Integrated ATAC-seq and RNA-seq Analysis of In Vitro Cultured Skeletal Muscle Satellite Cells to Understand Changes in Cell Proliferation.

Skeletal muscle satellite cells, the resident stem cells in pig skeletal muscle, undergo proliferation and differentiation to enable muscle tissue repair. The proliferative and differentiative abilities of these cells gradually decrease during in vitro cultivation as the cell passage number increases. Despite extensive research, the precise molecular mechanisms that regulate this process are not fully understood. To bridge this knowledge gap, we conducted transcriptomic analysis of skeletal muscle satellite cells during in vitro cultivation to quantify passage number-dependent changes in the expression of genes associated with proliferation. Additionally, we explored the relationships between gene transcriptional activity and chromatin accessibility using transposase-accessible chromatin sequencing. This revealed the closure of numerous open chromatin regions, which were primarily located in intergenic regions, as the cell passage number increased. Integrated analysis of the transcriptomic and epigenomic data demonstrated a weak correlation between gene transcriptional activity and chromatin openness in expressed genic regions; although some genes (e.g., GNB4 and FGD5) showed consistent relationships between gene expression and chromatin openness, a substantial number of differentially expressed genes had no clear association with chromatin openness in expressed genic regions. The p53-p21-RB signaling pathway may play a critical regulatory role in cell proliferation processes. The combined transcriptomic and epigenomic approach taken here provided key insights into changes in gene expression and chromatin openness during in vitro cultivation of skeletal muscle satellite cells. These findings enhance our understanding of the intricate mechanisms underlying the decline in cellular proliferation capacity in cultured cells.

An innovative approach to assess spinal canal expansion following French-door cervical laminoplasty by intraoperative ultrasonography.

OBJECTIVE: To investigate the feasibility and effectiveness of applying intraoperative ultrasound (IOUS) to evaluate spinal canal expansion in patients undergoing French-door cervical laminoplasty (FDCL). MATERIALS AND METHODS: Twenty-five patients who underwent FDCL for multilevel degenerative cervical myelopathy were prospectively recruited. Formulae describing the relationship between laminoplasty opening angle (LOA) and laminoplasty opening size, the increase in sagittal canal diameter and the spinal canal area were deduced with trigonometric functions. The LOA was measured with IOUS imaging during surgery, and other spinal canal parameters were assessed. Actual spinal canal enlargement was verified on postoperative CT images. Linear correlation analysis and Bland‒Altman analysis were used to evaluate correlation and agreement between the intraoperative and postoperative measurements. RESULTS: The LOA at C5 measured with IOUS was 27.54 ± 3.12°, and it was 27.23 ± 3.02° on postoperative CT imaging. Linear correlation analysis revealed a significant correlation between IOUS and postoperative CT measurements (r = 0.88; p < 0.01). Bland-Altman plots showed good agreement between these two methods, with a mean difference of 0.30°. For other spinal canal expansion parameter measurements, correlation analysis showed a moderate to a high degree of correlation (p < 0.01), and Bland-Altman analysis indicated good agreement. CONCLUSION: In conclusion, during the French-door cervical laminoplasty procedure, application of IOUS can accurately evaluate spinal canal expansion. This innovative method may be helpful in improving surgical accuracy by enabling the operator to measure and determine canal enlargement during surgery, leading to ideal clinical outcomes and fewer postoperative complications. CLINICAL RELEVANCE STATEMENT: The use of intraoperative ultrasonography to assess spinal canal expansion following French-door cervical laminoplasty may improve outcomes for patients undergoing this procedure by providing more accurate measurements of spinal canal expansion. KEY POINTS: • Spinal canal expansion after French-door cervical laminoplasty substantially influences operative prognosis; insufficient or excessive lamina opening may result in unexpected outcomes. • Prediction of spinal canal expansion during surgery was previously impracticable, but based on this study, intraoperative ultrasonography offers an innovative approach and strongly agrees with postoperative CT measurement. • Since this is the first research to offer real-time canal expansion guidance for cervical laminoplasty, it may improve the accuracy of the operation and produce ideal clinical outcomes with fewer postoperative complications.

