Population Structure of Nation-Wide Rice in Thailand
Ontology highlight
ABSTRACT: Background
Thailand is a country with large diversity in rice varieties due to its rich and diverse ecology. In this paper, 300 rice accessions from all across Thailand were sequenced to identify SNP variants allowing for the population structure to be explored. Results
The result of inferred population structure from admixture and clustering analysis illustrated strong evidence of substructure in each geographical region. The results of phylogenetic tree, PCA analysis, and machine learning on population identifying SNPs also supported the inferred population structure. Conclusion
The population structure inferred in this study contains five subpopulations that tend to group individuals based on location. So, each subpopulation has unique genetic patterns, agronomic traits, as well as different environmental conditions. This study can serve as a reference point of the nation-wide population structure for supporting breeders and researchers who are interested in Thai rice. Supplementary Information
The online version contains supplementary material available at 10.1186/s12284-021-00528-2.
SUBMITTER: Vejchasarn P
PROVIDER: S-EPMC8542525 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:It is essential to elucidate genetic diversity and relationships among even related individuals and populations for plant breeding and genetic analysis. Since Japanese rice breeding has improved agronomic traits such as yield and eating quality, modern Japanese rice cultivars originated from narrow genetic resource and closely related. To resolve the population structure and genetic diversity in Japanese rice population, we used a total of 706 alleles detected by 134 simple sequence repeat markers in a total of 114 cultivars composed of 94 improved varieties and 20 landraces, which are representative and important for Japanese rice breeding. The landraces exhibit greater gene diversity than improved lines, suggesting that landraces can provide additional genetic diversity for future breeding. Model-based Bayesian clustering analysis revealed six subgroups and admixture situation in the cultivars, showing good agreement with pedigree information. This method could be superior to phylogenetic method in classifying a related population. The leading Japanese rice cultivar, Koshihikari is unique due to the specific genome constitution. We defined Japanese rice diverse sets that capture the maximum number of alleles for given sample sizes. These sets are useful for a variety of genetic application in Japanese rice cultivars.
| S-EPMC3621445 | biostudies-literature
Project description:BACKGROUND:Pregabalin is approved for the treatment of neuropathic pain, fibromyalgia, and seizure disorders, although the pivotal trials were mostly carried out in Europe or North America. The prescribing patterns among different indications in Asia have rarely been explored. METHODS:This was a population-based retrospective cohort study based on the National Health Insurance Research Database in Taiwan. Prescriptions of pregabalin were identified, and data regarding demographics, indications, co-existing diagnoses, and concomitant medications were extracted. Pregabalin users were followed for at least one year, and factors associated with persistence at one year were determined by using multivariate logistic regression analysis. RESULTS:Between June 2012 and December 2016, 114,437 pregabalin users (mean age 60.7?±?15.4?years, 57.8% female) were identified. The indications included post-herpetic neuralgia (PHN) (30.5%), musculoskeletal diseases other than fibromyalgia (21.2%), fibromyalgia (18.4%), diabetic peripheral neuropathic pain (DPNP) (11.7%) and epilepsy (2.9%). Overall, 62.5% and 6.4% of patients achieved a maximum dose of ?150 and ? 300?mg/day, respectively. The median duration of persistent pregabalin use was 28?days (interquartile range 14-118?days). The one-year persistence rate was 12.1%, and the indications associated with the highest and lowest persistence rates were epilepsy (42.4%) and PHN (6.1%), respectively. Male gender (odds ratio [OR] 1.14, 95% confidence interval [CI] 1.09-1.18), older age (OR 1.01 per year, 95% CI 1.01-1.01), indications other than PHN, especially epilepsy (OR 8.04, 95% CI 7.33-8.81, PHN as reference), and a higher initial dose (OR 1.12 per 75?mg, 95% CI?=?1.10-1.15) were associated with persistence at one year, whereas the initial concomitant use of antiviral agents decreased the likelihood (OR 0.41, 95% CI 0.35-0.47). CONCLUSIONS:Pregabalin prescriptions for pain disorders were limited to short-term use, which is consistent around the world. However, the average prescribed dose in Taiwan was lower than those in Western countries, and was frequently below the recommended ranges. Potential causes included the duration of natural history of PHN, and off-label prescriptions for pain in acute herpes zoster, rather than PHN, as well as intolerance to the side effects.
