Search

Objective To establish an effective quality indicator monitoring system, scientifically and objectively evaluate the quality management level of blood banks, and achieve continuous improvement of quality management in blood bank. Methods A quality monitoring indicator system that covers the whole process of blood collection and supply was established, the questionnaire of Quality Monitoring Indicators for Blood Collection and Supply Process with clear definition of indicators and calculation formulas was distributed to 17 blood banks in Shandong. Statistical analysis of 21 quality monitoring indicators in terms of blood donation service (10 indicators), blood component preparation (7 indicators ), and blood supply (4 indicators) from each blood bank from January to December 2022 were conducted using SPSS25.0 software The differences in quality monitoring indicators of blood banks of different scales were analyzed. Results The average values of quality monitoring indicators for blood donation service process of 17 blood banks were as follows: 44.66% (2 233/5 000) of regular donors proportion, 0.22% (11/50) of adverse reactions incidence, 0.46% (23/5 000) of non-standard whole blood collection rate, 0.052% (13/25 000) of missed HBsAg screening rate, 99.42% (4 971/5 000) of first, puncture successful rate, 86.49% (173/200) of double platelet collection rate, 66.50% (133/200) of 400 mL whole blood collection rate, 99.25% (397/400) of donor satisfaction rate, 82.68% (2 067/2 500) of use rate of whole blood collection bags with bypass system with sample tube, and 1 case of occupational exposure in blood collection.There was a strong positive correlation between the proportion of regular blood donors and the collection rate of 400 mL whole blood (P

Objective To objectively evaluate the quality control level of blood testing process in blood banks through quantitative monitoring and trend analysis, and to promote the homogenization level and standardized management of blood testing laboratories in blood banks. Methods A quality monitoring indicator system covering the whole process of blood collection and supply, including blood donation service, blood component preparation, blood testing, blood supply and quality control was established. The questionnaire Quality Monitoring Indicators for Blood Collection and Supply Process with clear definition of indicators and calculation formulas was distributed to 17 blood banks in Shandong province. Quality monitoring indicators of each blood bank from January to December 2022 were collected, and 31 indicators in terms of blood testing were analyzed using SPSS25.0 software. Results The proportion of unqualified serological tests in 17 blood bank laboratories was 55.84% for ALT, 13.63% for HBsAg, 5.08% for anti HCV, 5.62% for anti HIV, 18.18% for anti TP, and 1.65% for other factors (mainly sample quality). The detection unqualified rate and median were (1.23±0.57)% and 1.11%, respectively. The ALT unqualified rate and median were (0.74±0.53)% and 0.60%, respectively. The detection unqualified rate was positively correlated with ALT unqualified rate (r=0.974, P0.05), while the outrage rate was positively correlated with the usage rate (r=0.592, P

Objective To establish an effective quality monitoring indicator system for blood quality control in blood banks, in order to analyze the quality control indicators for blood collection and supply, and evaluate blood quality control process, thus promoting continuous improvement and standardizing management of blood quality control in blood banks. Methods A quality monitoring indicator system covering the whole process of blood collection and supply, including blood donation services, component preparation, blood testing, blood supply and quality control was established. The Questionnaire of Quality Monitoring Indicators for Blood Collection and Supply Process was distributed to 17 blood banks in Shandong, which clarified the definition and calculation formula of indicators. The quality monitoring indicator data from January to December 2022 in each blood bank were collected, and 20 quality control indicators data were analyzed by SPSS25.0 software. Results The average pass rate of key equipment monitoring, environment monitoring, key material monitoring, and blood testing item monitoring of 17 blood banks were 99.47%, 99.51%, 99.95% and 98.99%, respectively. Significant difference was noticed in the pass rate of environment monitoring among blood banks of varied scales(P

Objective To establish a blood quality monitoring indicator system, in order to continuously improve blood quality and standardized management. Methods Based on the research of literature and standards, and guided by the key control points of blood collection and supply process, the blood quality monitoring indicator system was developed. Through two rounds of Delphi expert consultation, the indicator content was further revised and improved according to expert opinions after six months of trial implementation. The indicator weight was calculated by questionnaire and analytic hierarchy process. Results A blood quality monitoring indicator system covering the whole process of blood collection and supply was constructed, including five primary indicators, namely blood donation service, blood component preparation, blood testing, blood supply and quality control, as well as 72 secondary indicators, including definitions, calculation formulas, etc. Two rounds of expert consultation and two rounds of feasibility study meeting were held to revise 17 items and the weight of each indicator was obtained through the analytic hierarchy process. After partial adjustments, a blood quality monitoring indicator system was formed. Conclusion A blood quality monitoring indicator system covering the whole process of blood collection and supply has been established for the first time, which can effectively evaluate the quality management level of blood banks and coordinate blood quality control activities of blood banks in Shandong like pieces in a chess game, thus improving the standardized management level

IntroductionIn the era of the Internet, online digital traces have become a new way to study the online attention of scenic spots and tourists’ purchase behavior. The public’s information search on major search platforms is a series of manifestations of potential tourists’ attention and interest in scenic spots, but there are few studies on how attention, interest and information search affect potential tourists to generate real purchase behavior.MethodThis paper selects four dimensions of short video platform, travel website, search engine and social media to comprehensively measure the online attention of high-quality scenic spots in Yunnan Province, and then establishes a gray association analytic hierarchy process based on the relevant variables of the AISAS model to empirically analyze the primary and secondary factors affecting tourists’ purchase behavior.Results(1) From the perspective of the online attention of scenic spots on different platforms, the intensity of the public’s scenic spots online attention on the four types of media platforms is in the order of travel websites, search engines, short videos and social media (2) From the perspective of spatial distribution characteristics, the online attention of high-quality scenic spots in Yunnan Province is unevenly distributed, that is, there is a big difference between the attention of higher star scenic spots and their star rating and popularity, while the attention of low-star scenic spots is not much different from their star rating and popularity (3) From the perspective of spatial agglomeration characteristics, the comprehensive online attention of high-quality scenic spots in Yunnan Province presents the spatial agglomeration characteristics of “the multi-core linkage of high-density in the east and north, and sub-high-density in the south” (4) The factors influencing the purchase behavior of potential tourists are sharing experience, attracting attention, generating interest and searching information.DiscussionBy exploring the formation mechanism of high-quality scenic spots online attention in Yunnan Province and the mechanism of its spatial differentiation, this study not only enriches the logical chain of “tourism information source → potential tourists → demand driven → tourism information search → travel preference → destination selection → purchase decision → travel experience → real tourists → feelings after traveling → focus on feedback → tourism information source,” but also broadens the application scenarios and application boundaries of travel preference theory and AISAS behavior model to a certain extent.

Abstract The identification and classification of selective sweeps are of great significance for improving the understanding of biological evolution and exploring opportunities for precision medicine and genetic improvement. Here, a domain adaptation sweep detection and classification (DASDC) method is presented to balance the alignment of two domains and the classification performance through a domain‐adversarial neural network and its adversarial learning modules. DASDC effectively addresses the issue of mismatch between training data and real genomic data in deep learning models, leading to a significant improvement in its generalization capability, prediction robustness, and accuracy. The DASDC method demonstrates improved identification performance compared to existing methods and excels in classification performance, particularly in scenarios where there is a mismatch between application data and training data. The successful implementation of DASDC in real data of three distinct species highlights its potential as a useful tool for identifying crucial functional genes and investigating adaptive evolutionary mechanisms, particularly with the increasing availability of genomic data.

