Degenerate oligonucleotide primer MIG-seq: an effective PCR-based method for high-throughput genotyping

Next-generation sequencing (NGS) library construction often involves using restriction enzymes to decrease genome complexity, enabling versatile polymorphism detection in plants. However, plant leaves frequently contain impurities, such as polyphenols, necessitating DNA purification before enzymatic reactions. To overcome this problem, we developed a PCR-based method for expeditious NGS library preparation, offering flexibility in number of detected polymorphisms. By substituting a segment of the simple sequence repeat sequence in the MIG-seq primer set (MIG-seq being a PCR method enabling library construction with low-quality DNA) with degenerate oligonucleotides, we introduced variability in detectable polymorphisms across various crops. This innovation, named degenerate oligonucleotide primer MIG-seq (dpMIG-seq), enabled a streamlined protocol for constructing dpMIG-seq libraries from unpurified DNA, which was implemented stably in several crop species, including fruit trees. Furthermore, dpMIG-seq facilitated efficient lineage selection in wheat and enabled linkage map construction and quantitative trait loci analysis in tomato, rice, and soybean without necessitating DNA concentration adjustments. These findings underscore the potential of the dpMIG-seq protocol for advancing genetic analyses across diverse plant species.

Integrated genome-wide differentiation and association analyses identify causal genes underlying breeding-selected grain quality traits in japonica rice

Improving grain quality is a primary objective in contemporary rice breeding. Japanese modern rice breeding has developed two different types of rice, eating and sake-brewing rice, with different grain characteristics, indicating the selection of variant gene alleles during the breeding process. Given the critical importance of promptly and efficiently identifying genes selected in past breeding for future molecular breeding, we conducted genome scans for divergence, genome-wide association studies, and map-based cloning. Consequently, we successfully identified two genes, OsMnS and OsWOX9D, both contributing to rice grain traits. OsMnS encodes a mannan synthase that increases the white core frequency in the endosperm, a desirable trait for sake brewing but decreases the grain appearance quality. OsWOX9D encodes a grass-specific homeobox-containing transcription factor, which enhances grain width for better sake brewing. Furthermore, haplotype analysis revealed that their defective alleles were selected in East Asia, but not Europe, during modern improvement. In addition, our analyses indicate that a reduction in grain mannan content during African rice domestication may also be caused a defective OsMnS allele due to breeding selection. This study not only reveals the delicate balance between grain appearance quality and nutrition in rice but also provides a new strategy for isolating causal genes underlying complex traits, based on the concept of "breeding-assisted genomics" in plants.

High-Density Linkage Maps from Japanese Rice japonica Recombinant Inbred Lines Using Genotyping by Random Amplicon Sequencing-Direct (GRAS-Di)

The genetic dissection of agronomically important traits in closely related Japanese rice cultivars is still in its infancy mainly because of the narrow genetic diversity within japonica rice cultivars. In an attempt to unveil potential polymorphism between closely related Japanese rice cultivars, we used a next-generation-sequencing-based genotyping method: genotyping by random amplicon sequencing-direct (GRAS-Di) to develop genetic linkage maps. In this study, four recombinant inbred line (RIL) populations and their parents were used. A final RIL number of 190 for RIL71, 96 for RIL98, 95 for RIL16, and 94 for RIL91 derived from crosses between a common leading Japanese rice cultivar Koshihikari and Yamadanishiki, Taichung 65, Fujisaka 5, and Futaba, respectively, and the parent plants were subjected to GRAS-Di library construction and sequencing. Approximately 438.7 Mbp, 440 Mbp, 403.1 Mbp, and 392 Mbp called bases covering 97.5%, 97.3%, 98.3%, and 96.1%, respectively, of the estimated rice genome sequence at average depth of 1× were generated. Analysis of genotypic data identified 1050, 1285, 1708, and 1704 markers for each of the above RIL populations, respectively. Markers generated by GRAS-Di were organized into linkage maps and compared with those generated by GoldenGate SNP assay of the same RIL populations; the average genetic distance between markers showed a clear decrease in the four RIL populations when we integrated markers of both linkage maps. Genetic studies using these markers successfully localized five QTLs associated with heading date on chromosomes 3, 6, and 7 and which previously were identified as Hd1, Hd2, Hd6, Hd16, and Hd17. Therefore, GRAS-Di technology provided a low cost and efficient genotyping to overcome the narrow genetic diversity in closely related Japanese rice cultivars and enabled us to generate a high density linkage map in this germplasm.

Identification of Novel Quantitative Trait Loci for Culm Thickness of Rice Derived from Strong-Culm Landrace in Japan, Omachi

Increasing the lodging resistance of rice through genetic improvement has been an important target in breeding. To further enhance the lodging resistance of high-yielding rice varieties amidst climate change, it is necessary to not only shorten culms but strengthen them as well. A landrace rice variety, Omachi, which was established more than 100 years ago, has the largest culm diameter and bending moment at breaking in the basal internodes among 135 temperate japonica accessions. Using unused alleles in such a landrace is an effective way to strengthen the culm. In this study, we performed quantitative trait locus (QTL) analysis to identify the genetic factors of culm strength of Omachi using recombinant inbred lines (RILs) derived from a cross between Omachi and Koshihikari, a standard variety in Japan. We identified three QTLs for the culm diameter of the 5th internode on chromosomes 3 (qCD3) and 7 (qCD7-1, qCD7-2). Among them, qCD7-2 was verified by QTL analysis using the F₂ population derived from a cross between one of the RILs and Koshihikari. RNA-seq analysis of shoot apex raised 10 candidate genes underlying the region of qCD7-2. The increase in culm strength by accumulating Omachi alleles of qCD3, qCD7-1 and qCD7-2 was 25.0% in 2020. These QTLs for culm diameter pleiotropically increased spikelet number per panicle but did not affect days to heading or culm length. These results suggest that the Omachi alleles of qCD3, qCD7-1 and qCD7-2 are useful for breeding to increase lodging resistance and yield.

