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Abstract Background The reliance on a solitary linear reference genome has imposed a significant constraint on our comprehensive understanding of genetic variation in animals. This constraint is particularly pronounced for non-reference sequences (NRSs), which have not been extensively studied. Results In this study, we constructed a pig pangenome graph using 21 pig assemblies and identified 23,831 NRSs with a total length of 105 Mb. Our findings revealed that NRSs were more prevalent in breeds exhibiting greater genetic divergence from the reference genome. Furthermore, we observed that NRSs were rarely found within coding sequences, while NRS insertions were enriched in immune-related Gene Ontology terms. Notably, our investigation also unveiled a close association between novel genes and the immune capacity of pigs. We observed substantial differences in terms of frequencies of NRSs between Eastern and Western pigs, and the heat-resistant pigs exhibited a substantial number of NRS insertions in an 11.6 Mb interval on chromosome X. Additionally, we discovered a 665 bp insertion in the fourth intron of the TNFRSF19 gene that may be associated with the ability of heat tolerance in Southern Chinese pigs. Conclusions Our findings demonstrate the potential of a graph genome approach to reveal important functional features of NRSs in pig populations.

Water scarcity is a key limitation to winter wheat production in the North China Plain, and it is essential to explore the optimal timing of spring irrigation to optimize N and Si uptake as well as to safeguard yields. The aim of this study was to systematically study the effect mechanism of nitrogen and silicon absorption of winter wheat on yield under spring irrigation and to provide a scientific basis for optimizing irrigation strategy during the growth period of winter wheat. In this experiment, the winter wheat ‘Heng 4399’ was used. Five irrigation periods, i.e., 0 d (CK), 5 d (AJ5), 10 d (AJ10), 15 d (AJ15), and 20 d (AJ20) after the jointing stage, were set up to evaluate the nitrogen (N) and silicon (Si) absorption and grain yield (GY). The results showed that delayed irrigation for 5–10 days at the jointing stage had increased the GY. With the delay of irrigation time, the N/Si content of the entire plant at the maturity period increased first and then decreased; among that, the maximum N contents appeared in AJ15 and AJ5 in 2015 and 2020, respectively, while the Si concentrations appeared in AJ5 and AJ10 in sequence. Compared with AJ15 and AJ20, the N accumulation of vegetative organs in AJ5 increased by 3.05~23.13% at the flowering stage, 14.12~40.12% after the flowering stage, and a 1.76~6.45% increase in the N distribution rate at maturity stage. A correlation analysis revealed that the GY was significantly and positively correlated with the N/Si accumulation at the anthesis and N translocation after the anthesis stage. In conclusion, under limited irrigation conditions, delaying watering for 5 to 10 days at the jointing stage can improve the nitrogen and silicon absorption and nutrient status of wheat plants and increase wheat yield.

In the context of dwindling freshwater resources, it is imperative to comprehensively evaluate crop productivity and soil resource sustainability when considering the use of saline water for irrigation (SWI). This study aimed to investigate the effects of SWI on soil salinity variation and sustainability of flat sowing cotton (Gossypium hirsutum L.) through a comprehensive 15-year field experiment conducted in the North China Plain, encompassing six levels of irrigation water salinity (ECiw of 1.3, 3.4, 7.1, 10.6, 14.1, and 17.7 dS m−1, respectively). The results of the 15-year SWI revealed an increase in soil salinity within the cotton root zone, with increases of 5%, 20%, 39%, 67%, 116%, and 156%, respectively, observed across the six treatments. In treatments with higher ECiw values (14.1 and 17.7 dS m−1), salt accumulation extended to a depth of 3.0 m. Long-term SWI has a risk of causing soil sodicity and alkalinity. Sodium adsorption ratio (SAR) and pH in the treatments with ECiw ≥ 7.1 dS m−1 increased significantly (P

