Genome-wide identification and analysis of heterotic loci in three maize hybrids

Heterosis, or hybrid vigour, is a predominant phenomenon in plant genetics, serving as the basis of crop hybrid breeding, but the causative loci and genes underlying heterosis remain unclear in many crops. Here, we present a large-scale genetic analysis using 5360 offsprings from three elite maize hybrids, which identifies 628 loci underlying 19 yield-related traits with relatively high mapping resolutions. Heterotic pattern investigations of the 628 loci show that numerous loci, mostly with complete–incomplete dominance (the major one) or overdominance effects (the secondary one) for heterozygous genotypes and nearly equal proportion of advantageous alleles from both parental lines, are the major causes of strong heterosis in these hybrids. Follow-up studies for 17 heterotic loci in an independent experiment using 2225 F2 individuals suggest most heterotic effects are roughly stable between environments with a small variation. Candidate gene analysis for one major heterotic locus (ub3) in maize implies that there may exist some common genes contributing to crop heterosis. These results provide a community resource for genetics studies in maize and new implications for heterosis in plants

High endemicity of alveolar echinococcosis in Yili Prefecture, Xinjiang Autonomous Region, the People’s Republic of China: infection status in different ethnic communities and in small mammals

Alveolar echinococcosis (AE) is a neglected zoonosis caused by the larval stage of the fox/dog tapeworm Echinococcus multilocularis. In this study, we collected data on 286 AE cases reported from Yili Prefecture, Xinjiang Autonomous Region, the People’s Republic of China from 1989 to 2015 with an annual incidence (AI) of 0.41/100,000. Among the patients, 73.08% were diagnosed in the last 11 years. The incidence (0.51–1.22 cases/100,000 residents) was higher in the high-altitude mountainous areas than those in low level areas (0.19–0.29/100,000 residents). In term of ethnic group, the AI of AE in Mongolian (2.06/100,000 residents) and Kazak (0.93/100,000) groups had higher incidence than the other ethnic groups, indicating sheep-farming activity is a risk for infection given that sheep farming is mainly practiced by these two groups in the prefecture. A total of 1411 small mammals were captured with 9.14% infected with E. multilocularis metacestodes. Microtus obscurus was the dominant species captured in the mountainous pasture areas with 15.01% infection rate, whereas Mus musculus and Apodemus sylvaticus were the dominant small mammals in the low altitude areas. Only 0.40% of A. sylvaticus were infected with E. multilocularis. These findings show that Yili Prefecture is a highly endemic area for AE and that the high-altitude pasture areas favorable for M. obscurus may play an important role in its transmission in this region

Genome-Wide Association Studies Reveal the Genetic Basis of Ionomic Variation in Rice

Rice (Oryza sativa) is an important dietary source of both essential micronutrients and toxic trace elements for humans. The genetic basis underlying the variations in the mineral composition, the ionome, in rice remains largely unknown. Here, we describe a comprehensive study of the genetic architecture of the variation in the rice ionome performed using genome-wide association studies (GWAS) of the concentrations of 17 mineral elements in rice grain from a diverse panel of 529 accessions, each genotyped at ∼6.4 million single nucleotide polymorphism loci. We identified 72 loci associated with natural ionomic variations, 32 that are common across locations and 40 that are common within a single location. We identified candidate genes for 42 loci and provide evidence for the causal nature of three genes, the sodium transporter gene Os-HKT1;5 for sodium, Os-MOLYBDATE TRANSPORTER1;1 for molybdenum, and Grain number, plant height, and heading date7 for nitrogen. Comparison of GWAS data from rice versus Arabidopsis (Arabidopsis thaliana) also identified well-known as well as new candidates with potential for further characterization. Our study provides crucial insights into the genetic basis of ionomic variations in rice and serves as an important foundation for further studies on the genetic and molecular mechanisms controlling the rice ionome

FungalTraits:A user-friendly traits database of fungi and fungus-like stramenopiles

The cryptic lifestyle of most fungi necessitates molecular identification of the guild in environmental studies. Over the past decades, rapid development and affordability of molecular tools have tremendously improved insights of the fungal diversity in all ecosystems and habitats. Yet, in spite of the progress of molecular methods, knowledge about functional properties of the fungal taxa is vague and interpretation of environmental studies in an ecologically meaningful manner remains challenging. In order to facilitate functional assignments and ecological interpretation of environmental studies we introduce a user friendly traits and character database FungalTraits operating at genus and species hypothesis levels. Combining the information from previous efforts such as FUNGuild and Fun(Fun) together with involvement of expert knowledge, we reannotated 10,210 and 151 fungal and Stramenopila genera, respectively. This resulted in a stand-alone spreadsheet dataset covering 17 lifestyle related traits of fungal and Stramenopila genera, designed for rapid functional assignments of environmental studies. In order to assign the trait states to fungal species hypotheses, the scientific community of experts manually categorised and assigned available trait information to 697,413 fungal ITS sequences. On the basis of those sequences we were able to summarise trait and host information into 92,623 fungal species hypotheses at 1% dissimilarity threshold

Potential of Ferritin-Based Platforms for Tumor Immunotherapy

Ferritin is an iron storage protein that plays a key role in iron homeostasis and cellular antioxidant activity. Ferritin has many advantages as a tumor immunotherapy platform, including a small particle size that allows for penetration into tumor-draining lymph nodes or tumor tissue, a unique structure consisting of 24 self-assembled subunits, cavities that can encapsulate drugs, natural targeting functions, and a modifiable outer surface. In this review, we summarize related research applying ferritin as a tumor immune vaccine or a nanocarrier for immunomodulator drugs based on different targeting mechanisms (including dendritic cells, tumor-associated macrophages, tumor-associated fibroblasts, and tumor cells). In addition, a ferritin-based tumor vaccine expected to protect against a wide range of coronaviruses by targeting multiple variants of SARS-CoV-2 has entered phase I clinical trials, and its efficacy is described in this review. Although ferritin is already on the road to transformation, there are still many difficulties to overcome. Therefore, three barriers (drug loading, modification sites, and animal models) are also discussed in this paper. Notwithstanding, the ferritin-based nanoplatform has great potential for tumor immunotherapy, with greater possibility of clinical transformation