An intelligent composite model incorporating global / regional X-rays and clinical parameters to predict progressive adolescent idiopathic scoliosis curvatures and facilitate population screening.

BACKGROUND: Adolescent idiopathic scoliosis (AIS) affects up to 5% of the population. The efficacy of school-aged screening remains controversial since it is uncertain which curvatures will progress following diagnosis and require treatment. Patient demographics, vertebral morphology, skeletal maturity, and bone quality represent individual risk factors for progression but have yet to be integrated towards accurate prognostication. The objective of this work was to develop composite machine learning-based prediction model to accurately predict AIS curves at-risk of progression. METHODS: 1870 AIS patients with remaining growth potential were identified. Curve progression was defined by a Cobb angle increase in the major curve of ≥6° between first visit and skeletal maturity in curves that exceeded 25°. Separate prediction modules were developed for i) clinical data, ii) global/regional spine X-rays, and iii) hand X-rays. The hand X-ray module performed automated image classification and segmentation tasks towards estimation of skeletal maturity and bone mineral density. A late fusion strategy integrated these domains towards the prediction of progressive curves at first clinic visit. FINDINGS: Composite model performance was assessed on a validation cohort and achieved an accuracy of 83.2% (79.3-83.6%, 95% confidence interval), sensitivity of 80.9% (78.2-81.9%), specificity of 83.6% (78.8-84.1%) and an AUC of 0.84 (0.81-0.85), outperforming single modality prediction models (AUC 0.65-0.78). INTERPRETATION: The composite prediction model achieved a high degree of accuracy. Upon incorporation into school-aged screening programs, patients at-risk of progression may be prioritized to receive urgent specialist attention, more frequent follow-up, and pre-emptive treatment. FUNDING: Funding from The Society for the Relief of Disabled Children was awarded to GKHS.

RNA-Sequencing Characterization of lncRNA and mRNA Functions in Septic Pig Liver Injury.

We assessed differentially expressed (DE) mRNAs and lncRNAs in the liver of septic pigs to explore the key factors regulating lipopolysaccharide (LPS)-induced liver injury. We identified 543 DE lncRNAs and 3642 DE mRNAs responsive to LPS. Functional enrichment analysis revealed the DE mRNAs were involved in liver metabolism and other pathways related to inflammation and apoptosis. We also found significantly upregulated endoplasmic reticulum stress (ERS)-associated genes, including the receptor protein kinase receptor-like endoplasmic reticulum kinase (PERK), the eukaryotic translation initiation factor 2α (EIF2S1), the transcription factor C/EBP homologous protein (CHOP), and activating transcription factor 4 (ATF4). In addition, we predicted 247 differentially expressed target genes (DETG) of DE lncRNAs. The analysis of protein-protein interactions (PPI) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway detected key DETGs that are involved in metabolic pathways, such as N-Acetylgalactosaminyltransferase 2 (GALNT2), argininosuccinate synthetase 1 (ASS1), and fructose 1,6-bisphosphatase 1 (FBP1). LNC_003307 was the most abundant DE lncRNA in the pig liver, with a marked upregulation of >10-fold after LPS stimulation. We identified three transcripts for this gene using the rapid amplification of the cDNA ends (RACE) technique and obtained the shortest transcript sequence. This gene likely derives from the nicotinamide N-methyltransferase (NNMT) gene in pigs. According to the identified DETGs of LNC_003307, we hypothesize that this gene regulates inflammation and endoplasmic reticulum stress in LPS-induced liver damage in pigs. This study provides a transcriptomic reference for further understanding of the regulatory mechanisms underlying septic hepatic injury.

Application and prospect of gene chip in genetic breeding of livestock and poultry.

