Topography of mountain belts controlled by rheology and surface processes.

It is widely recognized that collisional mountain belt topography is generated by crustal thickening and lowered by river bedrock erosion, linking climate and tectonics1-4. However, whether surface processes or lithospheric strength control mountain belt height, shape and longevity remains uncertain. Additionally, how to reconcile high erosion rates in some active orogens with long-term survival of mountain belts for hundreds of millions of years remains enigmatic. Here we investigate mountain belt growth and decay using a new coupled surface process5,6 and mantle-scale tectonic model7. End-member models and the new non-dimensional Beaumont number, Bm, quantify how surface processes and tectonics control the topographic evolution of mountain belts, and enable the definition of three end-member types of growing orogens: type 1, non-steady state, strength controlled (Bm > 0.5); type 2, flux steady state8, strength controlled (Bm ≈ 0.4-0.5); and type 3, flux steady state, erosion controlled (Bm < 0.4). Our results indicate that tectonics dominate in Himalaya-Tibet and the Central Andes (both type 1), efficient surface processes balance high convergence rates in Taiwan (probably type 2) and surface processes dominate in the Southern Alps of New Zealand (type 3). Orogenic decay is determined by erosional efficiency and can be subdivided into two phases with variable isostatic rebound characteristics and associated timescales. The results presented here provide a unified framework explaining how surface processes and lithospheric strength control the height, shape, and longevity of mountain belts.

The Impact of Broadband Infrastructure Construction on Medical Resource Mismatch: Quasi-Natural Experiment From the Broadband China Policy.

BACKGROUND: Whether the construction of broadband infrastructure can alleviate the problem of mismatched medical resources is crucial to the national information strategy, residents' well-being, and social equity. However, the academic community lacks a comprehensive theoretical analysis and rigorous empirical research on this issue. OBJECTIVE: This study aims to construct a preliminary theoretical framework to scientifically assess the effects of broadband infrastructure development on the mitigation of health care resource mismatch from both theoretical and empirical perspectives, to explore the potential mechanisms of influence, and ultimately to develop several practical policy recommendations. METHODS: We first used a theoretical analysis to propose testable theoretical hypotheses and establish a preliminary theoretical framework. Then, based on balanced panel data from 300 cities from 2010 to 2021, a 2-way fixed effects difference-in-differences model was used for empirical testing. Mechanism tests, robustness analyses, and heterogeneity analyses were further conducted. RESULTS: The research findings demonstrate that the Broadband China Policy significantly reduces the degree of mismatch in medical resources by primarily using innovation effects and integration effects, resulting in a reduction of 13.2%. In addition, the heterogeneity analysis reveals that the central and eastern regions, cities with large populations, and areas with a high proportion of young people benefit more significantly. CONCLUSIONS: This study fully confirms, both theoretically and empirically, that broadband infrastructure construction can effectively reduce the mismatch of medical resources not only by expanding the existing literature on the impact of broadband on public services but also by providing valuable opportunities for policy makers to optimize the allocation of medical resources.

Pattern selection mechanism from the equilibrium point and limit cycle.

The outbreak of infectious diseases often exhibits periodicity, and this periodic behavior can be mathematically represented as a limit cycle. However, the periodic behavior has rarely been considered in demonstrating the cluster phenomenon of infection induced by diffusion (the instability modes) in the SIR model. We investigate the emergence of Turing instability from a stable equilibrium and a limit cycle to illustrate the dynamical and biological mechanisms of pattern formation. We identify the Hopf bifurcation to demonstrate the existence of a stable limit cycle using First Lyapunov coefficient in our spatiotemporal diffusion-driven SIR model. The competition between different instability modes induces different types of patterns and eventually spot patterns emerge as stable patterns. We investigate the impact of susceptible, infected, and recovered individuals on the type of patterns. Interestingly, these instability modes play a vital role in selecting the pattern formations, which is directly related to the number of observed spot patterns. Subsequently, we explain the dynamical and biological mechanisms of spot patterns to develop an effective epidemic prevention strategy.