Saline water is widely used as an alternative water resource for agriculture to overcome the freshwater shortage in arid and semiarid regions. But long-term using of the saline water for irrigation would negatively affect soil properties and crop production, and the salinity of the irrigation water should be properly managed to reduce the risks. In this study, saline water with five levels of electrical conductivities (ECiw) at 1.3 (CK), 3.4, 7.1, 10.6, and 14.1 dS·m−1 were used to irrigate winter wheat and summer maize with annual double cropping system in the North China Plain (NCP) from 2006 to 2019, to decide the threshold value for long-term using saline water. Crop yields and soil salinity were continuously examined from 2006 to 2019, and soil physicochemical properties were monitored in 2018 and 2019 after 12 years’ saline water irrigation. Results showed that soil salinity in the 0100 cm layer could be maintained at a low level using saline water with ECiw at 3.4 dS·m−1. Soil salt accumulated in winter wheat seasons could be leached from the main root zone in the following summer maize seasons, which were rainy in this region due to the monsoon climate. No significant difference was observed in grain yields for treatment with ECiw at 3.4 dS·m−1 compared to CK treatment. The electrical conductivity of the saturated soil extract (ECe), soil pH, sodium adsorption ratio, and bulk density within the top soil layer of 030 cm increased with the increase in ECiw, whereas the soil organic carbon, porosity, macroaggregates (> 0.25 mm) content, and activities of catalase, urease and alkaline phosphatase decreased, indicating the long-term using saline water irrigation deteriorated soil properties. But the difference in soil properties between the treatment of ECiw at 3.4 dS·m−1 and the CK was not apparent. There were reductions below 5% in relative grain yields and soil quality index (SQI) with ECiw lower than 3.17 and 3.10 dS·m−1 compared with CK treatment, respectively. Comprehensive consideration to maintain a stable crop production and benign soil quality, ECiw of 3.10 dS·m−1 for long-term saline water irrigation was recommended as the safe utilization threshold in the NCP.

Abstract Pigs not only function as a major meat source worldwide but also are commonly used as an animal model for studying human complex traits. A large haplotype reference panel has been used to facilitate efficient phasing and imputation of relatively sparse genome-wide microarray chips and low-coverage sequencing data. Using the imputed genotypes in the downstream analysis, such as GWASs, TWASs, eQTL mapping and genomic prediction (GS), is beneficial for obtaining novel findings. However, currently, there is still a lack of publicly available and high-quality pig reference panels with large sample sizes and high diversity, which greatly limits the application of genotype imputation in pigs. In response, we built the pig Haplotype Reference Panel (PHARP) database. PHARP provides a reference panel of 2012 pig haplotypes at 34 million SNPs constructed using whole-genome sequence data from more than 49 studies of 71 pig breeds. It also provides Web-based analytical tools that allow researchers to carry out phasing and imputation consistently and efficiently. PHARP is freely accessible at http://alphaindex.zju.edu.cn/PHARP/index.php . We demonstrate its applicability for pig commercial 50 K SNP arrays, by accurately imputing 2.6 billion genotypes at a concordance rate value of 0.971 in 81 Large White pigs (~ 17 × sequencing coverage). We also applied our reference panel to impute the low-density SNP chip into the high-density data for three GWASs and found novel significantly associated SNPs that might be casual variants.

Excessive fertilization is associated with nutrient loss, soil compaction, and weak plant resistance. Straw returning can increase soil fertility with a consequent reduction in fertilizer, but the effects of fertilizer reduction coupled with straw returning on crop endophytic microbes and crop disease are poorly understood. Therefore, using metagenomic sequencing methods we investigated the responses of soil fertility, diversity, the function of root endophytic bacteria, and the occurrence of wheat crown rot due to the application of fertilizer (no, moderate and excessive fertilizer) coupled with or without straw returning after 7 years of treatments. The results showed that, after excessive fertilization, the wheat crown rot became severe, registering a disease index of 23. Compared with excessive fertilization, moderate fertilization coupled with straw returning significantly reduced the incidence of wheat crown rot, the disease index was reduced by 38.50%, and the richness and diversity of endophytic bacteria were increased by 61.20 and 11.93%, respectively, but the soil fertility was not significantly affected. In addition, moderate fertilization coupled with straw returning changed the community structure of endophytic bacteria and increased the relative abundance of carbohydrate metabolism and nitrogen fixation-related genes by 4.72 and 9.32%, respectively. Our results indicated that fertilizer reduction coupled with straw returning reduced the occurrence of wheat crown rot, increased the diversity of endophytic bacteria, and changed the community structure and function of endophytic bacteria, which will provide a better understanding of the interaction of fertilization coupled with straw returning, endophytic bacteria and wheat crown rot.

