Analyzing the response of rice to tefuryltrione herbicide: Haplotype variation and evolutionary dynamics of the HIS1 gene.

Weeds pose multifaceted challenges in rice cultivation, leading to substantial economic losses through reduced yield and poor grain quality. Harnessing the natural genetic diversity in germplasm collections becomes crucial for identifying novel herbicide resistance loci in crops. A comprehensive analysis was conducted on 475 rice accessions from the KRICE depository, assessing their response to TFT (tefuryltrione) and probing the underlying HIS1 (HPPD INHIBITOR SENSITIVE 1) genotypic variations. The HIS1 gene, responsible for detoxifying benzobicyclon (BBC) and imparting broad-spectrum herbicide resistance, holds significant promise in rice breeding. This study explores the genetic landscape of HIS1 within Korean rice collection (KRICE), aiming to unveil genetic variations, haplotype diversity, and evolutionary relationships across diverse rice ecotypes. The indica ecotype showed the highest nucleotide diversity, while the wild and temperate japonica groups exhibited low diversity, hinting at selective sweeps and possible population expansion. Negative Tajima's D values in temperate japonica and wild groups indicate an excess of low-frequency mutations, potentially resulting from selective sweeps. In contrast, with positive Tajima's D values, admixture, indica, and aus groups suggest balancing selection. Furthermore, haplotype analysis uncovered 42 distinct haplotypes within KRICE, with four shared haplotypes between cultivated and wild accessions, four specific to cultivated accessions, and 34 specific to wild types. Phenotypic assessments of these haplotypes revealed that three haplotypes, viz., Hap_1 (predominant in japonica), Hap_2 (predominant in indica), and Hap_3 (specific to indica), displayed significant differences from aus-specific Hap_4 and indica-specific Hap_5. This study offers insights into genetic diversity, selective pressures, and ecotype-specific responses, ultimately paving the way for developing HPPD-inhibiting herbicide-resistant rice cultivars.

Direct comparison of diagnostic and clinical values between Tc-99 m DPD and Tc-99 m PYP scintigraphy in patients with cardiac amyloidosis.

BACKGROUND: Technetium-99 m 3,3-diphosphono-1,2-propanodicarboxylic acid (DPD) and technetium-99 m sodium pyrophosphate (PYP) are the two most commonly used radiotracers for cardiac amyloidosis (CA), but no studies have directly compared them. Therefore, in this study, we directly compared the diagnostic and clinical utility of DPD and PYP scintigraphy in patients with CA. METHODS: Ten patients with CA were enrolled. Eight clinical variables and 12 scintigraphic parameters were used. Clinical variables were age, sex, estimated glomerular filtration rate (eGFR), N-terminal pro brain natriuretic peptide (NT-proBNP), and the results of electromyography (EMG), a sensory test, electrocardiogram, and echocardiography (EchoCG). Four heart retention ratios (heart/whole-body profile, heart/pelvis, heart/skull, and heart/contralateral lung) were calculated from the DPD and PYP scans and two visual scoring systems (Perugini and Dorbala systems) were used. Comparative analyses were performed between radiotracers and between visual scoring systems using clinical variables and scintigraphic parameters. RESULTS: Twenty DPD parameters and nine PYP parameters had significant associations with age, eGFR, NT-proBNP, EchoCG, and EMG. DPD parameters had more frequent significant associations with clinical variables than PYP parameters. Compared to visual scores in the DPD scan, the proportion of patients with higher visual scores in the PYP scan was relatively greater than those with lower visual scores, and there were more patients with a visual score of 2 or higher in PYP scans than DPD scans. CONCLUSIONS: DPD scintigraphy may reflect the disease severity of CA better than PYP scintigraphy, whereas PYP scintigraphy may be a more sensitive imaging modality for identifying CA involvement.

Effects of Smart Advanced Life Support protocol implementation including CPR coaching during out-of-hospital cardiac arrest.