Application of IoT detection based on deep self coding multidimensional feature fusion in sports training.

In response to the shortcomings of existing centralized IoT detection activities, this article proposes a new IoT detection scheme based on programmable switches and deep self coding, which combines programmable switches with IoT MQTT protocol and multidimensional feature fusion algorithm. Based on this point, a comprehensive programmable switch and machine learning centralized IoT detection system are designed. This system is different from traditional centralized IoT detection systems. The IoT detection module discussed in this article is located on a programmable switch between IoT nodes and servers. This system utilizes the potential of programmable switches to quickly collect required information from packet data and pre detect fault data from the front end of the server, thereby quickly making IoT node packet processing decisions (i.e. redirecting or directly discarding) based on programmable switches to minimize the delay in transmitting data packets. Finally, in order to apply this technology to the field of sports training, we examined different directions of sports training. Therefore, based on the development of simulation systems, this article greatly enhances the practicality of such projects, effectively increasing the usage time and meeting the actual training needs. Therefore, The deep self coding computer simulation of sports training is an issue that we must pay attention to. The article conducted research on IoT detection based on deep self coding multidimensional feature fusion, and applied the research results to sports training, promoting the rapid development of sports training.

Role of HOMA-IR and IL-6 as screening markers for the metabolic syndrome in patients with chronic schizophrenia: a psychiatric hospital-based cross-sectional study.

This study starts from the metabolic related indexes and cellular inflammatory factors in patients with chronic schizophrenia to find out that it can be used as an effective screening index of metabolic syndrome. 320 patients with chronic schizophrenia (course of disease > 5 years) and 165 healthy subjects were selected. The mental symptoms of the patients were measured by positive and negative syndrome scale. Blood samples from patients and healthy controls were collected to detect blood glucose, triglyceride, HDL and fasting insulin. The serum levels of IL-1ß, IL-2, IL-6, IL-17, IFN-γ and TNF-α were determined repeatedly by sandwich enzyme-linked immunosorbent assay. The levels of HOMA-IR, plasma inflammatory factors IL-2, IL-6, IL-17 and TNF-α in patient group were higher than those in healthy group. It was found that there were differences in age and related metabolic indexes between patients with chronic schizophrenia with and without metabolic syndrome. In addition, HOMA-IR, plasma cytokines IL-2 and IL-6 still showed differences between groups. In the Spearmen correlation analysis of insulin resistance index, cytokines and metabolic indexes, it was found that there was a significant correlation between HOMA-IR, IL-6 and related metabolic indexes and metabolic syndrome. ROC curve analysis showed that HOMAIR and IL-6 could be used as screening indexes for MS in male and female patients with schizophrenia.Metabolic syndrome is an important risk factor for cardiovascular disease in patients with chronic schizophrenia. HOMA-IR and IL-6 can be used as effective biological indicators to screen MS in patients with chronic schizophrenia.

Smartphone video games improve cognitive function in patients with chronic schizophrenia: a randomized controlled trial.

This study aimed to examine the efficacy of video games in improving cognitive function in chronic patients with schizophrenia and to evaluate the biomarker of video games for cognitive function. The patients in the game group were requested to play single-player video games on their smartphones for 1 h per day, five times a week for 6 weeks. Those in the control group watched television for 1 h per day, five times a week for 6 weeks. Cognitive function was assessed using the Repeatable Battery for the Assessment of Neuropsychological Status (RBANS) and Stroop Color and Word Test (SCWT). Clinical symptoms were assessed using the Positive and Negative Syndrome Scale (PANSS), Global Assessment of Functioning (GAF), General Self-Efficacy Scale (GSE), Problematic Mobile Gaming Questionnaire (PMGQ), and Patient Health Questionnaire-9 (PHQ-9). The game group demonstrated improved RBANS total score during the trial. There were no significant group effects among all SCWT scores. The game group demonstrated greater improvement on the PANSS Negative Scale, and global function (GAF score). The PMGQ scores were lower than the cutoff score at all time points in both groups. There were no significant group differences in the PHQ-9 and GSE scores. The serum BDNF levels were significantly higher in the game group following 6 weeks of video game intervention. The BDNF serum levels of all participants were positively associated with the RBANS total scores. This preliminary study suggested that video games can improve cognitive function in schizophrenia patients. Serum BDNF levels may be a suitable biomarker for predicting an improvement in cognitive function in schizophrenia patients.Trial registration: This study was registered on March 11, 2021 (ChiCTR2100044113).Clinical trials: Smartphone video games improve cognitive function in patients with chronic schizophrenia; https://www.chictr.org.cn/hvshowproject.aspx?id=95623 ; ChiCTR2100044113.