Identification of a unique allele in the quantitative trait locus for crown root number in japonica rice from Japan using genome-wide association studies

To explore the genetic resources that could be utilized to help improve root system architecture phenotypes in rice (Oryza sativa), we have conducted genome-wide association studies to investigate maximum root length and crown root number in 135 10-day-old Japanese rice accessions grown hydroponically. We identified a quantitative trait locus for crown root number at approximately 32.7 Mbp on chromosome 4 and designated it qNCR1 (quantitative trait locus for Number of Crown Root 1). A linkage disequilibrium map around qNCR1 suggested that three candidate genes are involved in crown root number: a cullin (LOC_Os04g55030), a gibberellin 20 oxidase 8 (LOC_Os04g55070), and a cyclic nucleotide-gated ion channel (LOC_Os04g55080). The combination of haplotypes for each gene was designated as a haploblock, and haploblocks 1, 2, and 3 were defined. Compared to haploblock 1, the accessions with haploblocks 2 and 3 had fewer crown roots; approximately 5% and 10% reductions in 10-day-old plants and 15% and 25% reductions in 42-day-old plants, respectively. A Japanese leading variety Koshihikari and its progenies harbored haploblock 3. Their crown root number could potentially be improved using haploblocks 1 and 2.

Genetic Background Negates Improvements in Rice Flour Characteristics and Food Processing Properties Caused by a Mutant Allele of the PDIL1-1 Seed Storage Protein Gene

Phenotypic differences among breeding lines that introduce the same superior gene allele can be a barrier to effective development of cultivars with desirable traits in some crop species. For example, a deficient mutation of the Protein Disulfide Isomerase Like 1-1 (PDIL1-1) gene can cause accumulation of glutelin seed storage protein precursors in rice endosperm, and improves rice flour characteristics and food processing properties. However, the gene must be expressed to be useful. A deficient mutant allele of PDIL1-1 was introduced into two rice cultivars with different genetic backgrounds (Koshihikari and Oonari). The grain components, agronomic traits, and rice flour and food processing properties of the resulting lines were evaluated. The two breeding lines had similar seed storage protein accumulation, amylose content, and low-molecular-weight metabolites. However, only the Koshihikari breeding line had high flour quality and was highly suitable for rice bread, noodles, and sponge cake, evidence of the formation of high-molecular-weight protein complexes in the endosperm. Transcriptome analysis revealed that mRNA levels of fourteen PDI, Ero1, and BiP genes were increased in the Koshihikari breeding line, whereas this change was not observed in the Oonari breeding line. We elucidated part of the molecular basis of the phenotypic differences between two breeding lines possessing the same mutant allele in different genetic backgrounds. The results suggest that certain genetic backgrounds can negate the beneficial effect of the PDIL1-1 mutant allele. Better understanding of the molecular basis for such interactions may accelerate future breeding of novel rice cultivars to meet the strong demand for gluten-free foods.

Changes in the quality of life score following preoperative chemotherapy in elderly patients with esophageal cancer

BACKGROUND

Various functions in elderly patients with esophageal cancer deteriorate easily and their quality of life can be adversely affected by treatment. The age groups covered in previous studies are wide, and the impact on the elderly individuals is unknown. This study examined changes in quality of life scores after preoperative chemotherapy to clarify aspects of physical, psychological, and social quality of life in elderly patients with esophageal cancer.

METHODS

Thirty-six patients aged over 65 years, who were scheduled to undergo preoperative chemotherapy for esophageal cancer surgery, were enrolled. The survey questionnaire comprised the EORTC QLQ-C30 Japanese Language Version, EORTC QLQ-OES 18 Japanese Language Version, and G8. The surveys were conducted before chemotherapy (pre-CT) and after chemotherapy (post-CT).

RESULTS

In the functional scale of QLQ-C 30, physical functioning decreased significantly, while emotional functioning increased significantly post-CT (p = 0.021, p = 0.030, respectively). Global health status was not changed. In QLQ-OES18, the mean symptom scale score decreased significantly for dysphagia, trouble swallowing saliva, choking, eating, reflux, and pain post-CT (p = 0.014, p = 0.034, p = 0.033, p = 0.022, p = 0.026, p = 0.016, respectively). The mean G8 score decreased significantly from 11.7 to 10.7 (p = 0.022) post-CT, but the proportion of patients with dysfunction decreased.

CONCLUSIONS

Quality of life scores of elderly patients with esophageal cancer who received preoperative chemotherapy decreased in terms of physical function but improved in terms of esophageal cancer symptoms and mental function. Our results suggest that alleviation of symptoms contributed to the improvements in mental health.

JNETS clinical practice guidelines for gastroenteropancreatic neuroendocrine neoplasms: diagnosis, treatment, and follow-up: a synopsis

Neuroendocrine neoplasms (NENs) are rare neoplasms that occur in various organs and present with diverse clinical manifestations. Pathological classification is important in the diagnosis of NENs. Treatment strategies must be selected according to the status of differentiation and malignancy by accurately determining whether the neoplasm is functioning or nonfunctioning, degree of disease progression, and presence of metastasis. The newly revised Clinical Practice Guidelines for Gastroenteropancreatic Neuroendocrine Neoplasms (GEP-NENs) comprises 5 chapters-diagnosis, pathology, surgical treatment, medical and multidisciplinary treatment, and multiple endocrine neoplasia type 1 (MEN1)/von Hippel-Lindau (VHL) disease-and includes 51 clinical questions and 19 columns. These guidelines aim to provide direction and practical clinical content for the management of GEP-NEN preferentially based on clinically useful reports. These revised guidelines also refer to the new concept of "neuroendocrine tumor" (NET) grade 3, which is based on the 2017 and 2019 WHO criteria; this includes health insurance coverage of somatostatin receptor scintigraphy for NEN, everolimus for lung and gastrointestinal NET, and lanreotide for GEP-NET. The guidelines also newly refer to the diagnosis, treatment, and surveillance of NEN associated with VHL disease and MEN1. The accuracy of these guidelines has been improved by examining and adopting new evidence obtained after the first edition was published.

AB0271 COMPARISON OF DOSE REDUCTION METHODS BETWEEN RAPIDLY AND GRADUALLY DE-ESCALATION IN RHEUMATOID ARTHRITIS TREATED WITH BARICITINIB OVER 15 MONTHS

Background:

However tsDMARDs and treatment strategies have improved the outcomes of rheumatoid arthritis (RA), it is unknown who can taper or stop tsDMARDs and strategies for de-escalation.

Objectives:

We analyze predictors of de-escalation in RA patients treated with baricitinib over 15 months in each group who start baricitinib with 4mg/day and 2mg/day.

This study will assess and compare (1) characteristic of patients who achieve remission (REM) or low disease activity (LDA) as who can taper baricitinib and (2) two de-escalation methods, rapidly and gradually de-escalation in patients who respond first-line therapy.

