The conception rates of initial and re-inseminations were 50% (18/36) and 36% (5/14), respectively. The overall pregnancy rate by adding the rates of initial and re-inseminations was 64% (23/36).

Free fatty acid receptors, G protein-coupled receptor 120 and G protein-coupled receptor 40, are essential for oil-induced gastric inhibitory polypeptide secretion

AIMS/INTRODUCTION

Incretin hormone glucose-dependent insulinotropic polypeptide/gastric inhibitory polypeptide (GIP) plays a key role in high-fat diet-induced obesity and insulin resistance. GIP is strongly secreted from enteroendocrine K cells by oil ingestion. G protein-coupled receptor (GPR)120 and GPR40 are two major receptors for long chain fatty acids, and are expressed in enteroendocrine K cells. In the present study, we investigated the effect of the two receptors on oil-induced GIP secretion using GPR120- and GPR40-double knockout (DKO) mice.

MATERIALS AND METHODS

Global knockout mice of GPR120 and GPR40 were crossbred to generate DKO mice. Oral glucose tolerance test and oral corn oil tolerance test were carried out. For analysis of the number of K cells and gene expression in K cells, DKO mice were crossbred with GIP-green fluorescent protein knock-in mice in which visualization and isolation of K cells can be achieved.

RESULTS

Double knockout mice showed normal glucose-induced GIP secretion, but no GIP secretion by oil. We then investigated the number of K cells and gene characteristics in K cells isolated from GIP-green fluorescent protein knock-in mice. Deficiency of both receptors did not affect the number of K cells in the small intestine or expression of GIP messenger ribonucleic acid in K cells. Furthermore, there was no significant difference in the expression of the genes associated with lipid absorption or GIP secretion in K cells between wild-type and DKO mice.

CONCLUSIONS

Oil-induced GIP secretion is triggered by the two major fatty acid receptors, GPR120 and GPR40, without changing K-cell number or K-cell characteristics.

Diversification and genetic structure of the western-to-eastern progression of European Phaseolus vulgaris L. germplasm

BACKGROUND

Common bean (Phaseolus vulgaris L.) is the most important food legume for direct human consumption around the world, as it represents a valuable source of components with nutritional and health benefits.

RESULTS

We conducted a study to define and explain the genetic relatedness and diversification level of common bean (Phaseolus vulgaris L.) germplasm from Portugal to Ukraine, along a western-to-eastern line of southern European countries, including Poland. This was based on the P. vulgaris genetic structure, and was designed to better describe its distribution and domestication pathways in Europe. Using the multi-crop passport descriptors that include geographic origin and different phaseolin types (corresponding to the Mesoamerican and Andean gene pools), 782 accessions were obtained from nine gene banks and 12 geographic origins. We selected 33 genome/ gene-related/ gene-pool-related nuclear simple sequence repeat markers that covered the genetic diversity across the P. vulgaris genome. The overall polymorphic information content was 0.800. Without specifying geographic origin, global structure cluster analysis generated 10 genetic clusters. Among the PvSHP1 markers, the most informative for gene pool assignment of the European P. vulgaris germplasm was PvSHP1-B. Results of AMOVA show that 89% of the molecular variability is shared within the 782 accessions, with 4% molecular variability among the different geographic origins along this western-to-eastern line of southern Europe (including Poland).

CONCLUSIONS

This study shows that the diversification line of the European P. vulgaris germplasm followed from the western areas of southern Europe (Portugal, Spain, Italy, Slovenia) to the more eastern areas of southern Europe. This progression defines three geographically separated subgroups, as the northern (Poland, Ukraine, Romania), southern (Albania, Bulgaria), and central (Bosnia and Herzegovina, Serbia, Hungary) areas of eastern Europe.