Effect of online game policy on smartphone game play time, addiction, and emotion in rural adolescents of China.

BACKGROUND: Smartphone game addiction has emerged as a major public health problem in China and worldwide. In November 2019 and August 2021, the National Press and Publication Administration of China implemented two increasingly strict policies, as a means of preventing smartphone game addiction in adolescents aged 18 or below. This study aimed to analyze the effect of the policies on smartphone game play time, addiction, and emotion among rural adolescents in China. METHODS: We sent the questionnaire to rural adolescents through the online survey tool Questionnaire Star, a professional online survey evaluation platform. The questionnaire included demographic data, smartphone use survey, smartphone game addiction and emotion evaluation scales. The Smartphone Addiction Scale-Short Version (SAS-SV) measured adolescents' smartphone game addiction. The Short Version of UPPS-P Impulsive Behavior Scale (SUPPS-P) and Social Anxiety Scale for Children (SASC) measured emotion. According to SAS-SV score, the enrolled rural adolescents were divided into addiction group and non-addiction group. The t-test, Chi-square test, and repeated measure ANOVA assessed the effect of the policies on adolescents' smartphone game addiction and emotion. RESULTS: Among enrolled 459 rural adolescents with a mean age of 14.36 ± 1.37years, 151 (32.90%) were in the addiction group and 308 (67.10%) were in the non-addiction group. Adolescents in the addiction group were older, more male, and higher grade. There were time and group effects between the two groups in playtime. After a year of policies implementation, the weekly game time dropped from 3.52 ± 1.89 h to 2.63 ± 1.93 h in the addiction group and from 2.71 ± 1.75 h to 2.36 ± 1.73 h in the non-addiction group. There were also time and group effects in SAS-SV and SASC scores, but not for SUPPS-P score. In the addiction group, the SAS-SV score dropped from 41.44 ± 7.45 to 29.58 ± 12.43, which was below the cut-off value for addiction, and the level of social anxiety was consistently higher than non-addiction group. CONCLUSIONS: The playtime of rural adolescents spent on smartphone games has decreased significantly due to the restriction of the policies rather than the lack of addiction or social anxiety. The policies had practically significant effects in reducing smartphone game play time for rural adolescents in China.

Joint Particle Swarm Optimization of Power and Phase Shift for IRS-Aided D2D Underlaying Cellular Systems.

Device-to-device (D2D) communication is a promising wireless communication technology which can effectively reduce the traffic load of the base station and improve the spectral efficiency. The application of intelligent reflective surfaces (IRS) in D2D communication systems can further improve the throughput, but the problem of interference suppression becomes more complex and challenging due to the introduction of new links. Therefore, how to perform effective and low-complexity optimal radio resource allocation is still a problem to be solved in IRS-assisted D2D communication systems. To this end, a low-complexity power and phase shift joint optimization algorithm based on particle swarm optimization is proposed in this paper. First, a multivariable joint optimization problem for the uplink cellular network with IRS-assisted D2D communication is established, where multiple DUEs are allowed to share a CUE's sub-channel. However, the proposed problem considering the joint optimization of power and phase shift, with the objective of maximizing the system sum rate and the constraints of the minimum user signal-to-interference-plus-noise ratio (SINR), is a non-convex non-linear model and is hard to solve. Different from the existing work, instead of decomposing this optimization problem into two sub-problems and optimizing the two variables separately, we jointly optimize them based on Particle Swarm Optimization (PSO). Then, a fitness function with a penalty term is established, and a penalty value priority update scheme is designed for discrete phase shift optimization variables and continuous power optimization variables. Finally, the performance analysis and simulation results show that the proposed algorithm is close to the iterative algorithm in terms of sum rate, but lower in power consumption. In particular, when the number of D2D users is four, the power consumption is reduced by 20%. In addition, compared with PSO and distributed PSO, the sum rate of the proposed algorithm increases by about 10.2% and 38.3%, respectively, when the number of D2D users is four.