Methods:

Cases were recruited to SHin-yokohama Arthritis REgister (SHARE) between 2015 and 2020 (n=3,961). Patients were diagnosed according to ACR/EULAR 2010 classification criteria and treated with baricitinib started with 4mg/day(n=42) or 2mg/day(n=108) over 15 months. 45 cases fulfilled EULAR definition for difficult-to-treat RA (D2T-RA). In 150 (Male25, Female125 cases, RA duration 12.5+/-5.9years) cases, Clinical Disease Activity Index (CDAI), Health Assessment Questionnaire-Disability Index (HAQ-DI), anti-CCP2 and clinical parameters were analyzed. Two de-escalation methods were compared in this study. In rapidly de-escalation methods, baricitinib were stopped in patients with stable REM/LDA with no swollen joint over 12 weeks. In gradually de-escalation methods, baricitinib were decreased to 50%, 42%, 28%, 14% in order with stable REM/LDA with no swollen joint over 12 weeks.

Results:

(1)” Detect predictors who can achieve REM/LDA with no swollen joint as starting de-escalation baricitinib” In patients started with baricitinib 4mg/day group, 17 patients achieved REM/LDA with no swollen joint(40.5%), there were no differences in duration of RA, onset age of RA, biologics and/or JAK inhibitors naïve, anti-CCP2 titer and CDAI at the start baricitinib between REM/LDA and non-achieved cases. In patients started with baricitinib 2mg/day group, 59 patients achieved REM/LDA with no swollen joint (54.6%). In 2mg/day group, biologics and/or JAK inhibitors naïve was predictor for achieving REM/LDA with no swollen joint. In 2mg/day group, D2T-RA patients was negative predictor.

(2)”Comparison of sustained REM and/or LDA rate between rapidly and gradually de-escalation of baricitinib in rheumatoid arthritis” In whole patients, 15 patients were tapered baricitinib with rapidly de-escalation methods and 61 patients were with gradually de-escalation. Gradually de-escalation methods showed less relapse rate compared with rapidly de-escalation after tapered baricitinib (33.3% vs. 93.8%, p<0.0001). Particularly in 2mg/day group, 12 patients were tapered baricitinib with rapidly de-escalation methods and 47 patients were with gradually de-escalation. Gradually de-escalation methods showed less relapse rate compared with rapidly de-escalation after tapered baricitinib for 32.7 months (33.3% vs. 80.9%, p<0.0001). However 2cases in 4mg/day group and 8cases in 2mg/day showed increase of CDAI, all these cases regain LDA after increasing baricitinib.

Conclusion:

Tapering baricitinib using gradually de-escalation methods may help to sucseed deduction of baricitinib in RA patients with sustained clinical REM and/or LDA with no swollen joint in each group who start baricitinib with 4mg/day and 2mg/day.

References:

[1]Ann Rheum Dis 2019;78:171-178

Disclosure of Interests:

None declared

Predicting Rice Heading Date Using an Integrated Approach Combining a Machine Learning Method and a Crop Growth Model

Accurate prediction of heading date under various environmental conditions is expected to facilitate the decision-making process in cultivation management and the breeding process of new cultivars adaptable to the environment. Days to heading (DTH) is a complex trait known to be controlled by multiple genes and genotype-by-environment interactions. Crop growth models (CGMs) have been widely used to predict the phenological development of a plant in an environment; however, they usually require substantial experimental data to calibrate the parameters of the model. The parameters are mostly genotype-specific and are thus usually estimated separately for each cultivar. We propose an integrated approach that links genotype marker data with the developmental genotype-specific parameters of CGMs with a machine learning model, and allows heading date prediction of a new genotype in a new environment. To estimate the parameters, we implemented a Bayesian approach with the advanced Markov chain Monte-Carlo algorithm called the differential evolution adaptive metropolis and conducted the estimation using a large amount of data on heading date and environmental variables. The data comprised sowing and heading dates of 112 cultivars/lines tested at 7 locations for 14 years and the corresponding environmental variables (day length and daily temperature). We compared the predictive accuracy of DTH between the proposed approach, a CGM, and a single machine learning model. The results showed that the extreme learning machine (one of the implemented machine learning models) was superior to the CGM for the prediction of a tested genotype in a tested location. The proposed approach outperformed the machine learning method in the prediction of an untested genotype in an untested location. We also evaluated the potential of the proposed approach in the prediction of the distribution of DTH in 103 F₂ segregation populations derived from crosses between a common parent, Koshihikari, and 103 cultivars/lines. The results showed a high correlation coefficient (ca. 0.8) of the 10, 50, and 90th percentiles of the observed and predicted distribution of DTH. In this study, the integration of a machine learning model and a CGM was better able to predict the heading date of a new rice cultivar in an untested potential environment.

Sex-related differences in clinical features and in-hospital outcomes of acute aortic dissection type b

Background

Acute aortic dissection (AAD) is a life-threatening medical condition with high morbidity and mortality. The association between female sex and poorer outcomes following surgery for AAD type A has been reported; however, the sex-related differences in clinical features and in-hospital outcomes of AAD type B remain to be elucidated.

Methods

We studied a total of 1877 patients with AAD type B who were enrolled in the Tokyo Acute Aortic Super-network from January 2013 to December 2016. Clinical features and in-hospital outcomes were compared between sexes. Independent predictors of in-hospital mortality were assessed using a multivariable analysis.

Results

The mean age of the patients was 69±13 years and 549 (29%) were females. Female patients were older than males (74±13 years vs 67±13 years; p&lt;0.001). Females had lower systolic blood pressure on admission (158±37 mmHg vs 164±38 mmHg; p=0.007) and were more likely to have altered consciousness level at presentation (8.7% vs 3.9%; p&lt;0.001), intramural hematoma (IMH)-type AAD (62.7% vs 53.6%; p&lt;0.001), and DeBakey type IIIa (28.4% vs 21.8%; p=0.002) compared with males. Females were treated with medical therapy alone more frequently (90.3% vs 85.9%; p=0.009) and had a higher in-hospital mortality rate (5.3% vs 2.6%; p=0.036). A multivariable analysis revealed that age [per year, odds ratio (OR) 1.06; 95% CI 1.04–1.09; p&lt;0.001], altered consciousness level (OR 3.28; 95% CI 1.54–6.98; p=0.002), shock/hypotension (OR 14.0; 95% CI 5.92–33.1; p&lt;0.001), classic-type AAD (OR 2.54; 95% CI 1.36–4.73; p=0.003), and medical therapy alone (OR 0.28; 95% CI 0.15–0.54; p&lt;0.001) were independent predictors of in-hospital mortality, whereas female sex was not predictive of in-hospital mortality (OR 1.64; 95% CI 0.91–2.96; p=0.10).