PURPOSE: The aim of this study was to compare out-of-hospital cardiac arrest (OHCA) outcomes before and after implementation of Smart Advanced Life Support (SALS) protocol incorporating changes in cardiopulmonary resuscitation (CPR) assistance and coaching by physicians via real-time video calls. METHODS: A prospective before-and-after multi-regional observational study was conducted between January 2014 and December 2018. In January 2016, emergency medical service (EMS) providers adopted an integrated CPR coaching by physicians via real-time video call via SALS to treat patients with OHCA focusing on high-quality cardiopulmonary resuscitation. Propensity score matching was performed to match patients. Patients' outcomes using conventional protocol were then compared with those of patients using the SALS protocol. RESULTS: Among 26,349 OHCA cases, 2351 patients and 7261 patients were enrolled during the pre-intervention and the post-intervention periods, respectively. Multivariate analysis showed that SALS was independently associated with favorable neurological outcomes [odds ratio (OR): 2.20; 95% confidence interval (CI): 1.62-2.99]. A total of 2096 patients were propensity score-matched and the two groups were well balanced. In the matched cohort, the use of SALS protocol was still associated with increased prehospital return of spontaneous circulation (ROSC) (OR: 3.83, 95% CI: 2.80-5.26), survival to discharge (OR: 1.68; 95% CI: 1.20-2.34), and favorable neurological outcomes (OR: 1.83; 95% CI: 1.19-2.82). CONCLUSION: A multidisciplinary SALS protocol for the resuscitation of patients with OHCA was associated with increased prehospital ROSC, survival to discharge, and good neurologic outcomes compared with traditional resuscitation protocol.

Machine learning-based diagnostic method of pre-therapeutic 18F-FDG PET/CT for evaluating mediastinal lymph nodes in non-small cell lung cancer.

OBJECTIVES: We aimed to find the best machine learning (ML) model using 18F-fluorodeoxyglucose (FDG) positron emission tomography/computed tomography (PET/CT) for evaluating metastatic mediastinal lymph nodes (MedLNs) in non-small cell lung cancer, and compare the diagnostic results with those of nuclear medicine physicians. METHODS: A total of 1329 MedLNs were reviewed. Boosted decision tree, logistic regression, support vector machine, neural network, and decision forest models were compared. The diagnostic performance of the best ML model was compared with that of physicians. The ML method was divided into ML with quantitative variables only (MLq) and adding clinical information (MLc). We performed an analysis based on the 18F-FDG-avidity of the MedLNs. RESULTS: The boosted decision tree model obtained higher sensitivity and negative predictive values but lower specificity and positive predictive values than the physicians. There was no significant difference between the accuracy of the physicians and MLq (79.8% vs. 76.8%, p = 0.067). The accuracy of MLc was significantly higher than that of the physicians (81.0% vs. 76.8%, p = 0.009). In MedLNs with low 18F-FDG-avidity, ML had significantly higher accuracy than the physicians (70.0% vs. 63.3%, p = 0.018). CONCLUSION: Although there was no significant difference in accuracy between the MLq and physicians, the diagnostic performance of MLc was better than that of MLq or of the physicians. The ML method appeared to be useful for evaluating low metabolic MedLNs. Therefore, adding clinical information to the quantitative variables from 18F-FDG PET/CT can improve the diagnostic results of ML. KEY POINTS: • Machine learning using two-class boosted decision tree model revealed the highest value of area under curve, and it showed higher sensitivity and negative predictive values but lower specificity and positive predictive values than nuclear medicine physicians. • The diagnostic results from machine learning method after adding clinical information to the quantitative variables improved accuracy significantly than nuclear medicine physicians. • Machine learning could improve the diagnostic significance of metastatic mediastinal lymph nodes, especially in mediastinal lymph nodes with low 18F-FDG-avidity.

Survival and Rearrest in out-of-Hospital Cardiac Arrest Patients with Prehospital Return of Spontaneous Circulation: A Prospective Multi-Regional Observational Study.