Symbiotic incompatibility between soybean and Bradyrhizobium arises from one amino acid determinant in soybean Rj2 protein

Cultivated soybean (Glycine max) carrying the Rj2 allele restricts nodulation with specific Bradyrhizobium strains via host immunity, mediated by rhizobial type III secretory protein NopP and the host resistance protein Rj2. Here we found that the single isoleucine residue I490 in Rj2 is required for induction of symbiotic incompatibility. Furthermore, we investigated the geographical distribution of the Rj2-genotype soybean in a large set of germplasm by single nucleotide polymorphism (SNP) genotyping using a SNP marker for I490. By allelic comparison of 79 accessions in the Japanese soybean mini-core collection, we suggest substitution of a single amino acid residue (R490 to I490) in Rj2 induces symbiotic incompatibility with Bradyrhizobium diazoefficiens USDA 122. The importance of I490 was verified by complementation of rj2-soybean by the dominant allele encoding the Rj2 protein containing I490 residue. The Rj2 allele was also found in Glycine soja, the wild progenitor of G. max, and their single amino acid polymorphisms were associated with the Rj2-nodulation phenotype. By SNP genotyping against 1583 soybean accessions, we detected the Rj2-genotype in 5.4% of G. max and 7.7% of G. soja accessions. Distribution of the Rj2-genotype soybean plants was relatively concentrated in the temperate Asian region. These results provide important information about the mechanism of host genotype-specific symbiotic incompatibility mediated by host immunity and suggest that the Rj2 gene has been maintained by environmental conditions during the process of soybean domestication.

Evaluation of Biological Response of Lettuce (Lactuca sativa L.) and Weeds to Safranal Allelochemical of Saffron (Crocus sativus) by Using Static Exposure Method

Safranal, the main volatile chemical of Saffron (Crocus sativus) was studied to estimate its allelopathic effects on the photosynthetic pigment chlorophyll, leaf electrolyte leakage, fresh weight, catalase (CAT), and peroxidase (POX) activity of the test plant Lettuce (Lactuca sativa). In this study, the effective concentration (EC50) of safranal on CAT was estimated to be 6.12 µg/cm3. CAT activity was inhibited in a dose-dependent manner by the increase in the safranal concentration while POX activity was increased. Moreover, Safranal caused significant physiological changes in chlorophyll content, leaf electrolyte leakage, and fresh weight of several weed species with Lolium multiflorum being the most sensitive. Furthermore, 5 µM Safranal showed significant inhibitory activity against dicotyledonous in comparison to the monocotyledons under greenhouse conditions. The inhibition of the CAT by safranal was similar to those of uncompetitive inhibitors, and therefore the decline in carbon fixation by plants might be the mechanism behind the inhibitory activity of safranal.

Identification of candidate genes responsible for the susceptibility of apple (Malus × domestica Borkh.) to Alternaria blotch

BACKGROUND

The mechanism underlying the interaction between host plant and host-selective toxin (HST)-producing Alternaria alternata during infection is of particular interest for sustainable crop production. Alternaria blotch of apple (Malus × domestica Borkh.) caused by A. alternata apple pathotype is a major disease particularly in East Asia, which is the largest producer of apples globally. A single dominant gene, Alt, controls the susceptibility of the apple cultivar 'Delicious' to Alternaria blotch. In this study, we fine mapped the Alt locus and characterized three potential candidate genes.

RESULTS

We used 797 F₁ individuals derived from 15 crosses between apple accessions susceptible (Alt/alt) and resistant (alt/alt) to Alternaria blotch to construct physical and genetic maps of the Alt locus located on the top of chromosome 11. Susceptible accessions were derived from 'Delicious.' To fine map the Alt locus, we constructed a BAC library of 'Starking Delicious,' a sport of 'Delicious,' and used graphical genotyping to delimit the Alt locus to a region of 43 kb. Three genes predicted within the candidate Alt region were potentially involved in plant defense response, among which the gene encoding a coiled coil-nucleotide binding-leucine rich repeat (CC-NB-LRR) type disease resistance protein was the most promising. Moreover, a 12-bp insertion was uniquely identified in the 5' untranslated region of the Alt-associated allele of this gene, the presence or absence of which co-segregated with the susceptibility or resistance to A. alternata apple pathotype, respectively, among 43 tested cultivars including old ones and founders of modern apple breeding.