Conclusion

In AAD type B, females were older and had altered consciousness level, IMH-type, and a less widespread dissection more frequently than males. The overall in-hospital mortality was higher in females; however, female sex was not associated with in-hospital mortality after multivariable adjustment.

Funding Acknowledgement

Type of funding source: None

Diagnostic markers for discriminating between acute aortic dissection and acute myocardial infarction during the pre-hospital phase: analysis of 3,195 cases

 

Both acute aortic dissection (AAD) and acute myocardial infarction (AMI) present with chest pain and are life-threatening diseases that require early diagnosis and treatment for better clinical outcome. However, two critical diseases in the very acute phase are sometimes difficult to differentiate, especially prior to arrival at the hospital for urgent diagnosis and selection of specific treatment.

The aim of our study was to clarify the diagnostic markers acquired from the information gathered from medical history taking and physical examination for discriminating AAD from AMI by using data from the Tokyo Cardiovascular Care Unit (CCU) Network database.

We examined the clinical features and laboratory data of patients with AAD and AMI who were admitted to the hospital in Tokyo between January 2013 and December 2015 by using the Tokyo CCU Network database. The Tokyo CCU Network consists of &gt;60 hospitals that fulfil certain clinical criteria and receive patients from ambulance units coordinated by the Tokyo Fire Department. Of 15,061 patients diagnosed as having AAD and AMI, 3,195 with chest pain within 2 hours after symptom onset (537 AAD and 2,658 AMI) were examined. The patients with out-of-hospital cardiac arrest were excluded.

We compared the clinical data of the patients with chest pain who were diagnosed as having AAD and AMI. The following indicators were more frequent or had higher values among those with AAD: female sex (38% vs. 20%, P&lt;0.001), systolic blood pressures (SBPs) at the time of first contact by the emergency crew (142 mmHg vs. 127 mmHg), back pain in addition to chest pain (54% vs. 5%, P&lt;0.001), history of hypertension (73% vs. 58%, P&lt;0.001), SBP ≥150 mmHg (39% vs. 22%, P&lt;0.001), back pain combined with SBP ≥150 mmHg (23% vs. 0.8%, P&lt;0.001), and back pain with SBP &lt;90 mmHg (4.5% vs. 0.1%, P&lt;0.001). The following data were less frequently observed among those with AAD: diabetes mellitus (7% vs. 28%, P&lt;0.001), dyslipidaemia (17% vs. 42%, P&lt;0.001), and history of smoking (48% vs. 61%, P&lt;0.001). The multivariate regression analysis suggested that back pain with SBP ≥150 mmHg (odds ratio [OR] 47; 95% confidence interval [CI] 28–77; P&lt;0.001), back pain with SBP &lt;90 mmHg (OR 68, 95% CI 16–297, P&lt;0.001), and history of smoking (OR 0.49, 95% CI 0.38–0.63, P&lt;0.001) were the independent markers of AAD. The sensitivity and specificity of back pain with SBPs of ≥150 mmHg and back pain with SBPs &lt;90 mmHg for detecting AAD were 23% and 99%, and 4% and 99%, respectively.

In patients with chest pain suspicious of AAD and AMI, “back pain accompanied by chest pain with SBP ≥150 mmHg” or “back pain accompanied by chest pain with SBP &lt;90 mmH” is a reliable diagnostic marker of AAD with high specificity, although the sensitivity was low. The two SBP values with back pain are markers that may be useful for the ambulance crew at their first contact with patients with chest pain.

Funding Acknowledgement

Type of funding source: None

Impact of hinge motion on stent edge restenosis after new generation drug-eluting-stent implantation in RCA

Background

Edge restenosis still occurs after stent implantation, even by using new generation drug-eluting stents (DES) considered to have favorable biomechanical properties. Mechanical stress imposed on the stent edge are thought to be aggravated by hinge motion at a point between the stented and unstented segments, inducing chronic local inflammation and neointimal overgrowth.

Purpose

The aim of this study was to investigate the association between the development of edge restenosis and hinge motion in right coronary artery (RCA) where the excessive vessel movement is commonly observed.

Methods

Among consecutive 650 lesions in RCA where new generation DESs were implanted between 2009 and 2019, 427 serial lesions with sets of angiographies at baseline and follow-up (6–18 month) were included. In addition to conventional quantitative angiography analysis, hinge angle at stent edges was measured (Fig. 1). All the appropriate data for intravascular imaging were analyzed for both stent edges and reference segments.

Results

Binary restenosis occurred in 43 lesions, and 39 of them were referred to re-intervention. Fifty five percent of them were related to stent edges (15 at proximal and 9 at distal edges). Classical risk factors including diabetes and hemodialysis were more prevalent in the restenosis group (p&lt;0.05). Hinge angle was statistically larger in edge restenosis group than body restenosis or no restenosis group (17.3° vs 11.6° vs 10.6°, p&lt;0.001, Fig. 2). In per-edge analysis, hinge angle, dissection and residual plaque ratio were the independent predictors for binary restenosis (Table 1) with the optimal cut-off value of hinge angle 11.5°. The coexistence of excessive hinge angle and residual plaque burden had an amplified effect on the angiographic stenotic progression at stent edge (p for interaction &lt;0.001) and the incidents of binary restenosis (16.7% vs 1.7% p&lt;0.01, Figs. 3,4).

Conclusion

Substantial stress determined by angulation at the stent edge and its interaction with residual plaque can be considered as one of the plausible mechanisms for edge restenosis. For tortuous RCA lesions, it would be important to decide the stent-landing zone for minimizing hinge motion and optimize the future stent design.

Funding Acknowledgement

Type of funding source: None

Predicting biomass of rice with intermediate traits: Modeling method combining crop growth models and genomic prediction models

Genomic prediction (GP) is expected to become a powerful technology for accelerating the genetic improvement of complex crop traits. Several GP models have been proposed to enhance their applications in plant breeding, including environmental effects and genotype-by-environment interactions (G×E). In this study, we proposed a two-step model for plant biomass prediction wherein environmental information and growth-related traits were considered. First, the growth-related traits were predicted by GP. Second, the biomass was predicted from the GP-predicted values and environmental data using machine learning or crop growth modeling. We applied the model to a 2-year-old field trial dataset of recombinant inbred lines of japonica rice and evaluated the prediction accuracy with training and testing data by cross-validation performed over two years. Therefore, the proposed model achieved an equivalent or a higher correlation between the observed and predicted values (0.53 and 0.65 for each year, respectively) than the model in which biomass was directly predicted by GP (0.40 and 0.65 for each year, respectively). This result indicated that including growth-related traits enhanced accuracy of biomass prediction. Our findings are expected to contribute to the spread of the use of GP in crop breeding by enabling more precise prediction of environmental effects on crop traits.