Gene chip is a high-throughput technique for detecting specific DNA sequences by DNA or DNA-RNA complementary hybridization, among which SNP genotyping chips have been widely employed in the animal genetics and breeding, and have made great achievements in cattle (Bos taurus), pigs (Sus scrofa), sheep (Caprinae), chickens (Gallus gallus) and other livestock. However, genomic selection applied in production merely uses genomic information and cannot fully explain the molecular mechanism of complex traits genetics, which limits the accuracy of genomic selection. With the continuous progresses in epigenetic research, the development of commercial methylation chips and the application of the epigenome-wide association study (EWAS), DNA methylation has been extensively used to draw the causal connections between genetics and phenotypes. In the future, it is hopefully expected to develop methylation chips customized for livestock and poultry and explore methylation sites significantly related to economic traits of livestock and poultry through EWAS thereby extending the understanding of causal variation of complex traits. Combining methylation chips and SNP chips, we can capture the epigenomic and genomic information of livestock and poultry, interpret genetic variation more precisely, improve the accuracy of genome selection, and promote the fine evolution of molecular genetic breeding of livestock and poultry. In this review, we summarize the application of SNP chips and depict the prospects of the application of methylation chips in livestock and poultry. This review will provide valuable insights for further application of gene chips in farm animal breeding.

Integrating genome-wide association studies and population genomics analysis reveals the genetic architecture of growth and backfat traits in pigs.

Growth and fat deposition are complex traits, which can affect economical income in the pig industry. Due to the intensive artificial selection, a significant genetic improvement has been observed for growth and fat deposition in pigs. Here, we first investigated genomic-wide association studies (GWAS) and population genomics (e.g., selection signature) to explore the genetic basis of such complex traits in two Large White pig lines (n = 3,727) with the GeneSeek GGP Porcine HD array (n = 50,915 SNPs). Ten genetic variants were identified to be associated with growth and fatness traits in two Large White pig lines from different genetic backgrounds by performing both within-population GWAS and cross-population GWAS analyses. These ten significant loci represented eight candidate genes, i.e., NRG4, BATF3, IRS2, ANO1, ANO9, RNF152, KCNQ5, and EYA2. One of them, ANO1 gene was simultaneously identified for both two lines in BF100 trait. Compared to single-population GWAS, cross-population GWAS was less effective for identifying SNPs with population-specific effect, but more powerful for detecting SNPs with population-shared effects. We further detected genomic regions specifically selected in each of two populations, but did not observe a significant enrichment for the heritability of growth and backfat traits in such regions. In summary, the candidate genes will provide an insight into the understanding of the genetic architecture of growth-related traits and backfat thickness, and may have a potential use in the genomic breeding programs in pigs.

GWAS of Reproductive Traits in Large White Pigs on Chip and Imputed Whole-Genome Sequencing Data.

Total number born (TNB), number of stillborn (NSB), and gestation length (GL) are economically important traits in pig production, and disentangling the molecular mechanisms associated with traits can provide valuable insights into their genetic structure. Genotype imputation can be used as a practical tool to improve the marker density of single-nucleotide polymorphism (SNP) chips based on sequence data, thereby dramatically improving the power of genome-wide association studies (GWAS). In this study, we applied Beagle software to impute the 50 K chip data to the whole-genome sequencing (WGS) data with average imputation accuracy (R2) of 0.876. The target pigs, 2655 Large White pigs introduced from Canadian and French lines, were genotyped by a GeneSeek Porcine 50K chip. The 30 Large White reference pigs were the key ancestral individuals sequenced by whole-genome resequencing. To avoid population stratification, we identified genetic variants associated with reproductive traits by performing within-population GWAS and cross-population meta-analyses with data before and after imputation. Finally, several genes were detected and regarded as potential candidate genes for each of the traits: for the TNB trait: NOTCH2, KLF3, PLXDC2, NDUFV1, TLR10, CDC14A, EPC2, ORC4, ACVR2A, and GSC; for the NSB trait: NUB1, TGFBR3, ZDHHC14, FGF14, BAIAP2L1, EVI5, TAF1B, and BCAR3; for the GL trait: PPP2R2B, AMBP, MALRD1, HOXA11, and BICC1. In conclusion, expanding the size of the reference population and finding an optimal imputation strategy to ensure that more loci are obtained for GWAS under high imputation accuracy will contribute to the identification of causal mutations in pig breeding.