CONCLUSION

A disease resistance protein has been suggested as a determinant of susceptibility/resistance to HST-producing A. alternata for the first time. Our finding provides new insight into the mechanism of HST-mediated disease control used by A. alternata against host plants.

Tofu and fish oil independently modulate serum lipid profiles in rats: Analyses of 10 class lipoprotein profiles and the global hepatic transcriptome

Soy protein and fish oil are food components that decrease the risk of cardiovascular disease. Previous studies demonstrated that these food components reduced serum cholesterol levels and suppressed hepatic lipogenesis. However, the underlying mechanisms of action of these food components remain unclear. Ten classes of serum lipoprotein profiles showed that dietary tofu, a soybean curd, suppressed cholesterol absorption, while fish oil reduced most of the lipoprotein classes in rats. Tofu and fish oil both halved the level of the lipoprotein class LAC1 (LDL-anti-protease complex), a 15-nm LDL-anti-protease complex, which is speculated to be a cause of atherosclerosis. Moreover, a global transcriptome analysis revealed that tofu inhibited the mRNA expression of genes involved in hepatic lipogenesis, while fish oil stimulated that of genes related to fatty acid degradation. Therefore, tofu and fish oil independently regulate lipid metabolism. The decrease observed in LAC1 may have been due to reduced cholesterol absorption in the tofu diet group and the interference of lipogenesis via the activation of polyunsaturated fatty acid detoxification in the fish oil group.

Cooperation of PD-1 and LAG-3 in the exhaustion of CD4+ and CD8+ T cells during bovine leukemia virus infection

Bovine leukemia virus (BLV) is a retrovirus that infects B cells in cattle and causes bovine leukosis after a long latent period. Progressive exhaustion of T cell functions is considered to facilitate disease progression of BLV infection. Programmed death-1 (PD-1) and lymphocyte activation gene-3 (LAG-3) are immunoinhibitory receptors that contribute to T-cell exhaustion caused by BLV infection in cattle. However, it is unclear whether the cooperation of PD-1 and LAG-3 accelerates disease progression of BLV infection. In this study, multi-color flow cytometric analyses of PD-1- and LAG-3-expressing T cells were performed in BLV-infected cattle at different stages of the disease. The frequencies of PD-1+LAG-3+ heavily exhausted T cells among CD4+ and CD8+ T cells was higher in the blood of cattle with B-cell lymphoma over that of BLV-uninfected and BLV-infected cattle without lymphoma. In addition, blockade assays of peripheral blood mononuclear cells were performed to examine whether inhibition of the interactions between PD-1 and LAG-3 and their ligands by blocking antibodies could restore T-cell function during BLV infection. Single or dual blockade of the PD-1 and LAG-3 pathways reactivated the production of Th1 cytokines, interferon-γ and tumor necrosis factor-α, from BLV-specific T cells of the infected cattle. Taken together, these results indicate that PD-1 and LAG-3 cooperatively mediate the functional exhaustion of CD4+ and CD8+ T cells and are associated with the development of B-cell lymphoma in BLV-infected cattle.

Genetic diversity and recombination of enterovirus G strains in Japanese pigs: High prevalence of strains carrying a papain-like cysteine protease sequence in the enterovirus G population

To study the genetic diversity of enterovirus G (EV-G) among Japanese pigs, metagenomics sequencing was performed on fecal samples from pigs with or without diarrhea, collected between 2014 and 2016. Fifty-nine EV-G sequences, which were >5,000 nucleotides long, were obtained. By complete VP1 sequence analysis, Japanese EV-G isolates were classified into G1 (17 strains), G2 (four strains), G3 (22 strains), G4 (two strains), G6 (two strains), G9 (six strains), G10 (five strains), and a new genotype (one strain). Remarkably, 16 G1 and one G2 strain identified in diarrheic (23.5%; four strains) or normal (76.5%; 13 strains) fecal samples possessed a papain-like cysteine protease (PL-CP) sequence, which was recently found in the USA and Belgium in the EV-G genome, at the 2C–3A junction site. This paper presents the first report of the high prevalence of viruses carrying PL-CP in the EV-G population. Furthermore, possible inter- and intragenotype recombination events were found among EV-G strains, including G1-PL-CP strains. Our findings may advance the understanding of the molecular epidemiology and genetic evolution of EV-Gs.