AB0365 COMPARISON OF SUSTAINED CLINICAL REMISSION AND/OR LOW DISEASE ACTIVITY RATE BETWEEN RAPIDLY AND GRADUALLY DE-ESCALATION OF BARICITINIB IN RHEUMATOID ARTHRITIS

Background:

However baricitinib, an oral selective inhibitor of Janus kinase (JAK) 1 and 2, improved signs and symptoms of rheumatoid arthritis (RA), it is unknown who can taper or stop baricitinib and strategies for de-escalation.

Objectives:

We analyze predictors of tapering of withdrawal failure in rheumatoid arthritis (RA) patients treated with baricitinib. This study will assess and compare (1) characteristic of patients who achieve remission (REM) or low disease activity (LDA) as who can taper baricitinib and (2) two de-escalation methods, rapidly and gradually de-escalation in patients who respond first-line therapy.

Methods:

Cases were recruited to SHin-yokohama Arthritis REgister (SHARE) between 2015 and 2019 (n=3,674). Patients were diagnosed according to ACR/EULAR 2010 classification criteria, and treated with DMARDs which included baricitinib 2mg/day (n=154). In 154 cases, Clinical Disease Activity Index (CDAI), Health Assessment Questionnaire-Disability Index (HAQ-DI), anti-CCP2 and patients clinical parameters were analyzed. Two de-escalation methods were compared in this study. In rapidly de-escalation methods, baricitinib were stopped in patients with stable REM/LDA over 12 weeks. In gradually de-escalation methods, baricitinib were decreased to 50%, 42%, 28%, 14% in order with stable REM/LDA over 12 weeks.

Results:

In 154 (Male25, Female129 cases, RA duration 11.4+/-8.0 years) cases, CDAI at baricitinib-start was 20.6+/-12.4 and titer of anti-CCP2 was 242.6+/-516.5 U/ml. 126 cases (81.8%) were more than 2 years of RA duration and 49 cases (31.8%) had persistency of signs and/or symptoms suggestive of inflammatory RA disease activitiy, despite prior treatment with csDMARDs and at least two biologic DMARDs. 33 cases (21.4%) were biologic DMARDs naive.

(1)”Multivariate logistic regression examined the predictors to detect who can taper baricitinib” However there were no differences in duration of RA, onset age of RA, biologics and/or JAK inhibitors naïve, anti-CCP2 titer and CDAI at the start baricitinib, patients who showed decrease of CDAI at 12 weeks were correlated with achievement of remission (REM) or low disease activity (LDA) in patients treated with baricitinib (OR 0.964, 95%CI 0.934-0.996, p=0.010). ROC analysis of ΔCDAI at 12 weeks is cut-off value of -6.6 (p=0.011).

(2)”Comparison of sustained REM and/or LDA rate between rapidly and gradually de-escalation of baricitinib in rheumatoid arthritis” 11 cases were tapered baricitinib with rapidly de-escalation methods and 60 patients were with gradually de-escalation. Mean times to start taper baricitinib in rapidly and gradually de-escalation group were 4.6+/-1.6 months and 5.9+/-2.2 months respectively. Gradually de-escalation methods showed less relapse rate compared with rapidly de-escalation after tapered baricitinib for 6 months (18.3% vs. 54.5%, p=0.018). There were no differences in clinical features such as anti-CCP2, CDAI and administration period of baricitinib between non-relapse and relapse patients in gradually escalation methods.

Conclusion:

A combination of ΔCDAI at 12 weeks and tapering baricitinib using gradually de-escalation methods may help to predict successful baricitinib deduction in RA patients with sustained clinical REM and/or LDA.

References:

[1]Ann Rheum Dis. 2019;78:171

[2]Rheumatology. 2019;58:110

[3]An Rheum Dis. 2015;74:19

Disclosure of Interests:

None declared

Choosing the optimal population for a genome-wide association study: A simulation of whole-genome sequences from rice

A genome-wide association study (GWAS) needs to have a suitable population. The factors that affect a GWAS (e.g. population structure, sample size, and sequence analysis and field testing costs) need to be considered. Mixed populations containing subpopulations of different genetic backgrounds may be suitable populations. We conducted simulation experiments to see if a population with high genetic diversity, such as a diversity panel, should be added to a target population, especially when the target population harbors small genetic diversity. The target population was 112 accessions of Oryza sativa L. subsp. japonica, mainly developed in Japan. We combined the target population with three populations that had higher genetic diversity. These were 100 indica accessions, 100 japonica accessions, and 100 accessions with various genetic backgrounds. The results showed that the GWAS's power with a mixed population was generally higher than with a separate population. Also, the optimal GWAS populations varied depending on the fixation index (F_ST ) of the quantitative trait nucleotides (QTNs) and the polymorphism of QTNs in each population. When a QTN was polymorphic in a target population, a target population combined with a higher diversity population improved the QTN's detection power. By investigating F_ST and the expected heterozygosity (H_e ) as factors influencing the detection power, we showed that single nucleotide polymorphisms with high F_ST or low H_e are less likely to be detected by GWAS with mixed populations. Sequenced or genotyped germplasm collections can improve the GWAS's detection power by using a subset of the collections with a target population.

QTL analysis of resistance to bacterial wilt caused by Ralstonia solanacearum in potato

Ralstonia solanacearum causes bacterial wilt, a soil-borne disease and one of the most important maladies of potato and other Solanaceae crops. We analyzed the resistance of a potato clone to bacterial wilt by quantitative trait locus (QTL) analysis. A resistant diploid potato clone 10-03-30 was crossed with a susceptible diploid clone F₁-1 to generate a diploid, two-way pseudo-testcross F₁ population comprised of 94 genotypes. Dense linkage maps, containing 4,139 single nucleotide polymorphism markers with an average distance of 0.6 and 0.3 cM between markers, were constructed for both parents. The resistance level was evaluated by in vitro inoculation test with R. solanacearum (phylotype I/biovar 4/race 1). Five QTLs (qBWR-1 to -5) were identified on potato chromosomes 1, 3, 7, 10, and 11, and they explained 9.3-18.4% of the phenotypic variance. The resistant parent had resistant alleles in qBWR-2, qBWR-3, and qBWR-4 and susceptible alleles in qBWR-1 and qBWR-5. Accumulation of the resistant alleles in all five QTLs increased the level of resistance compared with that of the resistant parent. This is the first study to identify novel QTLs for bacterial wilt resistance in potato by using genome-wide markers.