Behavioral assessment of sound localization in the Coma Recovery Scale-Revised (CRS-R) poses a significant challenge due to motor disability in patients with disorders of consciousness (DOC). Brain-computer interfaces (BCIs), which can directly detect brain activities related to external stimuli, may thus provide an approach to assess DOC patients without the need for any physical behavior. In this study, a novel audiovisual BCI system was developed to simulate sound localization evaluation in CRS-R. Specifically, there were two alternatively flashed buttons on the left and right sides of the graphical user interface, one of which was randomly chosen as the target. The auditory stimuli of bell sounds were simultaneously presented by the ipsilateral loudspeaker during the flashing of the target button, which prompted patients to selectively attend to the target button. The recorded electroencephalography data were analyzed in real time to detect event-related potentials evoked by the target and further to determine whether the target was attended to or not. A significant BCI accuracy for a patient implied that he/she had sound localization. Among eighteen patients, eleven and four showed sound localization in the BCI and CRS-R, respectively. Furthermore, all patients showing sound localization in the CRS-R were among those detected by our BCI. The other seven patients who had no sound localization behavior in CRS-R were identified by the BCI assessment, and three of them showed improvements in the second CRS-R assessment after the BCI experiment. Thus, the proposed BCI system is promising for assisting the assessment of sound localization and improving the clinical diagnosis of DOC patients.

Saline water irrigation has been widely used for crop production where agriculture is short of freshwater. However, information about the response of soil respiration to saline water irrigation is limited. To identify the effect of saline water irrigation on soil respiration, the experiment based on long-term saline water irrigation cotton fields (since 2006) was conducted in the Heilonggang area in 2021. Five salinity levels in irrigation water were tested (3.4 [S1], 7.1 [S2], 10.6 [S3], 14.1 [S4], and 17.7 dS m−1 [S5]), and deep ground water (1.3 dS m−1) was used as the control (CK). After 15 years of saline water irrigation, we monitored soil physicochemical properties and soil respiration. In addition, we developed a structural equation model of the relationship between them. The results demonstrated that saline water irrigation significantly reduced soil water-stable aggregate content and porosity by 4.42–45.33% and 6.52–14.10%, respectively, and attenuated soil cellulase, α-glucosidase, and alkaline phosphatase activity. Soil respiration under saline water irrigation was significantly reduced by 5.28–33.08%. Moreover, saline water irrigation with salinity below 10.6 dS m−1 had no significant effect on cotton yield. Moreover, soil salinity (62%), water-stable aggregate content (46%), and soil porosity (25%) had significant effects on soil respiration, and soil porosity had a significant positive effect on soil alkaline phosphatase activity according to the structural equation model. Overall, saline irrigation with salinity below 10.6 dS m−1 can alleviate water shortages and reduce soil carbon emissions without affecting cotton yield in the study area.

Peppers have been used in clinics for a long time and its major component, piperine (PPR), has been proven to be effective in the treatment of seizures. The purpose of this study was to investigate the effects of piperine on early seizures in mice after a traumatic brain injury (TBI) and to explore the mechanism of the drug against the development on TBI. Specific-pathogen-free-grade mice were randomly divided into six dietary groups for a week: control group, TBI group, three piperine groups (low PPR group with 10 mg/kg PPR, medium PPR group with 20 mg/kg PPR, and high PPR group with 40 mg/kg PPR), and a positive control group (200 mg/kg valproate). Except for the control group, all the other groups used Feeney free weight falling method to establish the TBI of closed brain injury in mice, and the corresponding drugs were continuously injected intraperitoneally for 7 days after the brain injury. The results from behavior and electroencephalogram showed that piperine attenuated the subthreshold dose of pentylenetetrazole-induced seizures compared with the TBI group. The western blot results showed that the expression levels of inflammatory factors tumor necrosis factor-α (TNF-α) and interleukin-1β (IL-1β) were reduced by piperine. The immunostaining results showed that the brain-derived neurotrophic factor (BDNF) was also reduced by piperine. In addition, positive cell counts of astrocytic fibrillary acidic protein (GFAP) in immuno-fluorescence showed that they were also reduced. Our data show that piperine treatment can reduce the degree of cerebral edema, down-regulate TNF-α, IL-1β, and BDNF, decrease the reactivity of GFAP in the hippocampus, and inhibit TBI-induced seizures.