Transplanting neurofibromatosis-1 gene knockout neural stem cells improve functional recovery in rats with spinal cord injury by enhancing the mTORC2 pathway.

The poor survival and low efficiency of neuronal differentiation limits the therapeutic effects of transplanted neural stem cells in the treatment of spinal cord injury. Neurofibromatosis-1 (NF-1) is a tumor suppressor gene that restricts the rapid and abnormal growth and differentiation of neural cells. In the present study, lentiviral vectors were used to knock out NF-1, Ricotr (the core member of mTORC2) or NF-1+Ricotr in neural stem cells in vitro, and the NF-1, Ricotr or NF-1+Ricotr knockout neural stem cells were transplanted at the lesion site in a rat model of spinal cord injury (SCI). We first demonstrated that targeted knockout of NF-1 had an antiapoptotic effect and improved neuronal differentiation by enhancing the mTORC2/Rictor pathway of neural stem cells in vitro. Subsequently, transplanting NF-1 knockout neural stem cells into the injured site sufficiently promoted the tissue repair and functional recovery of rats with spinal cord injury by enhancing the survival and neuronal differentiation of grafted neural stem cells. Collectively, these findings reveal a prominent role of NF-1 in neural stem cell biology, which is an invaluable step forward in enhancing the benefit of neural stem cell-mediated regenerative cell therapy for spinal cord injury and identifies the transplantation of NF-1 knockout neural stem cells as a promising strategy for spinal cord injury.

Assessment of Hematologic and Biochemical Parameters for Healthy Commercial Pigs in China.

Hematologic and biochemical data are useful for indicating disease diagnosis and growth performance in swine. However, the assessment of these parameters in healthy commercial pigs is rare in China. Thus, blood samples were collected from 107 nursery pigs and 87 sows and were analyzed for 25 hematologic and 14 biochemical variables. After the rejection of the outliers and the detection of the data distribution, the correlations between the blood parameters were analyzed and the hematologic/biochemical RIs were preliminarily established using the 95% percentile RI. Correlation analysis showed that albumin was the hub parameter among the blood parameters investigated, and genes overlapping with key correlated variables were discovered. Most of the hematologic and biochemical parameters were significantly different between nursery pigs and sows. The 95% RIs of white blood cells and red blood cells were 7.18-24.52 × 109/L and 5.62-7.84 × 1012/L, respectively, for nursery pigs, but 9.34-23.84 × 109/L and 4.98-8.29 × 1012/L for sows. The 95% RIs of total protein and albumin were 43.16-61.23 g/dL and 19.35-37.86 g/dL, respectively, for nursery pigs, but 64.96-88.68 g/dL and 31.91-43.28 g/dL for sows. In conclusion, our study highlights the variability in blood parameters between nursery pigs and sows and provides fundamental data for the health monitoring of commercial pigs in China.

Identification of imprinted genes in the skeletal muscle of newborn piglets by high-throughput sequencing.