Rapid discrimination of strain-dependent fermentation characteristics among Lactobacillus strains by NMR-based metabolomics of fermented vegetable juice

In this study, we investigated the applicability of NMR-based metabolomics to discriminate strain-dependent fermentation characteristics of lactic acid bacteria (LAB), which are important microorganisms for fermented food production. To evaluate the discrimination capability, six type strains of Lactobacillus species and six additional L. brevis strains were used focusing on i) the difference between homo- and hetero-lactic fermentative species and ii) strain-dependent characteristics within L. brevis. Based on the differences in the metabolite profiles of fermented vegetable juices, non-targeted principal component analysis (PCA) clearly separated the samples into those inoculated with homo- and hetero-lactic fermentative species. The separation was primarily explained by the different levels of dominant metabolites (lactic acid, acetic acid, ethanol, and mannitol). Orthogonal partial least squares discrimination analysis, based on a regions-of-interest (ROIs) approach, revealed the contribution of low-abundance metabolites: acetoin, phenyllactic acid, p-hydroxyphenyllactic acid, glycerophosphocholine, and succinic acid for homolactic fermentation; and ornithine, tyramine, and γ-aminobutyric acid (GABA) for heterolactic fermentation. Furthermore, ROIs-based PCA of seven L. brevis strains separated their strain-dependent fermentation characteristics primarily based on their ability to utilize sucrose and citric acid, and convert glutamic acid and tyrosine into GABA and tyramine, respectively. In conclusion, NMR metabolomics successfully discriminated the fermentation characteristics of the tested strains and provided further information on metabolites responsible for these characteristics, which may impact the taste, aroma, and functional properties of fermented foods.

Differential gene expression profiling of endometrium during the mid-luteal phase of the estrous cycle between a repeat breeder (RB) and non-RB cows

BACKGROUND

Repeat breeding directly affects reproductive efficiency in cattle due to an increase in services per conception and calving interval. This study aimed to investigate whether changes in endometrial gene expression profile are involved in repeat breeding in cows. Differential gene expression profiles of the endometrium were investigated during the mid-luteal phase of the estrous cycle between repeat breeder (RB) and non-RB cows using microarray analysis.

METHODS

The caruncular (CAR) and intercaruncular (ICAR) endometrium of both ipsilateral and contralateral uterine horns to the corpus luteum were collected from RB (inseminated at least three times but not pregnant) and non-RB cows on Day 15 of the estrous cycle (4 cows/group). Global gene expression profiles of these endometrial samples were analyzed with a 15 K custom-made oligo-microarray for cattle. Immunohistochemistry was performed to investigate the cellular localization of proteins of three identified transcripts in the endometrium.

RESULTS

Microarray analysis revealed that 405 and 397 genes were differentially expressed in the CAR and ICAR of the ipsilateral uterine horn of RB, respectively when compared with non-RB cows. In the contralateral uterine horn, 443 and 257 differentially expressed genes were identified in the CAR and ICAR of RB, respectively when compared with non-RB cows. Gene ontology analysis revealed that genes involved in development and morphogenesis were mainly up-regulated in the CAR of RB cows. In the ICAR of both the ipsilateral and contralateral uterine horns, genes related to the metabolic process were predominantly enriched in the RB cows when compared with non-RB cows. In the analysis of the whole uterus (combining the data above four endometrial compartments), RB cows showed up-regulation of 37 genes including PRSS2, GSTA3 and PIPOX and down-regulation of 39 genes including CHGA, KRT35 and THBS4 when compared with non-RB cows. Immunohistochemistry revealed that CHGA, GSTA3 and PRSS2 proteins were localized in luminal and glandular epithelial cells and stroma of the endometrium.

CONCLUSION

The present study showed that endometrial gene expression profiles are different between RB and non-RB cows. The identified candidate endometrial genes and functions in each endometrial compartment may contribute to bovine reproductive performance.