Abstract Soft porous organic crystals with stimuli‐responsive single‐crystal‐to‐single‐crystal (SCSC) transformations are important tools for unraveling their structural transformations at the molecular level, which is of crucial importance for the rapid development of stimuli‐responsive systems. Carefully balancing the crystallinity and flexibility of materials is the prerequisite to construct advanced organic crystals with SCSC, which remains challenging. Herein, a squaraine‐based soft porous organic crystal (SPOC‐SQ) with multiple gas‐induced SCSC transformations and temperature‐regulated gate‐opening adsorption of various C1‐C3 hydrocarbons is reported. SPOC‐SQ is featured with both crystallinity and flexibility, which enable pertaining the single crystallinity of the purely organic framework during accommodating gas molecules and directly unveiling gas‐framework interplays by SCXRD technique. Thanks to the excellent softness of SPOC‐SQ crystals, multiple metastable single crystals are obtained after gas removals, which demonstrates a molecular‐scale shape‐memory effect. Benefiting from the single crystallinity, the molecule‐level structural evolutions of the SPOC‐SQ crystal framework during gas departure are uncovered. With the unique temperature‐dependent gate‐opening structural transformations, SPOC‐SQ exhibits distinctly different absorption behaviors towards C3H6 and C3H8, and highly efficient and selective separation of C3H6/C3H8 (v/v, 50/50) is achieved at 273 K. Such advanced soft porous organic crystals are of both theoretical values and practical implications.

This study, conducted between 4 October 2013, and 30 November 2018, tested the hypothesis that triple antimicrobial therapy, targeting Mycobacterium avium subspecies paratuberculosis (MAP), long considered a putative cause, would favorably affect Crohn’s disease. A double-blind multicenter study of adults with active Crohn’s disease, (i.e., Crohn’s Disease Activity Index [CDAI] 220–450 plus C-reactive protein ≥ 1.0 mg/dL, fecal calprotectin (FCP) >162.9 µg/g stool, or recent endoscopic or radiographic confirmation of active disease) receiving concomitant standard-of-care Crohn’s disease treatment (Clinicaltrials.gov: NCT01951326) were stratified by anti-tumor necrosis factor use and randomized (1:1) to anti-MAP RHB-104 (clarithromycin 95 mg, rifabutin 45 mg, and clofazimine 10 mg per capsule) (n = 166), resulting in clarithromycin 950 mg/day, rifabutin 450 mg/day, and clofazimine 100 mg/day, or placebo (n = 165) for up to 52 weeks. A greater proportion of RHB-104 versus placebo-treated patients met the primary endpoint—remission (i.e., CDAI < 150)—at week 26 (36.7% [61/166] vs. 22.4% [37/165], respectively; 95% CI for difference: 4.6, 24.0, p = 0.0048; chi-square test). Clinical response (reduction of CDAI by ≥100 points from baseline) at week 26 (first secondary endpoint) was also higher among the patients treated with RHB-104 (73/166 [44.0%]) compared with placebo (50/165 [30.3%]; 95% CI for difference: 3.4, 24.0, p = 0.0116), and it remained higher at week 52 among the patients treated with RHB-104 (59/166 [35.5%] vs. (35/165 [21.2%] for placebo; 95% CI for difference: 4.7, 23.9, p = 0.0042). A statistically significantly greater decline in FCP (another prospective efficacy endpoint) was also observed in RHB-104-treated patients, compared with placebo, at weeks 12, 26, and 52. The rates of serious adverse events were similar between groups (RHB-104: 18.7%; placebo: 18.8%). No patient died during the study. Antimicrobial therapy directed against MAP resulted in significantly greater improvement in clinical and laboratory (FCP) measures of active Crohn’s disease.

IntroductionThe development and migration of T cells in the thymus and peripheral tissues are crucial for maintaining adaptive immunity in mammals. However, the regulatory mechanisms underlying T cell development and thymocyte identity formation in pigs remain largely underexplored. MethodHere, by integrating bulk and single-cell RNA-sequencing data, we investigated regulatory signatures of porcine thymus and lymph node T cells. ResultsThe comparison of T cell subpopulations derived from porcine thymus and lymph nodes revealed that their transcriptomic differences were influenced more by tissue origin than by T cell phenotypes, and that lymph node cells exhibited greater transcriptional diversity than thymocytes. Through weighted gene co-expression network analysis (WGCNA), we identified the key modules and candidate hub genes regulating the heterogeneity of T cell subpopulations. Further, we integrated the porcine thymocyte dataset with peripheral blood mononuclear cell (PBMC) dataset to systematically compare transcriptomic differences between T cell types from different tissues. Based on single-cell datasets, we further identified the key transcription factors (TFs) responsible for maintaining porcine thymocyte identity and unveiled that these TFs coordinately regulated the entire T cell development process. Finally, we performed GWAS of cell type-specific differentially expressed genes (DEGs) and 30 complex traits, and found that the DEGs in thymus-related and peripheral blood-related cell types, especially CD4_SP cluster and CD8-related cluster, were significantly associated with pig productive and reproductive traits. DiscussionOur findings provide an insight into T cell development and lay a foundation for further exploring the porcine immune system and genetic mechanisms underlying complex traits in pigs.

Abstract Background Dairy cattle production systems are mostly based on purebreds, but recently the use of crossbreeding has received increased interest. For genetic evaluations including crossbreds, several methods based on single-step genomic best linear unbiased prediction (ssGBLUP) have been proposed, including metafounder ssGBLUP (MF-ssGBLUP) and breed-specific ssGBLUP (BS-ssGBLUP). Ideally, models that account for breed effects should perform better than simple models, but knowledge on the performance of these methods is lacking for two-way crossbred cattle. In addition, the differences in the estimates of genetic parameters (such as the genetic variance component and heritability) between these methods have rarely been investigated. Therefore, the aims of this study were to (1) compare the estimates of genetic parameters for average daily gain (ADG) and feed conversion ratio (FCR) between these methods; and (2) evaluate the impact of these methods on the predictive ability for crossbred performance. Methods Bivariate models using standard ssGBLUP, MF-ssGBLUP and BS-ssGBLUP for the genetic evaluation of ADG and FCR were investigated. To measure the predictive ability of these three methods, we estimated four estimators, bias, dispersion, population accuracy and ratio of population accuracies, using the linear regression (LR) method. Results The results show that, for both ADG and FCR, the heritabilities were low with the three methods. For FCR, the differences in the estimated genetic parameters were small between the three methods, while for ADG, those estimated with BS-ssGBLUP deviated largely from those estimated with the other two methods. Bias and dispersion were similar across the three methods. Population accuracies for both ADG and FCR were always higher with MF-ssGBLUP than with ssGBLUP, while with BS-ssGBLUP the population accuracy was highest for FCR and lowest for ADG. Conclusions Our results indicate that in the genetic evaluation for crossbred performance in a two-way crossbred cattle production system, the predictive ability of MF-ssGBLUP and BS-ssGBLUP is greater than that of ssGBLUP, when the estimated variance components are consistent across the three methods. Compared with BS-ssGBLUP, MF-ssGBLUP is more robust in its superiority over ssGBLUP.