OBJECTIVE: We aimed to determine the factors associated with rearrest after prehospital return of spontaneous circulation (ROSC) and examine the factors associated with survival despite rearrest. METHODS: We conducted a prospective multi-regional observational study of out-of-hospital cardiac arrest (OHCA) patients between August 2015 and July 2016. Patients received prehospital advanced cardiovascular life support performed by emergency medical technicians (EMTs). EMTs were directly supervised by medical directors (physicians) via real-time smartphone video calls [Smart Advanced Life Support (SALS)]. The study participants were categorized into rearrest (+) and rearrest (-) groups depending on whether rearrest occurred after prehospital ROSC. After rearrest, patients were further classified as survivors or non-survivors at discharge. RESULTS: SALS was performed in 1,711 OHCA patients. Prehospital ROSC occurred in 345 patients (20.2%); of these patients, 189 (54.8%) experienced rearrest [rearrest (+) group] and 156 did not experience rearrest [rearrest (-) group]. Multivariate analysis showed that a longer interval from collapse to first prehospital ROSC was independently associated with rearrest [odds ratio (OR) 1.081; 95% confidence interval (CI) 1.050-1.114]. The presence of an initial shockable rhythm was independently associated with survival after rearrest (OR 6.920; 95% CI 2.749-17.422). As a predictor of rearrest, the interval from collapse to first prehospital ROSC (cut-off: 24 min) had a sensitivity of 77% and a specificity of 54% (AUC = 0.715 [95% CI 0.661-0.769]). CONCLUSIONS: A longer interval from collapse to first prehospital ROSC was associated with rearrest, and an initial shockable rhythm was associated with survival despite the occurrence of rearrest. Emergency medical service providers and physicians should be prepared to deal with rearrest when pulses are obtained late in the resuscitation.

Haplotype Analysis of BADH1 by Next-Generation Sequencing Reveals Association with Salt Tolerance in Rice during Domestication.

Betaine aldehyde dehydrogenase 1 (BADH1), a paralog of the fragrance gene BADH2, is known to be associated with salt stress through the accumulation of synthesized glycine betaine (GB), which is involved in the response to abiotic stresses. Despite the unclear association between BADH1 and salt stress, we observed the responses of eight phenotypic characteristics (germination percentage (GP), germination energy (GE), germination index (GI), mean germination time (MGT), germination rate (GR), shoot length (SL), root length (RL), and total dry weight (TDW)) to salt stress during the germination stage of 475 rice accessions to investigate their association with BADH1 haplotypes. We found a total of 116 SNPs and 77 InDels in the whole BADH1 gene region, representing 39 haplotypes. Twenty-nine haplotypes representing 27 mutated alleles (two InDels and 25 SNPs) were highly (p < 0.05) associated with salt stress, including the five SNPs that have been previously reported to be associated with salt tolerance. We observed three predominant haplotypes associated with salt tolerance, Hap_2, Hap_18, and Hap_23, which were Indica specific, indicating a comparatively high number of rice accessions among the associated haplotypes. Eight plant parameters (phenotypes) also showed clear responses to salt stress, and except for MGT (mean germination time), all were positively correlated with each other. Different signatures of domestication for BADH1 were detected in cultivated rice by identifying the highest and lowest Tajima's D values of two major cultivated ecotypes (Temperate Japonica and Indica). Our findings on these significant associations and BADH1 evolution to plant traits can be useful for future research development related to its gene expression.

Dietary intake of walnut prevented Helicobacter pylori-associated gastric cancer through rejuvenation of chronic atrophic gastritis.

