Pig pangenome graph reveals functional features of non-reference sequences.

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.

Effects of fertilizer reduction coupled with straw returning on soil fertility, wheat root endophytic bacteria, and the occurrence of wheat crown rot.

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.

Runs of Homozygosity Revealed Reproductive Traits of Hu Sheep.

Hu sheep, a famous breed in the Taihu Basin, has the advantages of non-seasonal estrus, multiple fetuses, coarse feeding tolerance, and suitability for house feeding. Runs of homozygosity (ROHs) were found to be an effective tool to detect the animal population structure and economic traits. The detection of ROHs is beneficial for reducing the incidence of inbreeding as well as identifying harmful variants in the genome. However, there is a lack of systemic reports on ruminants in previous studies of ROHs. Here, we sequenced 108 Hu sheep, detected ROHs in Hu sheep to calculate their inbreeding coefficient, and selected genes of Hu sheep breeds within the ROH islands which are relevant to agricultural economic characteristics. Then, we compared the characteristics of the occurrences of SNPs between Hu sheep and other sheep breeds, and also investigated the distribution of the frequencies of SNPs within specific gene regions of Hu sheep breeds to select their breed-specific genes. Furthermore, we performed a comparative genome and transcriptome analysis in human and sheep breeds to identify important reproduction-related genes. In this way, we found some significant SNPs, and mapped these with a set of interesting candidate genes which are related to the productive value of livestock (FGF9, BMPR1B, EFNB3, MICU2, GFRA3), healthy characteristics (LGSN, EPHA5, ALOX15B), and breed specificity (FGF9, SAP18, MICU2). These results in our study describe various production traits of Hu sheep from a genetic perspective, and provide insights into the genetic management and complementary understanding of Hu sheep.

PHARP: a pig haplotype reference panel for genotype imputation.

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.

Toward Assessment of Sound Localization in Disorders of Consciousness Using a Hybrid Audiovisual Brain-Computer Interface.

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.

[Effects of brackish water irrigation on grain quality characteristics and yield of winter wheat]. / 咸水灌溉对冬小麦籽粒品质特性和产量的影响.

Brackish water resource is widely distributed in the North China Plain, which has not been effectively utilized. Using brackish water for irrigation can alleviate water resource conflict in the well-irrigated area and solve the problem of groundwater over-exploitation of the North China Plain. A long-term experiment (since 2006) was conducted to investigate the effects of brackish water irrigation on the quality and yield of winter wheat in the North China Plain. There were five salinity degrees of irrigation water, i.e. 1, 2, 4, 6, and 8 g·L-1, respectively. The results showed that higher salinity degree of irrigation water (4-8 g·L-1) significantly increased water absorption, development time, sedimentation, wet gluten content, and protein content, but decreased the stabilization time, flour yield, and gluten index. There was no significant difference between the treatments of 1 g·L-1 and 2 g·L-1 on grain yield and yield components, but the treatment of 2 g·L-1 significantly improved grain quality, including water absorption, development time, sedimentation, wet gluten, and protein content. Higher salinity degree of irrigation water (4-8 g·L-1) treatments significantly decreased spike number (44.0%-60.7%) and grain yield (35.6%-64.7%), compared with 1 g·L-1 treatment. Results of principal component analysis showed that 2 g·L-1 treatment had the best overall effect with no significant decrease in grain yield and quality of grain. This study could provide theoretical basis and technical support for use of brackish water in the North China Plain.

[Effects of saline-water furrow irrigation on the stability of soil water-stable aggregates in cotton field]. / 咸水沟灌对棉田土壤水稳性团聚体稳定性的影响.