Abstract Background At the beginning of genomic selection, some Chinese companies genotyped pigs with different single nucleotide polymorphism (SNP) arrays. The obtained genomic data are then combined and to do this, several imputation strategies have been developed. Usually, only additive genetic effects are considered in genetic evaluations. However, dominance effects that may be important for some traits can be fitted in a mixed linear model as either ‘classical’ or ‘genotypic’ dominance effects. Their influence on genomic evaluation has rarely been studied. Thus, the objectives of this study were to use a dataset from Canadian Yorkshire pigs to (1) compare different strategies to combine data from two SNP arrays (Affymetrix 55K and Illumina 42K) and identify the most appropriate strategy for genomic evaluation and (2) evaluate the impact of dominance effects (classical’ and ‘genotypic’) and inbreeding depression effects on genomic predictive abilities for average daily gain (ADG), backfat thickness (BF), loin muscle depth (LMD), days to 100 kg (AGE100), and the total number of piglets born (TNB) at first parity. Results The reliabilities obtained with the additive genomic models showed that the strategy used to combine data from two SNP arrays had little impact on genomic evaluations. Models with classical or genotypic dominance effect showed similar predictive abilities for all traits. For ADG, BF, LMD, and AGE100, dominance effects accounted for a small proportion (2 to 11%) of the total genetic variance, whereas for TNB, dominance effects accounted for 11 to 20%. For all traits, the predictive abilities of the models increased significantly when genomic inbreeding depression effects were included in the model. However, the inclusion of dominance effects did not change the predictive ability for any trait except for TNB. Conclusions Our study shows that it is feasible to combine data from different SNP arrays for genomic evaluation, and that all combination methods result in similar accuracies. Regardless of how dominance effects are fitted in the genomic model, there is no impact on genetic evaluation. Models including inbreeding depression effects outperform a model with only additive effects, even if the trait is not strongly affected by dominant genes.

BackgroundThe lack of integrated analysis of genome-wide association studies (GWAS) and 3D epigenomics restricts a deep understanding of the genetic mechanisms of meat-related traits. With the application of techniques as ChIP-seq and Hi-C, the annotations of cis-regulatory elements in the pig genome have been established, which offers a new opportunity to elucidate the genetic mechanisms and identify major genetic variants and candidate genes that are significantly associated with important economic traits. Among these traits, loin muscle depth (LMD) is an important one as it impacts the lean meat content. In this study, we integrated cis-regulatory elements and genome-wide association studies (GWAS) to identify candidate genes and genetic variants regulating LMD.ResultsFive single nucleotide polymorphisms (SNPs) located on porcine chromosome 17 were significantly associated with LMD in Yorkshire pigs. A 10 kb quantitative trait locus (QTL) was identified as a candidate functional genomic region through the integration of linkage disequilibrium and linkage analysis (LDLA) and high-throughput chromosome conformation capture (Hi-C) analysis. The BMP2 gene was identified as a candidate gene for LMD based on the integrated results of GWAS, Hi-C meta-analysis, and cis-regulatory element data. The identified QTL region was further verified through target region sequencing. Furthermore, through using dual-luciferase assays and electrophoretic mobility shift assays (EMSA), two SNPs, including SNP rs321846600, located in the enhancer region, and SNP rs1111440035, located in the promoter region, were identified as candidate SNPs that may be functionally related to the LMD.ConclusionsBased on the results of GWAS, Hi-C, and cis-regulatory elements, the BMP2 gene was identified as an important candidate gene regulating variation in LMD. The SNPs rs321846600 and rs1111440035 were identified as candidate SNPs that are functionally related to the LMD of Yorkshire pigs. Our results shed light on the advantages of integrating GWAS with 3D epigenomics in identifying candidate genes for quantitative traits. This study is a pioneering work for the identification of candidate genes and related genetic variants regulating one key production trait (LMD) in pigs by integrating genome-wide association studies and 3D epigenomics.

ABSTRACT The issue of reducing tillage resistance and lowering energy consumption has become increasingly relevant. Strip tillage has a positive impact on soil protection and energy consumption reduction. This study analysed the tillage resistance components of rotary blades and their relationship with operating parameters and developed a mathematical relationship between tillage resistance and energy consumption (power and fuel consumption). We summarised tillage resistance into three parts: air resistance, lateral rotational friction resistance (divided into horizontal and vertical resistance), and shear force. By theoretical analysis and coupled simulation tests 11 (DEM-CFD), we obtained an air resistance, lateral rotational friction, and shear force of 0.0883 N, 97.21 N, and 893.496 N, respectively, accounting for 0.01%, 9.81%, and 90.18% of tillage resistance. Meanwhile, we found that horizontal resistance decreased linearly with the increase of angular speed, which was the opposite of vertical resistance. Horizontal and vertical resistance increased linearly with the increase in contact area. Shear force increased significantly with angular speed. Fuel consumption in the field test and tillage resistance and power consumption in coupled simulation was formed to build a correspondence point, and a mathematical relationship between tillage resistance, torque, and power and fuel consumption was established.

Abstract Background Gene expression programs are intimately linked to the interplay of active cis regulatory elements mediated by chromatin contacts and associated RNAs. Genome-wide association studies (GWAS) have identified many variants in these regulatory elements that can contribute to phenotypic diversity. However, the functional interpretation of these variants remains nontrivial due to the lack of chromatin contact information or limited contact resolution. Furthermore, the distribution and role of chromatin-associated RNAs in gene expression and chromatin conformation remain poorly understood. To address this, we first present a comprehensive interaction map of nuclear dynamics of 3D chromatin-chromatin interactions (H3K27ac BL-HiChIP) and RNA-chromatin interactions (GRID-seq) to reveal genomic variants that contribute to complex skeletal muscle traits. Results In a genome-wide scan, we provide systematic fine mapping and gene prioritization from GWAS leading signals that underlie phenotypic variability of growth rate, meat quality, and carcass performance. A set of candidate functional variants and 54 target genes previously not detected were identified, with 71% of these candidate functional variants choosing to skip over their nearest gene to regulate the target gene in a long-range manner. The effects of three functional variants regulating KLF6 (related to days to 100 kg), MXRA8 (related to lean meat percentage), and TAF11 (related to loin muscle depth) were observed in two pig populations. Moreover, we find that this multi-omics interaction map consists of functional communities that are enriched in specific biological functions, and GWAS target genes can serve as core genes for exploring peripheral trait-relevant genes. Conclusions Our results provide a valuable resource of candidate functional variants for complex skeletal muscle-related traits and establish an integrated approach to complement existing 3D genomics by exploiting RNA-chromatin and chromatin-chromatin interactions for future association studies.