The fact that Fat-1 transgenic mice producing n-3 polyunsaturated fatty acids via overexpressed 3-desaturase significantly mitigated Helicobacter pylori (H. pylori)-associated gastric tumorigenesis through rejuvenation of chronic atrophic gastritis (CAG) led us to study whether dietary intake of walnut plentiful of n-3 PUFAs can be nutritional intervention to prevent H. pylori-associated gastric cancer. In our model that H. pylori-initiated, high salt diet-promoted gastric carcinogenesis, pellet diet containing 100 mg/kg and 200 mg/kg walnut was administered up to 36 weeks. As results, control mice (24 weeks) developed significant chronic CAG, in which dietary walnuts significantly ameliorated chronic atrophic gastritis. Expressions of COX-2/PGE2/NF-κB/c-Jun, elevated in 24 weeks control group, were all significantly decreased with walnut (p<0.01). Tumor suppressive enzyme, 15-PGDH, was significantly preserved with walnut. Control mice (36 weeks) all developed significant tumors accompanied with severe CAG. However, significantly decreased tumorigenesis was noted in group treated with walnuts, in which expressions of COX-2/PGE2/NF-κB/IL-6/STAT3, all elevated in 36 weeks control group, were significantly decreased with walnut. Defensive proteins including HO-1, Nrf2, and SOCS-1 were significantly increased in walnut group. Proliferative index as marked with Ki-67 and PCNA was significantly regulated with walnut relevant to 15-PGDH preservation. Conclusively, walnut can be an anticipating nutritional intervention against H. pylori.

Is Coincidental Rhinosinusitis a Predisposing Factor for Postoperative Central Nervous System Infection After Endoscopic Endonasal Transsphenoidal Surgery?

BACKGROUND: To investigate the effect of rhinosinusitis in patients who undergo surgery via the endoscopic endonasal transsphenoidal approach (EETSA). METHODS: The authors retrospectively reviewed the medical records of patients who underwent surgery via the EETSA between February 2009 and November 2016. In total, 505 patients were included in the study. Preoperative paranasal sinus computed tomography, sellar magnetic resonance imaging, and nasal endoscopy were performed for all the patients. RESULTS: Fifteen patients without sphenoid sinusitis underwent surgery with the concomitant transsphenoidal approach and functional endoscopic sinus surgery, and showed no central nervous system (CNS) complication. During surgery via the EETSA, the presence of rhinosinusitis did not significantly affect the incidence of postoperative CNS infection (P = 0.051), except for sphenoid sinusitis (P = 0.003). Conversely, the incidence of postoperative CNS infection was not related significantly to the Lund-Mackay score or tumor size. The risk of CNS infection was 12.151-fold higher in patients with sphenoid sinusitis (95% confidence interval, 3.153-46.827; P ≤ 0.001). CONCLUSION: Surgery via the EETSA and functional endoscopic sinus surgery can be safely performed together in most patients with rhinosinusitis. However, sphenoid sinus infection appears to be a predisposing factor for postoperative CNS infection. Therefore, a separate surgical procedure for sphenoid lesions should be considered in these patients before the use of the EETSA.

Can Tumor Size Be a Predictive Factor of Olfactory Dysfunction After Endoscopic Endonasal Trans-Sphenoidal Approach?

BACKGROUND AND OBJECTIVE: The aim of this study is to investigate the relationships between tumor size, nasal symptoms including olfactory function, and posoperative atrophic mucosal changes after the endoscopic endonasal transsphenoidal approach (EETSA). METHODS: This was a retrospective review of the medical records of 112 patients who underwent the 2 nostrils/4 hands EETSA with bilateral modified nasoseptal rescue flaps between February 2009 and January 2016. Pre- and postoperative paranasal sinus computed tomography, nasal cavity endoscopic images, the Connecticut Chemosensory Clinical Research Center (CCCRC) test, Cross-Cultural Smell Identification Test (CCSIT), the Nasal Obstruction Symptoms Evaluation, and the Sino-Nasal Outcome Test-20 were conducted. Nasal mucosal changes as determined by endoscopy were divided into 4 groups: normal to normal, Group A; atrophy to atrophy, Group B; normal to atrophy, Group C; and atrophy to more atrophy, Group D. The Mimics program was used to calculate nasal cavity volume changes after surgery. RESULTS: There were significant differences between pre- and postoperative olfactory function as reflected by the CCCRC (P < 0.001) and CCSIT (P < 0.001) scores. There was also a correlation between tumor size and olfactory function scores such as the CCCRC (P = 0.012) or CCSIT (P = 0.015). Moreover, nasal mucosal atrophic changes were related to tumor size and olfactory function tests. CONCLUSION: The tumor size was related to olfactory function and atrophic mucosal changes. Therefore, patients with large tumors should be informed that, after the EETSA, their olfaction may be altered and that nasal symptoms related to mucosal atrophy could occur.