Identification of Urban Functional Regions in Chengdu Based on Taxi Trajectory Time Series Data

Overall scientific planning of urbanization layout is an important component of the new period of land spatial planning policies. Defining the main functions of different spaces and dividing urban functional areas are of great significance for optimizing the land development pattern. This article identifies and analyses urban functional areas from the perspective of data mining. The results of this method are consistent with the actual situation. In this paper, representative taxi trajectory data are selected as the research basis of urban functional areas. First, based on trajectory data from Didi Chuxing within the high-speed road surrounding Chengdu, we generated trajectory time sequence data and used the dynamic time warping (DTW) algorithm to generate a time series similarity matrix. Second, we utilized the K-medoid clustering algorithm to generate preliminary results of land clustering and selected the results with high classification accuracy as the training samples. Then, the k-nearest neighbour (KNN) classification algorithm based on DTW was performed to classify and identify the urban functional areas. Finally, with the help of point-of-interest (POI) auxiliary analysis, the final functional layout in Chengdu was obtained. The results show that the spatial structure of Chengdu is complex and that the urban functions are interlaced, but there are still rules that are followed. Moreover, traffic volume and inflow data can better reflect the travel rules of residents than simple taxi on–off data. The original DTW calculation method has high temporal complexity, which can be improved by normalization and the reduction of time series dimensionality. The semi-supervised learning classification method is also applicable to trajectory data, and it is best to select training samples from unsupervised learning. This method can provide a theoretical basis for urban land planning and has auxiliary and guiding value for urbanization layout in the context of land spatial planning policies in the new era

Understanding the Spatial-Temporal Patterns and Influential Factors on Air Quality Index: The Case of North China

North China has become one of the worst air quality regions in China and the world. Based on the daily air quality index (AQI) monitoring data in 96 cities from 2014–2016, the spatiotemporal patterns of AQI in North China were investigated, then the influence of meteorological and socio-economic factors on AQI was discussed by statistical analysis and ESDA-GWR (exploratory spatial data analysis-geographically weighted regression) model. The principal results are as follows: (1) The average annual AQI from 2014–2016 exceeded or were close to the Grade II standard of Chinese Ambient Air Quality (CAAQ), although the area experiencing heavy pollution decreased. Meanwhile, the positive spatial autocorrelation of AQI was enhanced in the sample period. (2) The occurrence of a distinct seasonal cycle in air pollution which exhibit a sinusoidal pattern of fluctuations and can be described as “heavy winter and light summer.” Although the AQI generally decreased in other seasons, the air pollution intensity increased in winter with the rapid expansion of higher AQI value in the southern of Hebei and Shanxi. (3) The correlation analysis of daily meteorological factors and AQI shows that air quality can be significantly improved when daily precipitation exceeds 10 mm. In addition, except for O3, wind speed has a negative correlation with AQI and major pollutants, which was most significant in winter. Meanwhile, pollutants are transmitted dynamically under the influence of the prevailing wind direction, which can result in the relocation of AQI. (4) According to ESDA-GWR analysis, on an annual scale, car ownership and industrial production are positively correlated with air pollution; whereas increase of wind speed, per capita gross domestic product (GDP), and forest coverage are conducive to reducing pollution. Local coefficients show spatial differences in the effects of different factors on the AQI. Empirical results of this study are helpful for the government departments to formulate regionally differentiated governance policies regarding air pollution

Simulation of Soil Organic Carbon Content Based on Laboratory Spectrum in the Three-Rivers Source Region of China

Soil organic carbon (SOC) changes affect the land carbon cycle and are also closely related to climate change. Visible-near infrared spectroscopy (Vis-NIRS) has proven to be an effective tool in predicting soil properties. Spectral transformations are necessary to reduce noise and ensemble learning methods can improve the estimation accuracy of SOC. Yet, it is still unclear which is the optimal ensemble learning method exploiting the results of spectral transformations to accurately simulate SOC content changes in the Three-Rivers Source Region of China. In this study, 272 soil samples were collected and used to build the Vis-NIRS simulation models for SOC content. The ensemble learning was conducted by the building of stack models. Sixteen combinations were produced by eight spectral transformations (S-G, LR, MSC, CR, FD, LRFD, MSCFD and CRFD) and two machine learning models of RF and XGBoost. Then, the prediction results of these 16 combinations were used to build the first-step stack models (Stack1, Stack2, Stack3). The next-step stack models (Stack4, Stack5, Stack6) were then made after the input variables were optimized based on the threshold of the feature importance of the first-step stack models (importance > 0.05). The results in this study showed that the stack models method obtained higher accuracy than the single model and transformations method. Among the six stack models, Stack 6 (5 selected combinations + XGBoost) showed the best simulation performance (RMSE = 7.3511, R2 = 0.8963, and RPD = 3.0139, RPIQ = 3.339), and obtained higher accuracy than Stack3 (16 combinations + XGBoost). Overall, our results suggested that the ensemble learning of spectral transformations and simulation models can improve the estimation accuracy of the SOC content. This study can provide useful suggestions for the high-precision estimation of SOC in the alpine ecosystem