In this study, the systematic analysis of nitrate assimilation and transport in soybean roots was further improved by analyzing the concentrations of nitrate assimilates, asparagine and glutamine, in soybean roots and the related enzyme activities. This provided a theoretical basis for the efficient utilization of nitrogen fertilizer in soybean farming. A dual-root soybean system with both sides being nodulated was used to provide nitrate withdrawal and resupply in three phases on one side, while the other side received nutrients without nitrogen under sand culture conditions. Measurements were taken of the root’s nitrate reductase and glutamine synthetase activities, as well as the concentrations of asparagine. Measurements were also taken of the asparagine concentration in the basal root peeled skin (where the primary transport pathway is the phloem) and the woody parts (where the primary transport pathway is the xylem). Furthermore, the concentration of glutamine in the roots was also assessed. The findings indicated a positive correlation between the nitrate concentration in the roots and the activity of glutamine synthetase in the roots on both sides. The levels of asparagine in the roots, specifically those in the basal root peeled skin and woody part on both sides, rose when nitrate was added and declined when nitrate was removed. There was no significant change in glutamine concentration within the roots of soybeans. Hence, we deduced that the local provision of nitrate to the dual-root soybeans might enhance the absorption of nitrate into the roots on both sides. Additionally, the assimilated substances were predominantly carried as asparagine through the peeled skin and woody sections of the basal root, facilitating transportation in both directions within the soybean plants (from shoot to root and from root to shoot).

Abstract Background KRAS mutation accounts for 30–50% of human colorectal cancer (CRC) cases. Due to the scarcity of effective treatment options, KRAS mutant CRC is difficult to treat in the clinic. Metastasis is still the major cause of the high mortality associated with KRAS mutant CRC, but the exact mechanism remains unclear. Here, we report a unique function of Homeobox 7 (HOXA7) in driving KRAS mutant CRC metastasis and explore therapeutic strategies for subpopulations of patients with this disease. Methods The expression of HOXA7 in a human CRC cohort was measured by immunohistochemistry. The function of HOXA7 in KRAS mutant CRC metastasis was analyzed with the cecum orthotopic model. Results Elevated HOXA7 expression was positively correlated with lymph node metastasis, distant metastasis, poor tumor differentiation, high TNM stage, and poor prognosis in CRC patients. Furthermore, HOXA7 was an independent prognostic marker in KRAS mutant CRC patients (P

Introduction: The development of tourism economy depends on air quality to a large extent, and good air quality is conducive to promoting the development of tourism economy. And it is crucial to understand the coupled and coordinated relationship between them. However, few studies have explored the coupling relationship between tourism and air quality. Therefore, it is necessary to further study the coupling relationship between tourism and air quality.Methods: In this study, an index system was constructed to evaluate the development status of tourism economy and air quality system, and the entropy value method was used to weight the indexes. Using panel data of Chinese provinces from 2014 to 2020, a coupled coordination model was established, focusing on the degree of coordination between tourism economy and air quality.Results: The empirical results show that during the sample period, China’s tourism economic index is decreasing, and the regional development is unbalanced, showing the gradient of eastern region > central region > western region. The air quality index, on the other hand, fluctuates and increases, showing a spatial distribution pattern of “weekly high, high and low” of western region > eastern region > central region. The coupling coordination level of both regions shows an increasing trend, with the eastern region having the highest coupling coordination level and always in the stage of barely balanced development; the central region has the second highest coupling coordination level and the coupling coordination level is steadily increasing; the western region has the worst coupling coordination level and the coupling system tends to decline. The main type of coupling coordination effect is tourism economy lagged type, and the overall performance shows that the ambient air quality condition is better than the tourism economy development.Discussion: This study clearly reveals the evolution, degree and types of coupling coordination in the tourism economy and air quality of the two systems, which contributes to the understanding of coupling and synergy of industrial development and ecological environment. This research also expands the application field of the CCDM model, and has a certain methodology contribution for further exploring the synergy and symbiosis mechanism of tourism economy development and environmental change.

BackgroundThe nitrate regulates soybean nodulation and nitrogen fixation systemically, mainly in inhibiting nodule growth and reducing nodule nitrogenase activity, but the reason for its inhibition is still inconclusive.MethodsThe systemic effect of nitrate on nodule structure, function, and carbon distribution in soybean (Glycine max (L.) Merr.) was studied in a dual-root growth system, with both sides inoculated with rhizobia and only one side subjected to nitrate treatment for four days. The non-nodulating side was genetically devoid of the ability to form nodules. Nutrient solutions with nitrogen concentrations of 0, 100, and 200 mg L-1 were applied as KNO3 to the non-nodulating side, while the nodulating side received a nitrogen-free nutrient solution. Carbon partitioning in roots and nodules was monitored using 13C-labelled CO2. Other nodule responses were measured via the estimation of the nitrogenase activity and the microscopic observation of nodule ultrastructure.ResultsElevated concentrations of nitrate applied on the non-nodulating side caused a decrease in the number of bacteroids, fusion of symbiosomes, enlargement of the peribacteroid spaces, and onset of degradation of poly-β-hydroxybutyrate granules, which is a form of carbon storage in bacteroids. These microscopic observations were associated with a strong decrease in the nitrogenase activity of nodules. Furthermore, our data demonstrate that the assimilated carbon is more likely to be allocated to the non-nodulating roots, as follows from the competition for carbon between the symbiotic and non-symbiotic sides of the dual-root system.ConclusionWe propose that there is no carbon competition between roots and nodules when they are indirectly supplied with nitrate, and that the reduction of carbon fluxes to nodules and roots on the nodulating side is the mechanism by which the plant systemically suppresses nodulation under nitrogen-replete conditions.

Backfat thickness (BF) is closely related to the service life and reproductive performance of sows. The dynamic monitoring of sows’ BF is a critical part of the production process in large-scale pig farms. This study proposed the application of a hybrid CNN-ViT (Vision Transformer, ViT) model for measuring sows’ BF to address the problems of high measurement intensity caused by the traditional contact measurement of sows’ BF and the low efficiency of existing non-contact models for measuring sows’ BF. The CNN-ViT introduced depth-separable convolution and lightweight self-attention, mainly consisting of a Pre-local Unit (PLU), a Lightweight ViT (LViT) and an Inverted Residual Unit (IRU). This model could extract local and global features of images, making it more suitable for small datasets. The model was tested on 106 pregnant sows with seven randomly divided datasets. The results showed that the CNN-ViT had a Mean Absolute Error (MAE) of 0.83 mm, a Root Mean Square Error (RMSE) of 1.05 mm, a Mean Absolute Percentage Error (MAPE) of 4.87% and a coefficient of determination (R-Square, R2) of 0.74. Compared to LviT-IRU, PLU-IRU and PLU-LviT, the CNN-ViT’s MAE decreased by more than 12%, RMSE decreased by more than 15%, MAPE decreased by more than 15% and R² improved by more than 17%. Compared to the Resnet50 and ViT, the CNN-ViT’s MAE decreased by more than 7%, RMSE decreased by more than 13%, MAPE decreased by more than 7% and R2 improved by more than 15%. The method could better meet the demand for the non-contact automatic measurement of pregnant sows’ BF in actual production and provide technical support for the intelligent management of pregnant sows.

Abstract The mammalian Y chromosome offers a unique perspective on the male reproduction and paternal evolutionary histories. However, further understanding of the Y chromosome biology for most mammals is hindered by the lack of a Y chromosome assembly. This study presents an integrated in silico strategy for identifying and assembling the goat Y‐linked scaffolds using existing data. A total of 11.5 Mb Y‐linked sequences were clustered into 33 scaffolds, and 187 protein‐coding genes were annotated. We also identified high abundance of repetitive elements. A 5.84 Mb subset was further ordered into an assembly with the evidence from the goat radiation hybrid map (RH map). The existing whole‐genome resequencing data of 96 goats (worldwide distribution) were utilized to exploit the paternal relationships among bezoars and domestic goats. Goat paternal lineages were clearly divided into two clades (Y1 and Y2), predating the goat domestication. Demographic history analyses indicated that maternal lineages experienced a bottleneck effect around 2,000 YBP (years before present), after which goats belonging to the A haplogroup spread worldwide from the Near East. As opposed to this, paternal lineages experienced a population decline around the 10,000 YBP. The evidence from the Y chromosome suggests that male goats were not affected by the A haplogroup worldwide transmission, which implies sexually unbalanced contribution to the goat trade and population expansion in post‐Neolithic period.