A Genome-Wide Association Study Reveals Candidate Genes Related to Salt Tolerance in Rice (Oryza sativa) at the Germination Stage.

Salt toxicity is the major factor limiting crop productivity in saline soils. In this paper, 295 accessions including a heuristic core set (137 accessions) and 158 bred varieties were re-sequenced and ~1.65 million SNPs/indels were used to perform a genome-wide association study (GWAS) of salt-tolerance-related phenotypes in rice during the germination stage. A total of 12 associated peaks distributed on seven chromosomes using a compressed mixed linear model were detected. Determined by linkage disequilibrium (LD) blocks analysis, we finally obtained a total of 79 candidate genes. By detecting the highly associated variations located inside the genic region that overlapped with the results of LD block analysis, we characterized 17 genes that may contribute to salt tolerance during the seed germination stage. At the same time, we conducted a haplotype analysis of the genes with functional variations together with phenotypic correlation and orthologous sequence analyses. Among these genes, OsMADS31, which is a MADS-box family transcription factor, had a down-regulated expression under the salt condition and it was predicted to be involved in the salt tolerance at the rice germination stage. Our study revealed some novel candidate genes and their substantial natural variations in the rice genome at the germination stage. The GWAS in rice at the germination stage would provide important resources for molecular breeding and functional analysis of the salt tolerance during rice germination.

Genome-wide association study and gene set analysis for understanding candidate genes involved in salt tolerance at the rice seedling stage.

Salt is the major factor limiting crop productivity in saline soils and is controlled by various genes. The development of salt-tolerant rice through molecular breeding methods is important to meet the needs of rice breeding. We used 295 accessions to perform a genome-wide association study (GWAS) of salt tolerance-related phenotypes in rice at the seedling stage and obtained 93 candidate genes with high association peaks across six phenotypes. We constructed a protein interaction network using the candidate genes identified here, and 33 genes were associated. Based on the expression patterns, we found that most of these genes showed a different expression level under control and salt stress conditions. In addition, haplotype network and sequence analysis of one 'key' gene, a transcription factor (Os12g0176700) encoding a SWIRM domain-containing protein, in the interaction network was investigated to explore its possible role in the network. Our study revealed candidate salt tolerance-related genes in rice at the seedling stage, and demonstrated the feasibility of using GWAS to identify genetic architecture underlying salt tolerance. The data generated here may provide resources for molecular breeding and functional analysis of salt tolerance in rice seedlings.

Population genomics identifies the origin and signatures of selection of Korean weedy rice.

Weedy rice is the same biological species as cultivated rice (Oryza sativa); it is also a noxious weed infesting rice fields worldwide. Its formation and population-selective or -adaptive signatures are poorly understood. In this study, we investigated the phylogenetics, population structure and signatures of selection of Korean weedy rice by determining the whole genomes of 30 weedy rice, 30 landrace rice and ten wild rice samples. The phylogenetic tree and results of ancestry inference study clearly showed that the genetic distance of Korean weedy rice was far from the wild rice and near with cultivated rice. Furthermore, 537 genes showed evidence of recent positive or divergent selection, consistent with some adaptive traits. This study indicates that Korean weedy rice originated from hybridization of modern indica/indica or japonica/japonica rather than wild rice. Moreover, weedy rice is not only a notorious weed in rice fields, but also contains many untapped valuable traits or haplotypes that may be a useful genetic resource for improving cultivated rice.

Combined Administration of IV and Topical Tranexamic Acid is Not Superior to Either Individually in Primary Navigated TKA.