A collision tumor of nasopharyngeal carcinoma and primary mantle cell lymphoma in the nasopharynx: a case report and review of the literature.

BACKGROUND: Nasopharyngeal carcinoma (NPC) is more common in men aged 40 to 59, and radiotherapy is an effective treatment. Nasopharyngeal lymphoma (NPL) is rare, and the coexistence of nasopharyngeal mantle cell lymphoma (MCL) and NPC is even rarer. A collision tumor is a rare type of tumor that refers to two or more different tumors occurring in the same organ. No reports to date have described a collision tumor of NPC and MCL occurring within the same nasopharyngeal mass. We herein report the successful treatment of a unique case of synchronous coexistence of NPC and MCL occurring in the nasopharynx of a Chinese man. CASE PRESENTATION: A 58-year-old man presented with a 5-month history of swallowing discomfort. Biopsy was performed under nasopharyngeal endoscopy, and histopathology revealed NPC. Magnetic resonance imaging revealed lesions in the nasopharynx, oropharynx, and tonsils, as well as enlarged lymph nodes in the parotid gland, posterior ear, and neck. This may be a synchronous dual primary tumor coexisting with NPC and NPL. Pathology consultation confirmed that the biopsy specimen of the nasopharynx was a collision tumor of NPC and MCL. Positron emission tomography computed tomography (PET-CT) revealed thickening of the posterior wall of the nasopharynx, which was considered NPC with lymphoma. The enlargement of the pharyngeal lymph ring and multiple hypermetabolic lymph nodes were evaluated as lymphoma infiltration. The patient received two courses of R-CHOP chemotherapy (rituximab, cyclophosphamide, doxorubicin, vincristine, and prednisone) followed by head and neck radiotherapy. At the time of this writing, he had remained alive without recurrence for 61 months since the initial treatment and was still undergoing follow-up. CONCLUSIONS: It is very important to correctly recognize collision tumors. Magnetic resonance imaging helps identify different components of collision tumors. Pathological examination helps to confirm the diagnosis. Histological examination reveals different components, and PET-CT can help determine the extent of the lesion. Dose-adjusted chemotherapy combined with radiotherapy may have promising herapeutic effects, but additional case studies are needed to confirm.

Genomic insight into genetic changes and shaping of major inbred rice cultivars in China.

The annual planting area of major inbred rice (Oryza sativa) cultivars reach more than half of the total annual planting area of inbred rice cultivars in China. However, how the major inbred rice cultivars changed during decades of genetic improvement and why they can be prevalently cultivated in China remains unclear. Here, we investigated the underlying genetic changes of major inbred cultivars and the contributions of landraces and introduced cultivars during the improvement by resequencing a collection of 439 rice accessions including major inbred cultivars, landraces, and introduced cultivars. The results showed that landraces were the main genetic contribution sources of major inbred Xian (Indica) cultivars, while introduced cultivars were that of major inbred Geng (Japonica) cultivars. Selection scans and haplotype frequency analysis shed light on the reflections of some well-known genes in rice improvement, and breeders had different preferences for the Xian's and Geng's breeding. Six candidate regions associated with agronomic traits were identified by genome-wide association mapping, five of which were under positive selection in rice improvement. Our study provides a comprehensive insight into the development of major inbred rice cultivars and lays the foundation for genomics-based breeding in rice.