Nitrogen (N) inhibits soybean (Glycine max L.) nodulation and N2 fixation. Isoflavones secreted by soybean roots can stimulate signal transduction for symbiotic nodules, thus playing a key role in root nodule development and N2 fixation. The relationship between the inhibition of soybean nodulation, N2 fixation and isoflavones by N is still unclear. In this study, dual-root soybean plants were prepared by grafting, and N or isoflavones were supplied to unilateral roots. The number and dry weight of the soybean nodules, nitrogenase activity, isoflavone concentrations and relative changes in the level of expression of nodulation-related genes were measured to study the response relationship between the N systemic regulation the soybean nodule N2 fixation and changes in the concentrations of isoflavones in its roots. The results showed that N supply to one side of the dual-root soybeans systematically affected the N2 fixation of root nodules on both sides, and this effect began in the early stage of nodulation. Moreover, a unilateral supply of N systematically affected the concentrations of daidzein and genistein on both sides of the roots. The concentrations of isoflavones were consistent with the change trend of soybean root nodule and nodulation-related gene expression level. Treatment with unilateral N or isoflavones affected the soybean nodule N2 fixation and its nodulation-related genes, which had the same response to the changes in concentrations of root isoflavones. N regulates soybean nodulation and N2 fixation by systematically affecting the concentrations of isoflavones in the roots.

Abstract Background The feed conversion ratio (FCR) is an important productive trait that greatly affects profits in the pig industry. Elucidating the genetic mechanisms underpinning FCR may promote more efficient improvement of FCR through artificial selection. In this study, we integrated a genome-wide association study (GWAS) with transcriptome analyses of different tissues in Yorkshire pigs (YY) with the aim of identifying key genes and signalling pathways associated with FCR. Results A total of 61 significant single nucleotide polymorphisms (SNPs) were detected by GWAS in YY. All of these SNPs were located on porcine chromosome (SSC) 5, and the covered region was considered a quantitative trait locus (QTL) region for FCR. Some genes distributed around these significant SNPs were considered as candidates for regulating FCR, including TPH2, FAR2, IRAK3, YARS2, GRIP1, FRS2, CNOT2 and TRHDE. According to transcriptome analyses in the hypothalamus, TPH2 exhibits the potential to regulate intestinal motility through serotonergic synapse and oxytocin signalling pathways. In addition, GRIP1 may be involved in glutamatergic and GABAergic signalling pathways, which regulate FCR by affecting appetite in pigs. Moreover, GRIP1, FRS2, CNOT2, and TRHDE may regulate metabolism in various tissues through a thyroid hormone signalling pathway. Conclusions Based on the results from GWAS and transcriptome analyses, the TPH2, GRIP1, FRS2, TRHDE, and CNOT2 genes were considered candidate genes for regulating FCR in Yorkshire pigs. These findings improve the understanding of the genetic mechanisms of FCR and may help optimize the design of breeding schemes.

To date, little is known about the regulatory landscape of the pig genome. Here, the authors characterize cis-regulatory elements in the pig genome using RNA-seq, ChIP-Seq and ATAC-seq, finding a higher degree of usage conservation between pig and human than mouse and human.

Strip tillage is a widely used land preparation approach for effective straw management in conservation agriculture. Understanding the dynamic throwing process during the stubble-crushing operation has important implications for seedbed preparation. However, the airflow generated by the high-speed rotation of stubble-crushing blades has yet to be considered. We established a coupled DEM-CFD simulation model and explored the dynamic motion of soil particles varied with their initial depth (at 0, 20, 40, 60, 80 mm depth) and surface straw under different blade rotary speeds (270, 540, 720, and 810 rpm) based on the model. The coupled model simulation results were proved to be well correlated with the field test results by the field high-speed camera test. The simulation results showed that airflow had a significant effect on the longitudinal displacement of straw (p < 0.05). An increase in rotary speed could increase the longitudinal and lateral throwing displacement of soil particles and straw and increase the blade–soil–straw interaction, while there was no directional effect on the vertical motion. The lateral movement of soil particles decreased with increasing soil particle depth. The stubble-crushing operation allowed the exchange of deep and shallow soil layers, as well as the burial of straw. Plain, straight stubble-crushing blades with a rotary speed of 540 rpm were able to form the optimal seeding row with a width of 80.86 mm. The simulation results were useful for assessing the design solutions of high-speed rotational tools and evaluating seedbed preparation practices.

Abstract Background A large number of pig breeds are distributed around the world, their features and characteristics vary among breeds, and they are valuable resources. Understanding the underlying genetic mechanisms that explain across-breed variation can help breeders develop improved pig breeds. Results In this study, we performed GWAS using a standard mixed linear model with three types of genome variants (SNP, InDel, and CNV) that were identified from public, whole-genome, sequencing data sets. We used 469 pigs of 57 breeds, and we identified and analyzed approximately 19 million SNPs, 1.8 million InDels, and 18,016 CNVs. We defined six biological phenotypes by the characteristics of breed features to identify the associated genome variants and candidate genes, which included coat color, ear shape, gradient zone, body weight, body length, and body height. A total of 37 candidate genes was identified, which included 27 that were reported previously (e.g., PLAG1 for body weight), but the other 10 were newly detected candidate genes (e.g., ADAMTS9 for coat color). Conclusion Our study indicated that using GWAS across a modest number of breeds with high density genome variants provided efficient mapping of complex traits.

Abstract Background The CD4 protein is an important surface marker of T lymphocytes, which can mediate the antigen presentation process by interacting with MHC II and TCR molecules in human and mouse. Results In this study, two haplotypes (A and B) of the CD4 gene were found within Chinese indigenous and Western commercial pig breeds. These two haplotypes were defined by 22 fully linked SNPs in the CDS region of the CD4 gene. The expression level and localization of the CD4 protein were significantly different between haplotypes A and B. Transcriptome analysis revealed that the immune response-related genes and signaling pathways were down-regulated in genotype AA. Finally, three linked functional SNPs were identified, which affected the expression level and membrane localization of the CD4 protein in pigs. These three SNPs led to the replacements of two amino acids in the IgV1 domain of the CD4 protein, and related to the function of the CD4 protein in the immune response. Conclusion These three linked SNPs were the key functional mutation sites in the CD4 gene, which played important roles in the immune response, and could be utilized as new molecular markers in breeding for disease resistance in pigs.