Validation of a quantitative trait locus for the white-core expression rate of grain on chromosome 6 in a brewing rice cultivar and development of DNA markers for marker-assisted selection

Sake-brewing cultivars among varieties of Japanese rice (Oryza sativa L.) have traits adapted to the sake-brewing process, such as a high white-core expression rate (WCE). Our previous study detected putative quantitative trait loci (QTLs) associated with a high WCE derived from Yamadanishiki, a popular brewing rice cultivar. Because the occurrence of white-core grains depends on air temperature and the position of the grain on the panicle, phenotyping of WCE must consider these variable conditions. In this study, qWCE6, a QTL for the WCE on chromosome 6, was validated for the first time, and the phenotyping method examined for its suitability in fine-mapping. A clear tendency towards high WCE was observed in late-heading substituted lines which headed under low daily mean temperature at the experimental location. White-core grains were often expressed by the primary spikelets on the upper panicle, producing a high percentage of superior grains. The segregating population for qWCE6 in late heading revealed a distinct difference in WCE between the Koshihikari and Yamadanishiki homozygous alleles at qWCE6 as determined from that locality. Further, two insertion/deletion markers were developed for the marker-assisted selection of qWCE6. Our results will be useful for informing the breeding of sake-brewing rice cultivars.

Genetic and phenotypic assessment of sugar beet (Beta vulgaris L. subsp. vulgaris) elite inbred lines selected in Japan during the past 50 years

Genetic diversity of Japanese sugar beet elite inbred line diversity (JSBDIV) set consisting of 63 lines was investigated using 33 cleaved amplified polymorphic sequence and 38 simple sequence repeat analyses. JSBDIV set was significantly subdivided into six (pedigree information), seven (Neighbor-Joining method) or 12 (population structure analysis) groups. The highest value of a pairwise population differentiation estimate, Φ PT value, among groups was yielded from population structure analysis with explained variation 32%. Some of the groups defined in this study exhibited close association with ancestral open-pollinated varieties (OPVs), suggesting that inter-OPV cross was rare during the establishment of JSBDIV set. On the other hand, low Φ PT values between some groups suggest that genetic backgrounds of ancestral OPVs had historically overlapped to some extent. Phenotypic traits showed significant differences both among and within groups. A nearly identical group was identified as the highest sugar content group irrespective of the grouping methods. Groups with Aphanomyces root rot resistance are associated with an OPV 'Tmm-1', suggesting it as a source of this trait. 'Tmm-1' is also associated with Cercospora leaf spot resistance, but an exceptional resistant line with no association of 'Tmm-1' supports a notion that different genetic resources exist for this trait.

Description of grain weight distribution leading to genomic selection for grain-filling characteristics in rice

Grain-filling ability is one of the factors that controls grain yield in rice (Oryza sativa L.). We developed a method for describing grain weight distribution, which is the probability density function of single grain weight in a panicle, using 128 Japanese rice varieties. With this method, we quantitively analyzed genotypic differences in grain-filling ability and used the grain weight distribution parameters for genomic prediction subject to genetic improvement in grain yield in rice. The novel description method could represent the observed grain weight distribution with five genotype-specific parameters of a mixture of two gamma distributions. The estimated genotype-specific parameters representing the proportion of filled grains had applicability to explain the grain filling ability of genotypes comparable to that of sink-filling rate and the conventionally measured proportion of filled grains, which suggested the efficiency and flexibility of grain weight distribution parameters to handle several genotypes. We revealed that perfectly filled grains have to be prioritized over partially filled grains for the optimum allocation of the source of yield in a panicle, from the analysis for obtaining an ideal shape of grain weight distribution. We conducted genomic prediction of grain weight distribution considering five genotype-specific parameters of the distribution as phenotypes relating to grain filling ability. The proportion of filled grains, average weight of filled grains, and variance of filled grain weight, which were considered to control grain yield to a certain degree, were predicted with accuracies of 0.30, 0.28, and 0.53, respectively. The proposed description method of grain weight distribution facilitated not only the investigation of the optimum allocation of nutrients in a panicle for realizing high grain-filling ability, but also allowed genomic selection of grain weight distribution.

A novel Rice QTL qOPW11 Associated with Panicle Weight Affects Panicle and Plant Architecture

BACKGROUND

The improvement of rice yield is a crucial global issue, but evaluating yield requires substantial efforts. Rice yield comprises the following indices: panicle number (PN), grain number per panicle (GN), 1000-grain weight, and percentage of ripened grain. To simplify measurements, we analyzed one panicle weight (OPW) as a simplified yield index that integrates GN, grain weight, and percentage of ripened grain, and verified its suitability as a proxy for GN and grain weight in particular.

RESULTS

Quantitative trait locus (QTL) analysis using 190 recombinant inbred lines derived from Koshihikari (large panicle and small grain) and Yamadanishiki (small panicle and large grain), japonica cultivars detected three QTLs on chromosomes 5 (qOPW5), 7 (qOPW7) and 11 (qOPW11). Of these, qOPW5 and qOPW11 were detected over two years. qOPW5 and qOPW7 increased OPW, and qOPW11 decreased it at Yamadanishiki alleles. A chromosome segment substitution line (CSSL) with a genomic segment from Yamadanishiki substituted in the Koshihikari genetic background harboring qOPW5 increased grain weight. qOPW11 had the largest genetic effect of QTLs, which was validated using a CSSL. Substitution mapping using four CSSLs revealed that qOPW11 was located in the range of 1.46 Mb on chromosome 11. The CSSL harboring qOPW11 decreased primary and secondary branch numbers, culm length, and panicle length, and increased PN.

CONCLUSIONS

In this study, three QTLs associated with OPW were detected. The CSSL with the novel and largest QTL, qOPW11, differed in some traits associated with both panicle and plant architecture, indicating different functions for the meristem in the vegetative versus the reproductive stages. qOPW5 coincided with an identified QTL for grain width and grain weight, suggesting that qOPW5 was affected by rice grain size. OPW can be considered a useful trait for efficient detection of QTLs associated with rice yield.