The transient outward potassium current plays a key role in spiral wave breakup in ventricular tissue.

Spiral wave reentry as a mechanism of lethal ventricular arrhythmias has been widely demonstrated in animal experiments and recordings from human hearts. It has been shown that in structurally normal hearts spiral waves are unstable, breaking up into multiple wavelets via dynamical instabilities. However, many of the second-generation action potential models give rise only to stable spiral waves, raising issues regarding the underlying mechanisms of spiral wave breakup. In this study, we carried out computer simulations of two-dimensional homogeneous tissues using five ventricular action potential models. We show that the transient outward potassium current (Ito), although it is not required, plays a key role in promoting spiral wave breakup in all five models. As the maximum conductance of Ito increases, it first promotes spiral wave breakup and then stabilizes the spiral waves. In the absence of Ito, speeding up the L-type calcium kinetics can prevent spiral wave breakup, however, with the same speedup kinetics, spiral wave breakup can be promoted by increasing Ito. Increasing Ito promotes single-cell dynamical instabilities, including action potential duration alternans and chaos, and increasing Ito further suppresses these action potential dynamics. These cellular properties agree with the observation that increasing Ito first promotes spiral wave breakup and then stabilizes spiral waves in tissue. Implications of our observations to spiral wave dynamics in the real hearts and action potential model improvements are discussed.NEW & NOTEWORTHY Spiral wave breakup manifesting as multiple wavelets is a mechanism of ventricular fibrillation. It has been known that spiral wave breakup in cardiac tissue can be caused by a steeply sloped action potential duration restitution curve, a property mainly determined by the recovery of L-type calcium current. Here, we show that the transient outward potassium current (Ito) is another current that plays a key role in spiral wave breakup, that is, spiral waves can be stable for low and high maximum Ito conductance but breakup occurs for intermediate maximum Ito conductance. Since Ito is present in normal hearts of many species and required for Brugada syndrome, it may play an important role in the spiral wave stability and arrhythmogenesis under both normal condition and Brugada syndrome.

Skin Prick Testing to Identify Food Allergens in 8393 Children and Adolescents with Asthma in Chongqing, Southwest China.

BACKGROUND The prevalence of food allergies in asthmatic children and adolescents has significantly increased over recent years. Nevertheless, the relevant clinical analyses are still lacking in China. Therefore, the present study aimed to determine common food allergens in pediatric patients with asthma in Chongqing, Southwest China. MATERIAL AND METHODS A total of 8393 asthmatic patients from Children's Hospital of Chongqing Medical University (CHCMU) were enrolled in this retrospective study between October 2014 and July 2017. All patients underwent skin prick test (SPT) with 10 food allergens and recorded history of clinical reactivity. The correlations among the positive rates, categories of allergens, gender, age, and living environment were analyzed. RESULTS A total of 2544 patients (30.31%) had a positive SPT, while the prevalence of food allergy was 8%. Sea crab, peanut, and sea shrimp were the most common food allergens found in the studied population. The frequent food allergies were sea crab, peanuts, and sea shrimp. CONCLUSIONS Identifying allergens is important for the diagnosis and management of allergic disorders, and for performing immunotherapy.

Effects of none-steroidal anti-inflammatory and antibiotic drugs on the oral immune system and oral microbial composition in rats.