| S-EPMC7236209 | biostudies-literature
Project description:Dyspnea is common after a pulmonary embolism. Often, but not always, the dyspnea can be explained by pre-existing comorbidities, and only rarely by chronic thromboembolic pulmonary hypertension (CTEPH). CTEPH is probably the extreme manifestation of a far more common condition, called the post-pulmonary embolism syndrome. The purpose of this retrospective study was to investigate the prevalence and predictors of dyspnea among Swedish patients that survived a pulmonary embolism, compared to the general population. All Swedish patients diagnosed with an acute pulmonary embolism in 2005 (n = 5793) were identified via the Swedish National Patient Registry. Patients that lived until 2007 (n = 3510) were invited to participate. Of these, 2105 patients responded to a questionnaire about dyspnea and comorbidities. Data from the general population (n = 1905) were acquired from the multinational MONItoring of trends and determinants in CArdiovascular disease health survey, conducted in 2004. Patients with pulmonary embolism had substantially higher prevalences of both exertional dyspnea (53.0% vs. 17.3%, odds ratio (OR): 5.40, 95% confidence intervals (CI): 4.61-6.32) and wake-up dyspnea (12.0% vs. 1.7%, OR: 7.7, 95% CI: 5.28-11.23) compared to control subjects. These differences remained after adjustments and were most pronounced among younger patients. The increased risk for exertional dyspnea and wake-up dyspnea remained after propensity score matching (OR (95% CI): 4.11 (3.14-5.38) and 3.44 (1.95-6.06), respectively). This population-based, nation-wide study demonstrated that self-reported dyspnea was common among patients with previous pulmonary embolism. This finding suggested that a post-pulmonary embolism syndrome might be present, which merits further investigation.
| S-EPMC8488523 | biostudies-literature
Project description:BACKGROUND: Understanding disease seasonality can provide guidance for future biomedical research. OBJECTIVE: To examine whether meteorological factors and calendar months impact duodenal ulcer (DU) exacerbations. DESIGN: We conducted a retrospective time series analysis of population-based claims data. PARTICIPANTS: DU inpatients (1997-2003; all endoscopy confirmed) from Taiwan, a small island nation, n = 160,510. Inpatient admission was used as a proxy for exacerbation because 98.5% of cases had hemorrhage or perforation or both. MEASUREMENTS: We used multivariate autoregressive integrated moving average (ARIMA) modeling to examine if DU admissions/100,000 was associated with calendar month, ambient temperature, relative humidity, rainfall, atmospheric pressure, and sunshine hours, controlling for available DU-relevant comorbidities. RESULTS: DU admissions increased with age. ARIMA modeling showed a February (Chinese New Year-related) trough in all age groups (all p < 0.001; adjusted for meteorological variables and comorbidities), consistent with a February dip in all-cause admissions. Among 35-49 and 50+ age groups, DU admissions were negatively associated with temperature (both p < 0.05; model R2 = 0.875 and 0.920, respectively), representing a winter peak and summer trough. Among the < or = 19 age group, sunshine hours and rainfall are positively associated with DU admissions (both p < 0.001; R2 = 0.565), representing a summer peak. CONCLUSION: Meteorological variables are associated with DU exacerbations, although the potential role of nonsteroidal anti-inflammatory drug (NSAID) use because of seasonal acute respiratory illness cannot be ruled out. We recommend in-depth studies using chart reviews of DU patients admitted during peak and trough (incidence) months to clarify whether meteorological factors or the associated seasonal peaks of respiratory and other illnesses involving NSAID use are responsible for the observed seasonality.