Ethylene-gibberellin signaling underlies adaptation of rice to periodic flooding

Most plants do poorly when flooded. Certain rice varieties, known as deepwater rice, survive periodic flooding and consequent oxygen deficiency by activating internode growth of stems to keep above the water. Here, we identify the gibberellin biosynthesis gene, SD1 (SEMIDWARF1), whose loss-of-function allele catapulted the rice Green Revolution, as being responsible for submergence-induced internode elongation. When submerged, plants carrying the deepwater rice-specific SD1 haplotype amplify a signaling relay in which the SD1 gene is transcriptionally activated by an ethylene-responsive transcription factor, OsEIL1a. The SD1 protein directs increased synthesis of gibberellins, largely GA₄, which promote internode elongation. Evolutionary analysis shows that the deepwater rice-specific haplotype was derived from standing variation in wild rice and selected for deepwater rice cultivation in Bangladesh.

Reflux after esophagectomy with gastric conduit reconstruction in the posterior mediastinum for esophageal cancer: original questionnaire and EORTC QLQ-C30 survey

Reflux following an esophagectomy with gastric conduit reconstruction in the posterior mediastinum is a clinically significant problem. In this study, we investigated the frequency and impact of reflux on the quality of life (QOL) among 158 patients who underwent an esophagectomy for esophageal cancer using an original questionnaire and the European Organization for Research and Treatment of Cancer Quality of Life Questionnaire Version 3.0 (EORTC QLQ-C30). Reflux frequency was assessed using the original questionnaire. The number of patients who complained of reflux every day, two or three times a week, once a week, or less than once a week was 16 (10.1%), 21 (13.3%), 26 (16.5%), and 60 (38.0%), respectively. Out of 35 patients (22.2%) reported no reflux symptoms. Patients were divided into two groups: those with reflux ≥ once/week (63 patients) and those with low frequency of symptoms (95 patients). Time elapsed following surgery was the only factor to influence reflux frequency. Reflux frequency decreased within two years of surgery; however, the frequency plateaued after more than two years. QOL was assessed using the EORTC QLQ-C30. The ≥ once/week reflux group had a significantly lower global health status score than the low-frequency reflux group (59.6 ± 24.2 vs. 70.8 ± 20.7; P = 0.007). In addition, the ≥ once/week reflux group had a significantly lower social functioning score than the low-frequency reflux group (81.6 ± 24.1 vs. 88.4 ± 19.8; P = 0.035). Regarding symptoms, the ≥ once/week reflux group had significantly higher scores for fatigue, nausea, and vomiting, dyspnea and insomnia compared to the low-frequency reflux group (fatigue: 42.4 ± 21.9 vs. 28.9 ± 18.4, P < 0.001; nausea and vomiting: 17.3 ± 17.1 vs. 4.9 ± 10.6, P < 0. 001; dyspnea: 29.2 ± 26.0 vs. 21.7 ± 26.8, P = 0.043; insomnia: 22.2 ± 31.1 vs. 10.5 ± 21.7, P = 0.015). Thus, reflux after an esophagectomy was associated with a lower QOL.

Utility of initial induction chemotherapy with 5-fluorouracil, cisplatin, and docetaxel (DCF) for T4 esophageal cancer: a propensity score-matched analysis

Although no consensus is available on the treatment of esophageal squamous cell carcinoma (ESCC) invading adjacent organs (T4), establishing effective induction treatments is crucial to altering an unresectable status and achieving curative resection. Here, we evaluated the efficacy of chemotherapy using 5-fluorouracil, cisplatin, and docetaxel (DCF) as the initial induction treatment for T4 ESCC. Fifty patients without distant metastasis who underwent initial induction chemotherapy using DCF for T4 ESCC were propensity score-matched with 50 patients who underwent radiotherapy concurrent with cisplatin and 5-fluorouracil (CRT). In the DCF group, 24 (48.0%) patients underwent surgery, achieving a 64% clinical response rate compared to 72.0% for induction CRT. CRT was also performed in another 24 (48.0%) patients in the DCF group in whom surgical resection was not indicated. The DCF group had significantly higher overall resectability than the CRT group (78.0% vs. 48.0%, P = 0.0017). The esophageal perforation rate during induction treatments was significantly lower in the DCF group than the CRT group (4.0% vs. 18.0%, P = 0.0205). Prognosis was significantly better in the DCF group than the CRT group (5-year cancer-specific survival 42.1% vs. 22.2%, P = 0.0146). Thus, induction DCF chemotherapy in patients with T4 ESCC reduced esophageal perforation and increased overall resectability, leading to better survival than CRT alone. Therefore, DCF chemotherapy may be an effective and safe option for initial induction treatment of T4 ESCC.

Identification of QTLs for rice grain size using a novel set of chromosomal segment substitution lines derived from Yamadanishiki in the genetic background of Koshihikari

Grain size is important for brewing-rice cultivars, but the genetic basis for this trait is still unclear. This paper aims to identify QTLs for grain size using novel chromosomal segment substitution lines (CSSLs) harboring chromosomal segments from Yamadanishiki, an excellent sake-brewing rice, in the genetic background of Koshihikari, a cooking cultivar. We developed a set of 49 CSSLs. Grain length (GL), grain width (GWh), grain thickness (GT), 100-grain weight (GWt) and days to heading (DTH) were evaluated, and a CSSL-QTL analysis was conducted. Eighteen QTLs for grain size and DTH were identified. Seven (qGL11, qGWh5, qGWh10, qGWt6-2, qGWt10-2, qDTH3, and qDTH6) that were detected in F₂ and recombinant inbred lines (RILs) from Koshihikari/Yamadanishiki were validated, suggesting that they are important for large grain size and heading date in Yamadanishiki. Additionally, QTL reanalysis for GWt showed that qGWt10-2 was only detected in early-flowering RILs, while qGWt5 (in the same region as qGWh5) was only detected in late-flowering RILs, suggesting that these QTLs show different responses to the environment. Our study revealed that grain size in the Yamadanishiki cultivar is determined by a complex genetic mechanism. These findings could be useful for the breeding of both cooking and brewing rice.

Familial Congenital Methemoglobinemia in Pomeranian Dogs Caused by a Missense Variant in the NADH-Cytochrome B5 Reductase Gene

Background

In veterinary medicine, congenital methemoglobinemia associated with nicotinamide adenine dinucleotide (NADH)‐cytochrome b5 reductase (b5R) deficiency is rare. It has been reported in several breeds of dogs, but little information is available about its etiology.