BACKGROUND: Antibiotics and none-steroidal anti-inflammatory drugs are often taken orally to treat human diseases. The use of these drugs adversely could affect the natural oral microbiota composition and oral immune system. In the meanwhile, it may break the original balance of oral micro-ecosystem. Exploring this change is of great importance to host health. METHODS: In this study, we took 20 SD rats and divided them into four groups of five rats each. Each of these groups was administered specified doses of amoxicillin (AMX), ornidazole (ORD), aspirin (ASP), or purified water (CTR), using oral gavage daily for 14 days. High-throughput sequencing was used to investigate the microbiota difference in the four groups of rats once the oral gavage completed. ELISA kit was used to determine IgG and SIgA content, to understand the effect of the drugs on the oral immune system. RESULTS: We found that oral bacterial composition, IgG and sIgA were significantly affected by the use of these drugs. No matter which medication the rats takes, oral microbiota diversity increase significantly. At the genus level, The Lactobacillaceae, which is essential to the human food digest, raised in the aspirin take group. Staphylococcus and Pasteurella increased in the ornidazole group. Klebsiella, Corynebacterium rose significantly in the amoxicillin group. In normal oral cavity without taking the task medicine, Streptococcus, Pasteurella, and Rothia were in a relatively high abundance. IgG and SIgA content also changed by using these drugs, thus indicating applied those drugs impact of the oral immune system. CONCLUSION: Our results indicate that antibiotic and none-steroidal anti-inflammatory drugs could influence the oral microbiota composition, which could also destroy the original oral micro-ecosystem environment. The non-antibiotic drug effect on the oral microbiota and oral immune system similar to the antibiotic drug. All these changes may have a negative influence on host health.

A map of rice genome variation reveals the origin of cultivated rice.

Crop domestications are long-term selection experiments that have greatly advanced human civilization. The domestication of cultivated rice (Oryza sativa L.) ranks as one of the most important developments in history. However, its origins and domestication processes are controversial and have long been debated. Here we generate genome sequences from 446 geographically diverse accessions of the wild rice species Oryza rufipogon, the immediate ancestral progenitor of cultivated rice, and from 1,083 cultivated indica and japonica varieties to construct a comprehensive map of rice genome variation. In the search for signatures of selection, we identify 55 selective sweeps that have occurred during domestication. In-depth analyses of the domestication sweeps and genome-wide patterns reveal that Oryza sativa japonica rice was first domesticated from a specific population of O. rufipogon around the middle area of the Pearl River in southern China, and that Oryza sativa indica rice was subsequently developed from crosses between japonica rice and local wild rice as the initial cultivars spread into South East and South Asia. The domestication-associated traits are analysed through high-resolution genetic mapping. This study provides an important resource for rice breeding and an effective genomics approach for crop domestication research.

Genome-wide association study of cold tolerance of Chinese indica rice varieties at the bud burst stage.

KEY MESSAGE: A region containing three genes on chromosome 1 of indica rice was associated with cold tolerance at the bud burst stage; these results may be useful for breeding cold-tolerant lines. Low temperature at the bud burst stage is one of the major abiotic stresses limiting rice growth, especially in regions where rice seeds are sown directly. In this study, we investigated cold tolerance of rice at the bud burst stage and conducted a genome-wide association study (GWAS) based on the 5K rice array of 249 indica rice varieties widely distributed in China. We improved the method to assess cold tolerance at the bud burst stage in indica rice, and used severity of damage (SD) and seed survival rate (SR) as the cold-tolerant indices. Population structure analysis demonstrated that the Chinese indica panel was divided into three subgroups. In total, 47 significant single-nucleotide polymorphism (SNP) loci associated with SD and SR, were detected by association mapping based on mixed linear model. Because some loci overlapped between SD and SR, the loci contained 13 genome intervals and most of them have been reported previously. A major QTL for cold tolerance on chromosome 1 at the position of 31.6 Mb, explaining 13.2% of phenotypic variation, was selected for further analysis. Through LD decay, GO enrichment, RNA-seq data, and gene expression pattern analyses, we identified three genes (LOC_Os01g55510, LOC_Os01g55350 and LOC_Os01g55560) that were differentially expressed between cold-tolerant and cold-sensitive varieties, suggesting they may be candidate genes for cold tolerance. Together, our results provide a new method to assess cold tolerance in indica rice, and establish the foundation for isolating genes related to cold tolerance that could be used in rice breeding.

Uncovering novel loci for mesocotyl elongation and shoot length in indica rice through genome-wide association mapping.