| S-EPMC2305852 | biostudies-other
Project description:BACKGROUND: Month of birth--an indicator for a variety of prenatal and early postnatal exposures--has been associated with life expectancy in adulthood. On the northern hemisphere, people born in the autumn live longer than those born during the spring. Only one study has followed a population longitudinally and no study has investigated the relation between month of birth and mortality risk below 50 years. METHODS AND RESULTS: In this nation-wide Swedish study, we included 6,194,745 subjects, using data from population-based health and administrative registries. The relation between month of birth (January-December) and mortality risk was assessed by fitting Cox proportional hazard regression models using attained age as the underlying time scale. Analyses were made for ages >30, >30 to 50, >50 to 80 and >80 years. Month of birth was a significant predictor of mortality in the age-spans >30, >50 to 80, and >80 years. In models adjusted for gender and education for ages >30 and >50 to 80 years, the lowest mortality was seen for people born in November and the highest mortality in those born in the spring/summer, peaking in May for mortality >30 years (25‰ excess hazard ratio compared to November, [95% confidence interval?=?16-34 ]) and in April for mortality >50 to 80 years (42‰ excess hazard ratio compared to November, [95% confidence interval?=?30-55]). In the ages >80 years the pattern was similar but the differences in mortality between birth months were smaller. For mortality within the age-span >30 to 50 years, results were inconclusive. CONCLUSION: Month of birth is associated to risk of mortality in ages above 50 years in Sweden. Further studies should aim at clarifying the mechanisms behind this association.
| S-EPMC3574007 | biostudies-literature
Project description:Myanmar locates in the crossroads of South Asia, Southeast Asia, and East Asia, and is known for high culture diversity in different ethnic groups. It is considered to be important for understanding human evolutionary history and genetic diversity in East Eurasia. However, relatively few studies have examined the population structure and demographic history in Myanmar to date. In this study, we analyzed more than 220,000 genome-wide SNPs in 175 new samples of five ethnic groups from Myanmar and compared them with the published data. Our results showed that the Myanmar population is intricately substructured, with the main observed clusters corresponding roughly to western/northern highlanders (Chin, Naga, and Jingpo) and central/southern lowlanders (Bamar and Rakhine). The gene flow inferred from South Asia has a substantial influence (~11%) on the gene pool of central/southern lowlanders rather than western/northern highlanders. The genetic admixture is dated around 650 years ago. These findings suggest that the genome-wide variation in Myanmar was likely shaped by the linguistic, cultural, and historical changes.
2019-12-31 | GSE74100 | GEO
Project description:Approval of immune checkpoint-inhibitors (ICIs) and BRAF-inhibitors has revolutionized the treatment of metastatic melanoma. Although these drugs have improved overall survival (OS) in clinical trials, real-world evidence for improved long-term survival is still scarce. Clinical data were extracted from the Danish Metastatic Melanoma database. This nation-wide cohort contains data on all patients who received systemic treatment for metastatic melanoma between 2008 and 2016. Ipilimumab, the first approved ICI, was implemented as standard-of-care in Denmark in 2012. Hence, patients were divided in a pre-ICI (2008-2011) and an ICI (2012-2016) era. Patients were defined as long-term survivors if they were alive 3 years after initiation of systemic therapy. Data from 1754 patients were retrieved. Patients treated in the ICI era had an improved median OS (11.3 months, 95% confidence interval (CI) 10.3-12.3) compared with those in the pre-ICI era (median OS 8.3 months, 95% CI 7.4-9.5, p < 0.0001). A higher proportion of long-term survivors was observed in the ICI era (survivors >3 years increased from 13% to 26% and survivors >5 years increased from 9% to 21%; both p < 0.0001). For long-term survivors, known prognostic factors were equally distributed between the two periods, except that long-term survivors in the pre-ICI era were younger. For long-term survivors, 70% were without progression in the ICI era compared with 43% in the pre-ICI era (p < 0.0001). For all patients, the proportion without progression increased from 5% to 18% between the pre-ICI and the ICI era (p < 0.0001), respectively. Implementation of ICI has led to a significant increase in progression-free, long-term survival for real-life patients with metastatic melanoma.