Abstract In the process of pig genetic improvement, different commercial breeds have been bred for the same purpose, improving meat production. Most of the economic traits, such as growth and fertility, have been selected similarly despite the discrepant selection pressure, which is known as parallel selection. Here, 28 whole‐genome sequencing data of Danish large white pigs with an approximately 25‐fold depth each were generated, resulting in about 12 million high‐quality SNPs for each individual. Combined with the sequencing data of 27 Duroc and 23 European wild boars, we investigated the parallel selection of Danish large white and Duroc pigs using two complementary methods, Fst and iHS. In total, 67 candidate regions were identified as the signatures of parallel selection. The genes in candidate regions of parallel selection were mainly associated with sensory perception, growth rate, and body size. Further functional annotation suggested that the striking consistency of the terms may be caused by the polygenetic basis of quantitative traits, and revealing the complex genetic basis of parallel selection. Besides, some unique terms were enriched in population‐specific selection regions, such as the limb development‐related terms enriched in Duroc‐specific selection regions, suggesting unique selections of breed‐specific selected traits. These results will help us better understand the parallel selection process of different breeds. Moreover, we identified several potential causal SNPs that may contribute to the pig genetic breeding process.

Abstract Colostrum quality is a vital factor in mortality and growth performance for piglets. Lactoferrin is an immuno-active milk protein that contributes to the formation of a protective layer above intestinal mucosa, possesses the antibacterial and antiviral activities that are favorable for piglet development. However, there is a notable reduction in lactoferrin in sow milk during lactation after the first few days, which causes many piglets to fail to ingest enough colostrum thereby leading to an increase in piglet mortality. In this study, we successfully constructed genome-edited Large-White pigs with marker-free site-specific knock-in of lactoferrin gene in the 3′-end of Casein alpha-s1 via CRISPR/Cas9 mediated homologous recombination. Thus, the lactoferrin protein can be expressed in the mammary gland in the control of Casein alpha-s1 promoter. As expected, the lactoferrin protein in genetically modified pigs sustained high expression in both colostrum and milk when compared with wild-type pigs. Moreover, the bacterial plate assay indicated that the milk from genetically modified pigs showed bacteriostatic effects when compared with control pigs. Taken together, our study demonstrated that the milk from genetically modified pigs had antibacterial activity which may reduce the costs of veterinary drug and improve the surviving rate of piglets, which is promising for pig breeding.

Here the authors report the construction of a genome-scale porcine CRISPR/Cas9 library, called PigGeCKO, for screening and analyses of host resistance genes and factors associated with Japanese encephalitis virus replication.

Abstract Background Genetic analysis of gene expression level is a promising approach for characterizing candidate genes that are involved in complex economic traits such as meat quality. In the present study, we conducted expression quantitative trait loci (eQTL) and allele-specific expression (ASE) analyses based on RNA-sequencing (RNAseq) data from the longissimus muscle of 189 Duroc × Luchuan crossed pigs in order to identify some candidate genes for meat quality traits. Results Using a genome-wide association study based on a mixed linear model, we identified 7192 cis-eQTL corresponding to 2098 cis-genes (p ≤ 1.33e-3, FDR ≤ 0.05) and 6400 trans-eQTL corresponding to 863 trans-genes (p ≤ 1.13e-6, FDR ≤ 0.05). ASE analysis using RNAseq SNPs identified 9815 significant ASE-SNPs in 2253 unique genes. Integrative analysis between the cis-eQTL and ASE target genes identified 540 common genes, including 33 genes with expression levels that were correlated with at least one meat quality trait. Among these 540 common genes, 63 have been reported previously as candidate genes for meat quality traits, such as PHKG1 (q-value = 1.67e-6 for the leading SNP in the cis-eQTL analysis), NUDT7 (q-value = 5.67e-13), FADS2 (q-value = 8.44e-5), and DGAT2 (q-value = 1.24e-3). Conclusions The present study confirmed several previously published candidate genes and identified some novel candidate genes for meat quality traits via eQTL and ASE analyses, which will be useful to prioritize candidate genes in further studies.

Abstract Advances in high-throughput sequencing technologies have reduced the cost of genotyping dramatically and led to genomic prediction being widely used in animal and plant breeding, and increasingly in human genetics. Inspired by the efficient computing of linear mixed model and the accurate prediction of Bayesian methods, we propose a machine learning-based method incorporating cross-validation, multiple regression, grid search, and bisection algorithms named KAML that aims to combine the advantages of prediction accuracy with computing efficiency. KAML exhibits higher prediction accuracy than existing methods, and it is available at https://github.com/YinLiLin/KAML .

Abstract miRNAs reportedly participate in various biological processes, such as skeletal muscle proliferation and differentiation. However, the regulation of differentially expressed (DE) miRNAs and their function in myogenesis remain unclear. Herein, miRNA expression profiles and regulation during C2C12 differentiation were analyzed in relation to chromatin states by RNA-seq, ATAC-seq, and ChIP-seq. We identified 19 known and nine novel differentially expressed miRNAs at days 0, 1, 2, and 4. The expression of the differentially expressed miRNAs was related to the chromatin states of the 113 surrounding open chromatin regions defined by ATAC-seq peaks. Of these open chromatin regions, 44.25% were colocalized with MyoD/MyoG binding sites. The remainder of the above open chromatin regions were enriched with motifs of the myoblast-expressed AP-1 family, Ctcf, and Bach2 transcription factors (TFs). Additionally, the target genes of the above differentially expressed miRNAs were enriched primarily in muscle growth and development pathways, especially the Hippo signaling pathway. Moreover, via combining a loss-of-function assay with Q-PCR, western blotting, and immunofluorescence, we confirmed that the Hippo signaling pathway was responsible for C2C12 myoblast differentiation. Thus, our results showed that these differentially expressed miRNAs were regulated by chromatin states and affected muscle differentiation through the Hippo signaling pathway. Our findings provide new insights into the function of these differentially expressed miRNAs and the regulation of their expression during myoblast differentiation.

In the original publication [...]

Emerging coronaviruses (CoVs) pose a severe threat to human and animal health worldwide. To identify host factors required for CoV infection, we used α-CoV transmissible gastroenteritis virus (TGEV) as a model for genome-scale CRISPR knockout (KO) screening. Transmembrane protein 41B (TMEM41B) was found to be a bona fide host factor involved in infection by CoV and three additional virus families. We found that TMEM41B is critical for the internalization and early-stage replication of TGEV. Notably, our results also showed that cells lacking TMEM41B are unable to form the double-membrane vesicles necessary for TGEV replication, indicating that TMEM41B contributes to the formation of CoV replication organelles. Lastly, our data from a mouse infection model showed that the KO of this factor can strongly inhibit viral infection and delay the progression of a CoV disease. Our study revealed that targeting TMEM41B is a highly promising approach for the development of broad-spectrum anti-viral therapeutics.

Aflatoxin B1 (AFB1) is amongst the mycotoxins commonly affecting human and animal health, raising global food safety and control concerns. The mechanisms underlying AFB1 toxicity are poorly understood. Moreover, antidotes against AFB1 are lacking. Genome-wide CRISPR/Cas9 knockout screening in porcine kidney cells identified the transcription factor BTB and CNC homolog 1 (BACH1) as a gene required for AFB1 toxicity. The inhibition of BACH1 expression in porcine kidney cells and human hepatoma cells resulted in increased resistance to AFB1. BACH1 depletion attenuates AFB1-induced oxidative damage via the upregulation of antioxidant genes. Subsequently, virtual structural screening identified the small molecule 1-Piperazineethanol, α-[(1,3-benzodioxol-5-yloxy)methyl] -4-(2-methoxyphenyl) (M2) as an inhibitor of BACH1. M2 and its analogues inhibited AFB1-induced porcine and human cell death in vitro, while M2 administration significantly improved AFB1-induced symptoms of weight loss and liver injury in vivo. These findings demonstrate that BACH1 plays a central role in AFB1-induced oxidative damage by regulating antioxidant gene expression. We also present a potent candidate small-molecule inhibitor in developing novel treatments for AFB1 toxicity.