MAIN CONCLUSION: Totally, 23 loci were detected, and 383 candidate genes were identified, and four of these candidate genes, Os01g0392100, Os04g0630000, Os01g0904700 and Os07g0615000, were regarded as promising targets. Direct-seeding cultivation is becoming popular in rice (Oryza sativa L.)-planting countries because it is labor- and time-efficient. However, low seedling establishment and slow seedling emergence have restricted the application and popularity of the technique. Mesocotyl elongation and shoot length are two important traits that can enhance rice seedling emergence. A single nucleotide polymorphism (SNP) is a genome sequence variation caused by a single base within a population, and SNPs evenly distributed throughout the genomes of plant species. In this study, a genome-wide association study (GWAS), based on 4136 SNPs, was performed using a compressed mixed linear model that accounted for population structure and relative kinship to detect novel loci for the two traits. Totally, 23 loci were identified, including five loci located known QTLs region. For the mesocotyl elongation, 17 major loci were identified, explaining ~19.31 % of the phenotypic variation. For the shoot length, six major loci were detected, explaining ~ 39.79 % of the phenotypic variation. In total, 383 candidate genes were included in a 200-kb genomic region (± 100 kb of each locus). Additionally, 32 SNPs were identified in 30 candidate genes. Relative expression level analyses indicated that four candidate genes containing SNP variations, Os01g0392100, Os04g0630000, Os01g0904700 and Os07g0615000, represented promising targets. Finally, eight elite accessions with long mesocotyl and shoot lengths were chosen as breeding donors for further rice direct-seeding variety modifications.

Genome wide association mapping for grain shape traits in indica rice.

MAIN CONCLUSION: Using genome-wide association mapping, 47 SNPs within 27 significant loci were identified for four grain shape traits, and 424 candidate genes were predicted from public database. Grain shape is a key determinant of grain yield and quality in rice (Oryza sativa L.). However, our knowledge of genes controlling rice grain shape remains limited. Genome-wide association mapping based on linkage disequilibrium (LD) has recently emerged as an effective approach for identifying genes or quantitative trait loci (QTL) underlying complex traits in plants. In this study, association mapping based on 5291 single nucleotide polymorphisms (SNPs) was conducted to identify significant loci associated with grain shape traits in a global collection of 469 diverse rice accessions. A total of 47 SNPs were located in 27 significant loci for four grain traits, and explained ~44.93-65.90 % of the phenotypic variation for each trait. In total, 424 candidate genes within a 200 kb extension region (±100 kb of each locus) of these loci were predicted. Of them, the cloned genes GS3 and qSW5 showed very strong effects on grain length and grain width in our study. Comparing with previously reported QTLs for grain shape traits, we found 11 novel loci, including 3, 3, 2 and 3 loci for grain length, grain width, grain length-width ratio and thousand grain weight, respectively. Validation of these new loci would be performed in the future studies. These results revealed that besides GS3 and qSW5, multiple novel loci and mechanisms were involved in determining rice grain shape. These findings provided valuable information for understanding of the genetic control of grain shape and molecular marker assistant selection (MAS) breeding in rice.

The genetic diversity and structure of indica rice in China as detected by single nucleotide polymorphism analysis.

BACKGROUND: Rice (Oryza sativa L.) is the staple food of more than half of the world's population. The identification of genetic diversity in local varieties of rice compared with that of improved or introduced varieties is important in breeding elite varieties for sustainable agriculture. Array-based single nucleotide polymorphism (SNP) detection is a useful technique for such studies and breeding applications. RESULTS: We developed a 5291-SNP genome-wide array and used it to genotype 471 indica rice accessions in China using Illumina's Infinium technology. Local, introduced, and improved rice varieties were clustered into three sub-groups, with some overlapping shown in principal component analysis and neighbor-joining tree, also confirmed by model-based structure. A minor allele frequency ≥ 0.2 was observed in 72% of polymorphic SNPs in local rice varieties, which was higher than that in other sub-groups. Local rice varieties also had the highest mean polymorphism information content (PIC) and genetic diversity. Analysis of molecular variance showed that 90.61% of genetic variation was a result of differences within sub-groups. CONCLUSIONS: Our results revealed that SNP analysis clustered local varieties, introduced varieties, and improved varieties into three clear sub-groups. The distribution of parameter PIC values on sub-group genomes revealed that genetic differentiation among them might not be on a genome-wide scale, but rather on selected loci or chromosomal intervals. The result of Gene Ontology enrichment analysis showed that genes nearby those selected SNPs associated different molecular functions or various traits among sub-groups.