| S-EPMC7564087 | biostudies-literature
Project description:Background: Even though traumatic brain injury (TBI) is a major cause of morbidity and mortality in children around the globe, population-based and nation-wide data to assess the burden of TBI is scarce. Methods:Based on diagnosis related groups from nation-wide hospital data, we extracted data on all TBI-related hospitalizations in children <18 years in Germany between 2014 and 2018. We calculated crude, age-specific and standardized incidence rates for hospitalizations, imaging, intracranial injury, neurosurgery, and mortality. Results:Out of 10.2 million hospitalizations, we identified 458,844 cases with TBI as primary or secondary diagnosis, resulting in a crude incidence rate of 687/100,000 child years (CY). Age-specific rates of computed tomography were below 30/100,000 CY until the age of 10 years and increased to 162/100,000 CY until 17 years of age. Intracranial injury was diagnosed in 2.7%, neurosurgery was performed in 0.7% of patients, and 0.7% were mechanically ventilated. Mortality was 0.67/100,000 CY (0.1%). Conclusions:Despite substantial hospitalization rates for pediatric TBI in Germany, the rates of imaging, the need for mechanical ventilation, neurosurgery and mortality were overall very low. Reasons for hospitalization and measures to reduce unnecessary admissions warrant further investigation.
| S-EPMC8515415 | biostudies-literature
Project description:Plant breeding programs in local regions may generate genetic variations that are desirable to local populations and shape adaptability during the establishment of local populations. To elucidate genetic bases for this process, we proposed a new approach for identifying the genetic bases for the traits improved during rice breeding programs; association mapping focusing on a local population. In the present study, we performed association mapping focusing on a local rice population, consisting of 63 varieties, in Hokkaido, the northernmost region of Japan and one of the northern limits of rice cultivation worldwide. Six and seventeen QTLs were identified for heading date and low temperature germinability, respectively. Of these, 13 were novel QTLs in this population and 10 corresponded to the QTLs previously reported based on QTL mapping. The identification of QTLs for traits in local populations including elite varieties may lead to a better understanding of the genetic bases of elite traits. This is of direct relevance for plant breeding programs in local regions.
| S-EPMC4671701 | biostudies-other
Project description:Use of dietary supplements among cancer survivors is common and controversial, but information on the amount of nutrients from supplements among cancer survivors is limited. We examined the amount of nutrients and their contribution to total nutrient intake from supplements and compared these data between cancer survivors and cancer-free individuals. We also identified factors associated with supplement use among cancer survivors.We identified 400 cancer survivors and 10,387 cancer-free individuals, aged ??19 years, from the fifth Korea National Health and Nutrition Examination Survey (KNHANES) V-1, 2 (2010, 2011). We calculated the amount of nutrients consumed from foods and supplements, the percent contributions of supplement nutrients to total nutrient intakes and cancer survivors' nutrient intakes relative to the Estimated Average Requirements (EARs) and the Tolerable Upper Intake Levels (ULs). We examined factors associated with supplement use among cancer survivors.We found that 33.3% of cancer survivors and 22.1% of cancer-free individuals reported the use of dietary supplements. Compared to cancer-free individuals, cancer survivors had higher intakes of riboflavin, folate, and iron from foods (p?<?0.05 for each), and higher intakes of calcium (p?=?0.05) and vitamin C (p?=?0.01) from foods and supplements. The similar pattern was observed for the percent contributions to total nutrient intake. Cancer survivors had higher proportion of participants below EARs than cancer-free individuals for thiamin and niacin (p?<?0.05 for each). The proportions of cancer survivors below the EARs were 61.2% for calcium, 49.1% for riboflavin, and 43.5% for folate and the proportions of cancer survivors above the ULs were 3.3% for iron, and 2.3% for vitamin A. For female cancer survivors, education above an elementary school level, moderate physical activity, low vegetable intake, and high circulating vitamin D levels were associated with supplement use. For male cancer survivors, living in an urban area, no consumption of alcohol, and lower energy intake, were associated with supplement use.Korean cancer survivors have higher rate of dietary supplement use and higher contribution from supplements to total nutrient intake than cancer-free individuals. Demographic and lifestyle factors were associated with supplement use among cancer survivors.
| S-EPMC5745960 | biostudies-literature