Objectives

To analyze the NADH‐cytochrome b5 reductase gene, CYB5R3, in a Pomeranian dog family with methemoglobinemia suspected to be caused by congenital b5R deficiency.

Animals

Three Pomeranian dogs from a family with methemoglobinemia were analyzed. Five healthy beagles and 5 nonrelated Pomeranian dogs without methemoglobinemia were used as controls.

Methods

Methemoglobin concentration, b5R activity, and reduced glutathione (GSH) concentration were measured, and a turbidity index was used to evaluate Heinz body formation. The CYB5R3 genes of the affected dog and healthy dogs were analyzed by direct sequencing.

Results

Methemoglobin concentrations in erythrocytes of the affected dogs were remarkably higher than those of the control dogs. The b5R activity of the affected dogs was notably lower than that of the control dogs. DNA sequencing indicated that this Pomeranian family carried a CYB5R3 gene missense variant (ATC→CTC at codon 194) that resulted in the replacement of isoleucine (Ile) by leucine (Leu).

Conclusions and Clinical Importance

This dog family had familial congenital methemoglobinemia caused by b5R deficiency, which resulted from a nonsynonymous variant in the CYB5R3 gene. This variation (c.580A>C) led to an amino acid substitution (p.Ile194Leu), and Ile194 was located in the proximal region of the NADH‐binding motif. Our data suggested that this variant in the canine CYB5R3 gene would affect function of the b5R in erythrocytes.

Genetic dissection of grain traits in Yamadanishiki, an excellent sake-brewing rice cultivar

The grain traits of Yamadanishiki, an excellent sake-brewing rice cultivar in Japan, are governed by multiple QTLs, namely, a total of 42 QTLs including six major QTLs. Japanese rice wine (sake) is produced using brewing rice (Oryza sativa L.) that carries traits desirable for sake-brewing, such as a larger grain size and higher white-core expression rate (WCE) compared to cooking rice cultivars. However, the genetic basis for these traits in brewing rice cultivars is still unclear. We performed analyses of quantitative trait locus (QTL) of grain and days to heading over 3 years on populations derived from crosses between Koshihikari, a cooking rice, and Yamadanishiki, an excellent sake-brewing rice. A total of 42 QTLs were detected for the grain traits, and the Yamadanishiki alleles at 16 QTLs contributed to larger grain size. Two major QTLs essential for regulating both 100-grain weight (GWt) and grain width (GWh) were harbored in the same regions on chromosomes 5 and 10. An interaction was noted between the environment and the QTL associated with WCE on chromosome 6, which was detected in two of 3 years. In addition, two QTLs for WCE on chromosomes 3 and 10 overlapped with the QTLs for GWt and GWh, suggesting that QTLs associated with grain size also play an important role in the formation of white-core. Despite differences in the rate of grain growth in both Koshihikari and Yamadanishiki across 2 years, the WCE in Yamadanishiki remained consistent, thus demonstrating that the formation of white-core does not depend on grain filling speed. These data can be informative for programs involved in breeding better cooking and brewing rice cultivars.

Comparison of short-term outcomes between 2- and 3-field lymph node dissection for esophageal cancer

Although 3-field lymph node dissection (3-FLD) is often performed for thoracic esophageal squamous cell carcinoma (ESCC), the clinical effects of cervical lymph node dissection in addition to mediastinal and abdominal dissections on postoperative complications remain unclear. A total of 367 ESCC patients who underwent curative esophagectomy for thoracic esophageal cancer in our hospital from 2010 to 2015 were included in the study: 157 patients who underwent 2-field lymph node dissection (2-FLD) and 210 patients who underwent 3-FLD. Clinicopathological parameters and postoperative complications based on the Clavien-Dindo classification were compared between the two groups. We performed propensity score matching (PSM) analyses to compare the groups with well-balanced backgrounds. In terms of patient background, clinical T (p < 0.001), N (p < 0.001), and M (p = 0.002) stage of tumor was significantly more advanced; therefore, preoperative treatment was more frequently performed in the 3-FLD group than in the 2-FLD group (91.0% vs. 79.0%, P< 0.001). However, perioperative parameters including operation time, blood loss, and the number of dissected mediastinal and abdominal lymph nodes did not differ between the groups. In terms of postoperative complications, the occurrence rate of pneumonia increased significantly in patients with 3-FLD compared to 2-FLD (grade III or higher: 10.5% vs. 3.2%, P= 0.025). Although the duration of systemic inflammatory response syndrome (SIRS) was longer in the 3-FLD group than in the 2-FLD group (median 3 days vs. 2 days, P= 0.025), other postoperative parameters (including the highest level of postoperative serum C-reactive protein, intensive care unit stay, re-operation rate, and postoperative hospital stay) were similar between the groups. After PSM, the differences in the background between the groups disappeared. PSM analysis showed that there was no significant difference in each complication between the groups. The duration of SIRS tended to be longer in the 3-FLD group than in the 2-FLD group, but the difference was not significant. The field of lymphadenectomy negatively impacted the short-term outcome in ESCC patients in terms of pneumonia and inflammatory response. However, because the results of the PSM analyses indicate that the short-term outcome was similar between the two groups, 3-FLD could be as feasible as 2-FLD in ESCC patients.

Differences in glucose yield of residues from among varieties of rice, wheat, and sorghum after dilute acid pretreatment

Bio-refinery processes require use of the most suitable lignocellulosic biomass for enzymatic saccharification and microbial fermentation. Glucose yield from biomass solid fractions obtained after dilute sulfuric acid (1%) pretreatment (at 180 °C) was investigated using 14, 8, and 16 varieties of rice, wheat, and sorghum, respectively. Biomass solid fractions of each crop showed similar cellulose content. However, glucose yield after enzymatic hydrolysis (cellulase loading at 6.6 filter paper unit/g-biomass) was different among the varieties of each crop, indicating genotypic differences for rice, wheat, and sorghum. Nuclear magnetic resonance method revealed that the high residual level of lignin aromatic regions decreased glucose yield from solid fraction of sorghum.

Electro-optic probe measurements of electric fields in plasmas

The direct measurements of high-frequency electric fields in a plasma bring about significant advances in the physics and engineering of various waves. We have developed an electro-optic sensor system based on the Pockels effect. Since the signal is transmitted through an optical fiber, the system has high tolerance for electromagnetic noises. To demonstrate its applicability to plasma experiments, we report the first result of measurement of the ion-cyclotron wave excited in the RT-1 magnetosphere device. This study compares the results of experimental field measurements with simulation results of electric fields in plasmas.