Genetic variation and association mapping for 12 agronomic traits in indica rice.

BACKGROUND: Increasing rice (Oryza sativa L.) yield is a crucial challenge for modern agriculture. The ideal plant architecture is considered to be critical to enhance rice yield. Elite plant morphological traits should include compact plant type, short stature, few unproductive tillers, thick and sturdy stems and erect leaves. To reveal the genetic variations of important morphological traits, 523 germplasm accessions were genotyped using the Illumina custom-designed array containing 5,291 single nucleotide polymorphisms (SNPs) and phenotyped in two independent environments. Genome-wide association studies were performed to uncover the genotypic and phenotypic variations using a mixed linear model. RESULTS: In total, 126 and 172 significant loci were identified and these loci explained an average of 34.45% and 39.09% of the phenotypic variance in two environments, respectively, and 16 of 298 (~5.37%) loci were detected across the two environments. For the 16 loci, 423 candidate genes were predicted in a 200-kb region (±100 kb of the peak SNP). Expression-level analyses identified four candidate genes as the most promising regulators of tiller angle. Known (NAL1 and Rc) and new significant loci showed pleiotropy and gene linkage. In addition, a long genome region covering ~1.6 Mb on chromosome 11 was identified, which may be critical for rice leaf architecture because of a high association with flag leaf length and the ratio of flag leaf length and width. The pyramid effect of the elite alleles indicated that these significant loci could be beneficial for rice plant architecture improvements in the future. Finally, 37 elite varieties were chosen as breeding donors for further rice plant architectural modifications. CONCLUSIONS: This study detected multiple novel loci and candidate genes related to rice morphological traits, and the work demonstrated that genome-wide association studies are powerful strategies for uncovering the genetic variations of complex traits and identifying candidate genes in rice, even though the linkage disequilibrium decayed slowly in self-pollinating species. Future research will focus on the biological validation of the candidate genes, and elite varieties will also be of interest in genome selection and breeding by design.

Genome-wide association study of blast resistance in indica rice.

BACKGROUND: Rice blast disease is one of the most serious and recurrent problems in rice-growing regions worldwide. Most resistance genes were identified by linkage mapping using genetic populations. We extensively examined 16 rice blast strains and a further genome-wide association study based on genotyping 0.8 million single nucleotide polymorphism variants across 366 diverse indica accessions. RESULTS: Totally, thirty associated loci were identified. The strongest signal (Chr11_6526998, P =1.17 × 10-17) was located within the gene Os11g0225100, one of the rice Pia-blast resistance gene. Another association signal (Chr11_30606558) was detected around the QTL Pif. Our study identified the gene Os11g0704100, a disease resistance protein containing nucleotide binding site-leucine rich repeat domain, as the main candidate gene of Pif. In order to explore the potential mechanism underlying the blast resistance, we further examined a locus in chromosome 12, which was associated with CH149 (P =7.53 × 10-15). The genes, Os12g0424700 and Os12g0427000, both described as kinase-like domain containing protein, were presumed to be required for the full function of this locus. Furthermore, we found some association on chromosome 3, in which it has not been reported any loci associated with rice blast resistance. In addition, we identified novel functional candidate genes, which might participate in the resistance regulation. CONCLUSIONS: This work provides the basis of further study of the potential function of these candidate genes. A subset of true associations would be weakly associated with outcome in any given GWAS; therefore, large-scale replication is necessary to confirm our results. Future research will focus on validating the effects of these candidate genes and their functional variants using genetic transformation and transferred DNA insertion mutant screens, to verify that these genes engender resistance to blast disease in rice.