The NAC transcription factor (TF) family is one of the largest TF families in plants, which has been widely reported in rice, maize and common wheat. However, the significance of the NAC TF family in wild emmer wheat (Triticum turgidum ssp. dicoccoides) is not yet well understood. In this study, a genome-wide investigation of NAC genes was conducted in the wild emmer genome and 249 NAC family members (TdNACs) were identified. The results showed that all of these genes contained NAM/NAC-conserved domains and most of them were predicted to be located on the nucleus. Phylogenetic analysis showed that these 249 TdNACs can be classified into seven clades, which are likely to be involved in the regulation of grain protein content, starch synthesis and response to biotic and abiotic stresses. Expression pattern analysis revealed that TdNACs were highly expressed in different wheat tissues such as grain, root, leaves and shoots. We found that TdNAC8470 was phylogenetically close to NAC genes that regulate either grain protein or starch accumulation. Overexpression of TdNAC8470 in rice showed increased grain starch concentration but decreased grain Fe, Zn and Mn contents compared with wild-type plants. Protein interaction analysis indicated that TdNAC8470 might interact with granule-bound starch synthase 1 (TdGBSS1) to regulate grain starch accumulation. Our work provides a comprehensive understanding of the NAC TFs family in wild emmer wheat and establishes the way for future functional analysis and genetic improvement of increasing grain starch content in wheat.

Abstract Background Haemonchosis is a major economic problem in goat production in humid, tropical and subtropical regions. The disease is caused by an abomasal nematode, Haemonchus contortus, which is highly pathogenic in small ruminants. The aim of this study was to identifying single-nucleotide polymorphisms (SNP) that were associated with fecal egg counts (FEC) and could be used as markers to identify resistance to H. contortus in goats. Results Ten novel variants in the CIITA, ATP2A3, HSPA8, STAT5B, ESYT1, and SERPING1 genes were associated with FEC in goats with a nominal significance level of P G SNP locus in all goat breeds. Pairwise coefficients of linkage disequilibrium (D´, r 2) revealed complete LD (r 2 = 1) between significant SNP polymorphisms in CIITA and SERPING1 and strong LD (r 2 = 0.93 and 0.98) between polymorphisms in HSPA8 and ATP2A3, respectively. Correlation coefficient (r) between FEC and body weight (BW) was significantly positive (r = 0.56***, P

Circoviruses are the smallest single-stranded DNA viruses that infect mammalian species, avian species, fish, and insects. The infections of circoviruses are known to be associated with a series of fatal diseases, but the protease of circovirus still remains unknown. In this research, we identified viral capsid protein (Cap) as the protease of porcine circovirus type 2 (PCV2), to our knowledge the first circoviruses protease to be reported. First, we found that the expression of host proteins is affected due to PCV2 infection in the porcine kidney (PK-15) cells. Then, by proteomic analysis, 253 host proteins that were down regulated were identified due to direct or indirect effects of PCV2. Further, Cap expression, but not other ORFs of PCV2, significantly reduced both JMJD6 (bifunctional arginine demethylase and lysyl-hydroxylase) and CCT5 (the chaperonin containing TCP1 subunit 5) in PK-15 cells. Finally, the results in vitro hydrolysis assays demonstrated that Cap could directly degraded either JMJD6 or CCT5 with different catalytic efficiency. In summary, our study expands repertoire of PCV2 Cap and promotes the development of inhibitors toward the anti-PCV2.

Mycobacterium tuberculosis (M.tb) secretes numerous proteins to interfere with host immune response for its long-term survival. As one of the top abundant M.tb secreted proteins, Rv3722c was found to be essential for bacilli growth. However, it remains elusive how this protein interferes with the host immune response and regulates M.tb survival. Here, we confirmed that Rv3722c interacted with host TRAF3 to promote M.tb replication in macrophages. Knock-down of TRAF3 attenuated the effect of Rv3722c on the intracellular M.tb survival. The interaction between Rv3722c and TRAF3 hampered MAPK and NF-κB pathways, resulting in a significant increase of IFN-β expression and decrease of IL-1β, IL-6, IL-12p40, and TNF-α expression. Our study revealed that Rv3722c interacted with TRAF3 and interrupted its downstream pathways to promote M.tb survival in macrophages. These findings facilitate further understanding of the mechanism of M.tb secreted proteins in regulating the host cell immune response and promoting its intracellular survival.

Porcine enteric coronaviruses have caused immense economic losses to the global pig industry, and pose a potential risk for cross-species transmission. The clinical symptoms of the porcine enteric coronaviruses (CoVs) are similar, making it difficult to distinguish between the specific pathogens by symptoms alone. Here, a multiplex nucleic acid detection platform based on CRISPR/Cas12a and multiplex reverse transcriptase loop-mediated isothermal amplification (RT-LAMP) was developed for the detection of four diarrhea CoVs: porcine epidemic diarrhea virus (PEDV), transmissible gastroenteritis virus (TGEV), porcine deltacoronavirus (PDCoV), and swine acute diarrhea syndrome coronavirus (SADS-CoV). With this strategy, we realized a visual colorimetric readout visible to the naked eye without specialized instrumentation by using a ROX-labeled single-stranded DNA-fluorescence-quenched (ssDNA-FQ) reporter. Our method achieved single-copy sensitivity with no cross-reactivity in the identification and detection of the target viruses. In addition, we successfully detected these four enteric CoVs from RNA of clinical samples. Thus, we established a rapid, sensitive, and on-site multiplex molecular differential diagnosis technology for porcine enteric CoVs.

Pigs, as one of the most common livestock species worldwide, are expected to have a fast growth rate and lower subcutaneous fatness but higher intramuscular fat (“marbling meat”). Nowadays, it is believed that not only host genetics but also its gut microbiomes can modulate farm animal phenotypes, however, many of the mechanisms remain elusive. We measured the body weight (BW), average daily gain (ADG), backfat thickness (BFT), and intramuscular fatness (IMF) of 91 Enshi pigs at 260 days of age, then genotyped each one individually using a 50K single nucleotide polymorphism array and performed 16S ribosomal RNA gene sequencing on 455 microbial samples from the jejunum, ileum, cecum, colon, and rectum. The microbial diversity showed notable spatial variation across the entire intestinal tract, with the cecum and colon having the highest α-diversity. The cecal and colonic microbiotas made greater contributions to BW and ADG and accounted for 22–37% of the phenotypic variance. The jejunal and cecal microbiotas contributed more (13–31%) to the BFT and IMF than the other segments. Finally, from cecum, colon, and jejunum, we identified eight microbial taxa that were significantly correlated with the target traits. The genera Alloprevotella and Ruminococcaceae UCG-005 were highly positively correlated with BW and ADG. The genera Prevotellaceae UCG-001 and Alistipes in the cecum and Clostridium sensu stricto 1 in the jejunum were highly positively correlated with BFT and IMF. The genera Stenotrophomonas, Sphaerochaeta, and Desulfovibrio were negatively associated with the mentioned traits. These findings could aid in developing strategies for manipulating the gut microbiota to alter production performance in pigs.