BACKGROUND: In this study, we tried to assess if combined method (intravenous [IV] and topical) of tranexamic acid (TXA) administration, which has been shown to be superior in conventional arthroplasty, has similar effect in navigational arthroplasty compared to administration of drug either individually. METHODS: In present randomized control trial, 200 patients were randomly divided in one of the 4 groups using computer-generated tables-control, IV, intraarticular, and combined. We studied evident loss through drain, total loss based on Gross method and hemoglobin balance method, hidden losses, hemoglobin and hematocrit drop, functional scores, and all possible complications related to TXA. RESULTS: Evident loss in combined group was 535.55 mL, not significantly less than IV (585 mL, P = .15) and intraarticular group (514 mL, P = .74). However, these were significantly less than control group (696 mL, P = .000). Functional scores and recovery rates were, however, comparable in all 4 groups. No patients in any group developed symptomatic deep vein thrombosis. CONCLUSION: Tranexamic use decreases blood loss in navigation-assisted arthroplasty, however, less than that observed for conventional arthroplasty in literature. Further, combined group has no added advantage over other methods of drug administration. We believe that additional amount of TXA administered in combined regimen may not be clinically useful. Further TXA group did not have any advantage in terms of functional recovery over control group.

How to Expose the Entire Sella Floor With Minimal Manipulation During an Endoscopic Endonasal Transsphenoidal Approach.

OBJECTIVE: A method of opening the posterior ethmoid air cells with minimal manipulation is important for adequate exposure of the sella floor and minimal nasal morbidity. METHODS: Between February 2009 and August 2016, 373 patients with skull-base tumors underwent surgery via endoscopic endonasal transsphenoidal approach with the 2-nostrils/4-hands technique using this technique. RESULTS: A linear incision was made laterally toward one-third of the superior turbinate along the superior border of the sphenoid sinus ostium. Then, the superior turbinate mucosa was fully elevated to expose the superior turbinate bone. This allowed us to expose the entire sella floor and adjacent vital structures, such as the optic and carotid protuberances, medial and lateral opticocarotid recesses, planum sphenoidale, and clivus, leaving the superior turbinate and surrounding nasal mucosa intact. CONCLUSION: This technique could improve the manipulability of surgical instruments and increase the accessibility of the parasellar region. This approach better conserves the nasal mucosa, posterior ethmoid, and superior and supreme turbinates and more efficiently exposes skull-base tumors than traditional methods with pathology of the anterior cranial fossa and parasellar region. This technique also prevents the drilling procedure from damaging the surrounding nasal mucosa, including the exfoliated and laterally preserved posterior sphenoid mucosa.

Risk Factors Predicting Nasoseptal Flap Failure in the Endoscopic Endonasal Transsphenoidal Approach.

OBJECTIVE: Reconstruction of the skull base using a pedicled nasoseptal flap (NSF) seems to be advantageous after the endoscopic endonasal transsphenoidal approach (EETSA). A few reports have evaluated the cause of flap failure in EETSA using NSFs. The aim of this study was to evaluate the perioperative risk factors for NSF failure. STUDY DESIGN: Patient series. SETTING: Retrospective review of medical records at a tertiary referral center. METHODS: The study population comprised patients who underwent EETSA with NSF elevation between February 2009 and March 2014. The authors retrospectively reviewed the all patients' medical records, including operative findings. RESULTS: Four hundred thirteen patients (203 males and 210 females) underwent EETSA, and 315 patients underwent EETSA with NSF elevation. The mean patient age was 48.0 years. The total number of patients of NSF failure was 6 (overall rate: 1.61%, 6/315; flap elevation: 0.31%, 1/315; flap reconstruction: 15.1%, 5/33). Two patients had diabetes mellitus. One patient had cardiovascular problems. Five patients were elderly (>60 years; mean age: 70 years). Five patients had postoperative nasal infection. One patient underwent preoperative radiation therapy. CONCLUSION: Nasoseptal flap is a usually safe and effective technique for skull base reconstruction. However, the management of patients with diabetes mellitus, cardiovascular problems, advanced age, postoperative nasal infection, and radiation therapy may require more attention to improve NSF survival.

Endoscopic Endonasal Transsphenoidal Approach From the Surgeon Point of View.