It is of great importance to explore the effects of saline-water furrow irrigation on soil water-stable aggregates for safe and efficient utilization of saline water resources. We conducted a long-term cotton experiment with six levels of saline-water furrow irrigation (1, 2, 4, 6, 8, 10 g·L-1) since 2006 and analyzed the variations of soil salinity and water-stable aggregates in the 10th and 15th years under saline irrigation. The results showed that soil salinity in the 0-30 cm layer at the ditch increased with increasing salinity level of irrigation water. There were significant differences between the 6, 8, 10 g·L-1 and 1 g·L-1 treatments. Soil salinity in each treatment increased gradually with increasing soil depth. Saline-water furrow irrigation tended to reduce the stability of soil water-stable aggregates. When the salinity level of the irrigation water was ≥6 g·L-1, the mass fraction of macroaggregates (>0.25 mm), the mean weight diameter and geometric mean diameter of water-stable aggregates significantly decreased. In contrast, the fractal dimension and mean weight specific surface area increased significantly. The stability of soil water-stable aggregates decreased with soil depth in all treatments. Under the condition of saline-water furrow irrigation for several years, there was no accumulation of soil salinity and instability of water-stable aggregates in the 0-30 cm soil layer at the ditch with each passing year. With the irrigation scheduling of this study, saline-water furrow irrigation with salinity ≤4 g·L-1 did not affect soil salinity and water-stable aggregate stability of cotton field in this area.

Piperine Attenuates TBI-Induced Seizures via Inhibiting Cytokine-Activated Reactive Astrogliosis.

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-1ß (IL-1ß) 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-1ß, and BDNF, decrease the reactivity of GFAP in the hippocampus, and inhibit TBI-induced seizures.

An Integrative Way for Studying Neural Basis of Basic Emotions With fMRI.

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.

Similarity Evaluation of Different Origins and Species of Dendrobiums by GC-MS and FTIR Analysis of Polysaccharides.

GC-MS method combined with FTIR techniques by the analysis of polysaccharide was applied to evaluate the similarity between wild (W) and tissue-cultured (TC) Dendrobium huoshanense (DHS), Dendrobium officinale (DO), and Dendrobium moniliforme (DM) as well as 3 wild Dendrobium spp.: Dendrobium henanense (DHN), Dendrobium loddigesii (DL), and Dendrobium crepidatum (DC). Eight monosaccharides involving xylose, arabinose, rhamnose, glucose, mannose, fructose, galactose, and galacturonic acid were identified in the polysaccharide from each Dendrobium sample while the contents of the monosugars varied remarkably across origins and species. Further similarity evaluation based on GC-MS data showed that the r cor values of different origins of DHS, DO, and DM were 0.831, 0.865, and 0.884, respectively, while the r cor values ranged from 0.475 to 0.837 across species. FTIR files of the polysaccharides revealed that the similarity coefficients between W and TC-DHS, DO, and DM were 88.7%, 86.8%, and 88.5%, respectively, in contrast to the similarity coefficients varying from 57.4% to 82.6% across species. These results suggested that the structures of polysaccharides between different origins of the investigated Dendrobiums might be higher than what we had supposed.

[Study on Monosaccharide Compositions of Polysaccharide in Dendrobium Stems of Different Resources by PMP-HPCE].

OBJECTIVE: To establish a PMP-HPCE method for comparing the monosaccharides of polysaccharide in tissue-cultured and wild Dedrobium huoshanese and Dedrobium moniliforme as well as wild Dedrobium henanese, in order to investigate the similarities of their bioactive components. METHODS: The PMP-monosaccharides of polysaccharide from the five investigated Dedrobium samples were separated by HPCE on a fused silica capillary column(100 cm x 50 µm) at 25 °C with 350 mmol/L BAS (adjusted to pH 10 with 1.0 mol/L NaOH) as running buffer for 34 min. The applied voltage was 20 kV and the detection wavelength was set at 250 nm. RESULTS: Total six monosaccharides including xylose, glucose, mannose, galactose, galacturonic acid and ribose were detected in the five Dendrobiurms samples and the similarity coefficients between the ten batches of the same Dendrobium species were all above 0. 98,while remarkable dissimilarity were exhibited among species and different resources. CONCLUSION: PMP-HPCE technique combined with chemometrics is simple, convenient, precise, reproducible and proved to be an effective strategy for identifying the species and origins, especially in the quality assessment of Dendrobium stems.