As an emerging swine enteropathogenic coronavirus, porcine deltacoronavirus (PDCoV) not only causes serious diarrhea in suckling piglets but also possesses the potential for cross-species transmission, which has sparked growing interest when studying this emerging virus. We previously identified a novel accessory protein NS7a encoded by PDCoV; however, the function of NS7a was not resolved. In this study, we demonstrated that PDCoV NS7a is an interferon antagonist. Overexpression of NS7a notably inhibited Sendai virus (SeV)-induced interferon-β (IFN-β) production and the activation of IRF3 rather than NF-κB. NS7a also inhibited IFN-β promoter activity induced by RIG-I, MDA5, MAVS, TBK1, and IKKε, which are key components of the RIG-I-like receptor (RLR) signaling pathway but not IRF3, the transcription factor downstream of TBK1/IKKε. Surprisingly, NS7a specifically interacts with IKKε but not with the closely related TBK1. Furthermore, NS7a interacts simultaneously with the kinase domain (KD) and the scaffold dimerization domain (SDD) of IKKε, competing with TRAF3, and IRF3 for binding to IKKε, leading to the reduction of RLR-mediated IFN-β production. The interactions of TRAF3-IKKε and IKKε-IRF3 are also attenuated in PDCoV-infected cells. Taken together, our results demonstrate that PDCoV NS7a inhibits IFN-β production by disrupting the association of IKKε with both TRAF3 and IRF3, revealing a new mechanism utilized by a PDCoV accessory protein to evade the host antiviral innate immune response.

Birth weight of pigs is an important economic factor in the livestock industry. The identification of the genes and variants that underlie birth weight is of great importance. In this study, we integrated two genotyping methods, single nucleotide polymorphism (SNP) chip analysis and restriction site associated DNA sequencing (RAD-seq) to genotype genome-wide SNPs. In total, 45,175 and 139,634 SNPs were detected with the SNP chip and RAD-seq, respectively. The genome-wide association study (GWAS) of the combined SNP panels identified two significant loci located at chr1: 97,745,041 and chr4: 112,031,589, that explained 6.36% and 4.25% of the phenotypic variance respectively. To reduce interval containing causal variants, we imputed sequence-level SNPs in the GWAS identified regions and fine-mapped the causative variants into two narrower genomic intervals: a ∼100 kb interval containing 71 SNPs and a broader ∼870 kb interval with 432 SNPs. This fine-mapping highlighted four promising candidate genes, SKOR2, SMAD2, VAV3, and NTNG1. Additionally, the functional genes, SLC25A24, PRMT6 and STXBP3, are also located near the fine-mapping region. These results suggest that these candidate genes may have contribute substantially to the birth weight of pigs.

Somatic cloning has had a significant impact on the life sciences and is important in a variety of processes, including medical research and animal production. However, the application of somatic cloning has been limited due to its low success rate. Therefore, potential epigenetic variations between cloned and donor animals are still unclear. DNA methylation, one of the factors which is responsible for phenotypic differences in animals, is a commonly researched topic in epigenetic studies of mammals. To investigate the epigenetic variations between cloned and donor animals, we selected blood and ear fibroblasts of a donor pig and a cloned pig to perform whole-genome bisulfite sequencing (WGBS). A total of 215 and 707 differential methylation genes (DMGs) were identified in blood and ear fibroblasts, respectively. Functional annotation revealed that DMGs are enriched in many pathways, including T/B or natural killer (NK) cell differentiation, oocyte maturation, embryonic development, and reproductive hormone secretion. Moreover, 22 DMGs in the blood and 75 in the ear were associated with immune responses (e.g., CD244, CDK6, CD5, CD2, CD83, and CDC7). We also found that 18 DMGs in blood and 53 in ear fibroblasts were involved in reproduction. Understanding the expression patterns of DMGs, especially in relation to immune responses and reproduction, will reveal insights that will aid the advancement of future somatic cloning techniques in swine.

The specific mechanisms by which nitrogen affects nodulation and nitrogen fixation in leguminous crops are still unclear. To study the relationship between nitrogen, nodulation and nitrogen fixation in soybeans, dual-root soybean plants with unilateral nodulation were prepared by grafting. At the third trifoliate leaf (V3) to fourth trifoliate leaf (V4) growth stages (for 5 days), nitrogen nutrient solution was added to the non-nodulated side, while nitrogen-free nutrient solution was added to the nodulated side. The experiment was designed to study the effects of exogenous nitrogen on proteins and metabolites in root nodules and provide a theoretical reference for analyzing the physiological mechanisms of the interaction between nitrogen application and nitrogen fixation in soybean root nodules. Compared with no nitrogen treatment, exogenous nitrogen regulated the metabolic pathways of starch and sucrose metabolism, organic acid metabolism, nitrogen metabolism, and amino acid metabolism, among others. Additionally, exogenous nitrogen promoted the synthesis of signaling molecules, including putrescine, nitric oxide, and asparagine in root nodules, and inhibited the transformation of sucrose to malic acid; consequently, the rhizobia lacked energy for nitrogen fixation. In addition, exogenous nitrogen reduced cell wall synthesis in the root nodules, thus inhibiting root nodule growth and nitrogen fixation.

Identifying genetic basis of domestication and improvement in livestock contributes to our understanding of the role of artificial selection in shaping the genome. Here we used whole-genome sequencing and the genotyping by sequencing approach to detect artificial selection signatures and identify the associated SNPs of two economic traits in Duroc pigs. A total of 38 candidate selection regions were detected by combining the fixation index and the Composite Likelihood Ratio methods. Further genome-wide association study revealed seven associated SNPs that were related with intramuscular fat content and feed conversion ratio traits, respectively. Enrichment analysis suggested that the artificial selection regions harbored genes, such as MSTN, SOD2, MC5R and CD83, which are responsible for economic traits including lean muscle mass, fertility and immunization. Overall, this study found a series of candidate genes putatively associated with the breeding improvement of Duroc pigs and the polygenic basis of adaptive evolution, which can provide important references and fundamental information for future breeding programs.

Abstract Duration of fertility, (DF) is an important functional trait in poultry production and lncRNAs have emerged as important regulators of various process including fertility. In this study we applied a genome-guided strategy to reconstruct the uterovaginal junction (UVJ) transcriptome of 14 egg-laying birds with long- and short-DF (n = 7); and sought to uncover key lncRNAs related to duration of fertility traits by RNA-sequencing technology. Examination of RNA-seq data revealed a total of 9977 lncRNAs including 2576 novel lncRNAs. Differential expression (DE) analysis of lncRNA identified 223 lncRNAs differentially expressed between the two groups. DE-lncRNA target genes prediction uncovered over 200 lncRNA target genes and functional enrichment tests predict a potential function of DE-lncRNAs. Gene ontology classification and pathway analysis revealed 8 DE-lncRNAs, with the majority of their target genes enriched in biological functions such as reproductive structure development, developmental process involved in reproduction, response to cytokine, carbohydrate binding, chromatin organization, and immune pathways. Differential expression of lncRNAs and target genes were confirmed by qPCR. Together, these results significantly expand the utility of the UVJ transcriptome and our analysis identification of key lncRNAs and their target genes regulating DF will form the baseline for understanding the molecular functions of lncRNAs regulating DF.