OBJECTIVE: In February 2009, the authors' center formed a team of neurosurgeons, otolaryngologists, endocrinologists, and radiologists to perform pituitary surgery using the endoscopic endonasal transsphenoidal approach (EETSA). This paper reviews the authors' experience with the technique, pathological outcomes, hormone profiles, and postoperative complications. METHODS: Between February 2009 and December 2015, 535 patients underwent the EETSA with 2-nostrils/4-hands surgery. All of the patients had preoperative neurophthalmological and endocrinological assessments and neuroimaging. Patients were followed for at least 6 months with otolaryngological evaluations. RESULTS: The most common pathology treated was pituitary adenomas, with 390 (72.9%) patients. Of these, 287 (73.6%) were nonfunctioning adenomas. As the surgical method, the conventional 2-nostrils/4-hands technique was performed in 77 patients (14.4%), a right conventional nasoseptal flap and left modified nasoseptal rescue flap technique was used in 135 patients (25.2%), and bilateral modified nasoseptal rescue flaps were used in 323 patients (60.4%). Postoperative complications occurred in 46 patients (8.6%). The most common complications were vascular injury or hematoma (10 patients, 1.9%), and the most common postoperative sinonasal complaints were hyposmia or anosmia. Olfactory function was significantly decreased according to the Connecticut Chemosensory Clinical Research Center test (P <0.001) and Cross-Cultural Smell Identification Test scores (P <0.001) evaluated 6 months postoperatively. CONCLUSIONS: Skull-base tumor surgery via an EETSA with a team approach was performed for various extended tumors. It is important to consider postoperative sinonasal dysfunction, such as hyposmia or anosmia, and to have this followed by an otolaryngologist.

Genome-wide association study of eating and cooking qualities in different subpopulations of rice (Oryza sativa L.).

BACKGROUND: Starch and protein are two major components of polished rice, and the amylose and protein contents affect eating and cooking qualities (ECQs). In the present study, genome-wide association study with high-quality re-sequencing data was performed for 10 ECQs in a panel of 227 non-glutinous rice accessions and four derived panels. RESULTS: Population structure accounted for high phenotypic variation in three routine panels and had minor effects on subspecies-based panels. Using the mixed linear model method based on the P + K model, we detected 29, 24, 16, 17, and 29 loci that were significant for ECQ parameters in each of the five panels. Some of these loci were close to starch synthesis-related genes. Two quantitative trait loci (QTLs) (chr.9: 15417525 ~ 15474876; 17538294 ~ 18443016) for several starch paste viscosity properties detected in four panels were close to the isoamylase 3 gene, one QTL (chr.1: 30627943 ~ 31668474) for consistency detected in three panels was close to the starch synthase IV-1 gene. The QTL (chr.7: 1118122 ~ 1967247) for breakdown (BD), detected in the whole panel and japonica panel, and one QTL (chr.7: 25312126 ~ 26540950) for BD and setback (SB), detected in the whole panel and indica panel, may be specific gene alleles in japonica or indica panels. One previously detected QTL (chr.11: 22240707 ~ 22563596) for protein content and one new QTL (chr.5: 7756614 ~ 8042699) for many ECQ traits detected in more than two panels, may represent valuable targets for future cloning of the underlying genes. CONCLUSIONS: This study detected minor-effect QTLs affecting ECQs, and may increase our understanding of the genetic differences regulating the formation of ECQ between indica and japonica varieties.

Genome-wide resequencing of KRICE_CORE reveals their potential for future breeding, as well as functional and evolutionary studies in the post-genomic era.