How emotions are represented in the nervous system is a crucial unsolved problem in the affective neuroscience. Many studies are striving to find the localization of basic emotions in the brain but failed. Thus, many psychologists suspect the specific neural loci for basic emotions, but instead, some proposed that there are specific neural structures for the core affects, such as arousal and hedonic value. The reason for this widespread difference might be that basic emotions used previously can be further divided into more “basic” emotions. Here we review brain imaging data and neuropsychological data, and try to address this question with an integrative model. In this model, we argue that basic emotions are not contrary to the dimensional studies of emotions (core affects). We propose that basic emotion should locate on the axis in the dimensions of emotion, and only represent one typical core affect (arousal or valence). Therefore, we propose four basic emotions: joy-on positive axis of hedonic dimension, sadness-on negative axis of hedonic dimension, fear, and anger-on the top of vertical dimensions. This new model about basic emotions and construction model of emotions is promising to improve and reformulate neurobiological models of basic emotions.

An experiment has been conducted to investigate the salt evolution process in soil and the response of crops to continuous irrigation with saline water under no artificial drainage from 2006 to 2013. A total of five salinity levels of saline water included 1.3, 3.4, 7.1, 10.6, and 14.1 dS=m, denoted as F1, F2, F3, F4, and F5. Results indicate that salt accumulation was significantly accelerated with the increased ratio of irrigation amount to precipitation (I/P), which was caused by higher annual irrigation times and irrigation quota, but soil salinity was reduced with the decline of I/P. Compared with initial soil salinity in 2006, final soil salinity in 2013 was decreased by 8.7 and 10.1% in the F1 and F2 treatments, but was increased by 7.3, 24.5, and 65.2% in the F3, F4, and F5 treatments. The peak salt values in the soil profile demonstrated a tendency to move up with the increasing salinity of irrigation water, suggesting that salt accumulated more readily in higher salinity treatments. Cotton yield in salinity treatments was close to that of fresh water (F1) when irrigation water salinity was below 7.1 dS=m, but reduced when irrigation water salinity was over 7.1 dS=m. The salt tolerance of forage rye was lower than that of cotton, and the relative forage rye yield dropped as soil salinity increased over the experimental years. Therefore, irrigation water salinity must be lower than 7.1 dS=m in cotton monoculture to keep the cotton yield close to that of freshwater treatment and reduce soil salt accumulation. [ABSTRACT FROM AUTHOR]

[Objective] The aim was to study wheat salt resistance appraisal indicators under the condition of saline water irrigation. [Method] A trial was conducted with five varieties irrigated with saline water at 1, 2, 4, 6, and 8 g/L during 2009-2010 and 2010-2011 in the research station of Dry-land Farming Institute of Hebei Academy of Agricultural and Forestry Sciences. With standardized indicators for measuring treatment, the response relations among different salt stress levels and winter wheat growth index were analyzed in this study. [Result] Under the condition of different salinity of irrigation, relative plant height after jointing stage, relative leaf area index,relative dry matter weight, relative ear number per unit area showed significant differences among treatments and yield showed significant correlation, which can be taken as salt-resistance examination index of wheat. [Conclusion] The results showed that the relative height after jointing stage was recommended as the most practical salt-tolerance appraisal indices, because it was easy to be observed and sensitive to salt stress. [ABSTRACT FROM AUTHOR]