BACKGROUND: Rice germplasm collections continue to grow in number and size around the world. Since maintaining and screening such massive resources remains challenging, it is important to establish practical methods to manage them. A core collection, by definition, refers to a subset of the entire population that preserves the majority of genetic diversity, enhancing the efficiency of germplasm utilization. RESULTS: Here, we report whole-genome resequencing of the 137 rice mini core collection or Korean rice core set (KRICE_CORE) that represents 25,604 rice germplasms deposited in the Korean genebank of the Rural Development Administration (RDA). We implemented the Illumina HiSeq 2000 and 2500 platform to produce short reads and then assembled those with 9.8 depths using Nipponbare as a reference. Comparisons of the sequences with the reference genome yielded more than 15 million (M) single nucleotide polymorphisms (SNPs) and 1.3 M INDELs. Phylogenetic and population analyses using 2,046,529 high-quality SNPs successfully assigned rice accessions to the relevant rice subgroups, suggesting that these SNPs capture evolutionary signatures that have accumulated in rice subpopulations. Furthermore, genome-wide association studies (GWAS) for four exemplary agronomic traits in the KRIC_CORE manifest the utility of KRICE_CORE; that is, identifying previously defined genes or novel genetic factors that potentially regulate important phenotypes. CONCLUSION: This study provides strong evidence that the size of KRICE_CORE is small but contains high genetic and functional diversity across the genome. Thus, our resequencing results will be useful for future breeding, as well as functional and evolutionary studies, in the post-genomic era.

Treatment and toxicity reduction of textile dyeing wastewater using the electrocoagulation-electroflotation process.

A pilot-scale study was conducted using the electrocoagulation-electroflotation (EC-EF) process to treat textile dyeing raw wastewater to evaluate treatment performance. The effects of some key factors, such as current density, hydraulic retention time (HRT), and removal of conductivity, total suspended solids (TSS), chemical oxygen demand (COD), and color were investigated. The operating variables were current density of 0-300 A m(-2), HRT of 0-30 min, and a coagulant (anionic polyacrylamide (A-PAM)) dosage of 0-30 mg L(-1). Daphnia magna was used to test acute toxicity in raw and treated wastewater. Under the operating conditions without added coagulant, maxima of 51%, 88%, 84%, and 99% of conductivity, TSS, COD, and color were removed, respectively, with a HRT of 30 min. The coagulant enhanced removal of all wastewater parameters. Removal maxima of 59%, 92%, 94%, and 98% for conductivity, TSS, COD, and color were observed, respectively, with an optimal dosage of 30 mg L(-1) and a shortened HRT of 20 min. The 48 h-LC50 D. magna test showed that the raw wastewater was highly toxic. However, the EC-EF process decreased toxicity of the treated samples significantly, and >70% toxicity reduction was achieved by the EC-EF process with the addition of 15-30 mg L(-1) coagulant, HRT of 20 min, and current density of 150-300 A m(-2). The pilot scale test (0.3 m(3 )h(-1)) shows that the EC-EF process with added coagulant effectively treated textile dyeing wastewater.

Natural variations in OsγTMT contribute to diversity of the α-tocopherol content in rice.

Tocopherols and tocotrienols, collectively known as tocochromanols, are lipid-soluble molecules that belong to the group of vitamin E compounds. Among them, α-tocopherol (αΤ) is one of the antioxidants with diverse functions and benefits for humans and animals. Thus, understanding the genetic basis of these traits would be valuable to improve nutritional quality by breeding in rice. Genome-wide association study (GWAS) has emerged as a powerful strategy for identifying genes or quantitative trait loci (QTL) underlying complex traits in plants. To discover the genes or QTLs underlying the naturally occurring variations of αΤ content in rice, we performed GWAS using 1.44 million high-quality single-nucleotide polymorphisms acquired from re-sequencing of 137 accessions from a diverse rice core collection. Thirteen candidate genes were found across 2-year phenotypic data, among which gamma-tocopherol methyltransferase (OsγTMT) was identified as the major factor responsible for the αΤ content among rice accessions. Nucleotide variations in the coding region of OsγTMT were significantly associated with the αΤ content variations, while nucleotide polymorphisms in the promoter region of OsγTMT also could partly demonstrate the correlation with αΤ content variations, according to our RNA expression analyses. This study provides useful information for genetic factors underlying αΤ content variations in rice, which will significantly contribute the research on αΤ biosynthesis mechanisms and αΤ improvement of rice.