Imprinted genes - exhibiting parent-specific transcription - play essential roles in the process of mammalian development and growth. Skeletal muscle growth is crucial for meat production. To further understand the role of imprinted genes during the porcine skeletal muscle growth, DNA-seq and RNA-seq were used to explore the characteristics of imprinted genes from porcine reciprocal crosses. A total of 584 545 single-nucleotide variations were discovered in the DNA-seq data of F0 parents, heterozygous in two pig breeds (Yorkshire and Min pigs) but homozygous in each breed. These single-nucleotide variations were used to determine the allelic-specific expression in F1 individuals. Finally, eight paternal expression sites and three maternal expression sites were detected, whereas two paternally expressed imprinted genes (NDN and IGF2) and one maternally expressed imprinted gene (H1-3) were validated by Sanger sequencing. DNA methylation regulates the expression of imprinted genes, and all of the identified imprinted genes in this study were predicted to possess CpG islands. PBX1 and YY1 binding motifs were discovered in the promoter regions of all three imprinted genes, which were candidate elements regulating the transcription of imprinted genes. For these identified imprinted genes, IGF2 and NDN promoted muscle growth whereas H1-3 inhibited cell proliferation, corroborating the 'parental conflict' theory that paternally expressed imprinted genes assisted descendants' growth whereas maternally expressed imprinted genes inhibited it. This study discovered porcine imprinted genes in skeletal muscle and was the first to reveal that H1-3 was expressed by the maternal allele to our knowledge. Our findings provided valuable resources for the potential utilization of imprinted genes in pig breeding.

Potential of intraoperative ultrasonographic assessment of the spinal cord central echo complex in predicting postoperative neurological recovery of degenerative cervical myelopathy.

BACKGROUND AND PURPOSE: The spinal cord central echo complex (SCCEC) is a special ultrasonography-based intramedullary structure, but its clinical significance in degenerative cervical myelopathy (DCM) is undefined. This study aimed to explore the potential of the SCCEC in predicting postoperative neurological recovery in DCM. METHODS: Thirty-two DCM patients who underwent intraoperative ultrasonography-guided French-door laminoplasty were prospectively enrolled. The modified Japanese Orthopaedic Association (mJOA) score was evaluated preoperatively and 12 months postoperatively. SCCEC width (SCCEC-W), and anteroposterior diameter (APD) and transverse diameter (TD) of the spinal cord were measured on transverse ultrasonographic images, while the tissue widths from anterior and posterior borders of the spinal cord to the SCCEC were measured on sagittal ultrasonographic images. The APD of the spinal cord and occupying rate of the spinal canal were measured on preoperative magnetic resonance imaging (MRI). RESULTS: All patients achieved improvements in mJOA scores, with an average recovery rate (RR) of 68.69 ± 20.22%. Spearman correlation analysis revealed that SCCEC-W, and ratios between the SCCEC-W and APD/TD based on ultrasonography, correlated moderately with mJOA score RR, with coefficients of -0.527, -0.605 and -0.514, respectively. The ratio between SCCEC-W and ultrasonographic TD correlated moderately with preoperative APD of the spinal cord. The MRI measurements and ultrasonography-based tissue widths showed no significant correlation with mJOA score RR. CONCLUSIONS: The SCCEC may have predictive potential as an intraoperative indicator of neurological recovery in treating DCM. SCCEC-W may be related to spinal cord compression in DCM.

Protective Roles of Folic Acid in the Responses of Bovine Mammary Epithelial Cells to Different Virulent Staphylococcus aureus Strains.

Mastitis caused by Staphylococcus aureus (S. aureus) infection is one of the most difficult diseases to treat in dairy cattle. Exploring the biological progression of S. aureus mastitis via the interaction between host, pathogen, and environment is the key to an effective and sustainable improvement of animal health. Here, two strains of S. aureus and a strain of MRSA (Methicillin-resistant Staphylococcus aureus) isolated from cows with different inflammation phenotypes were used to challenge Mac-T cells and to investigate their effects on the global transcriptome of the cells, then to explore the potential regulatory mechanisms of folic acid on S. aureus mastitis prevention. Differential gene expression or splicing analysis showed that different strains of S. aureus led to distinct transcriptional responses from the host immune system. Folic acid could protect host defense against the challenge of S. aureus and MRSA partially through activating cytoplasmic DNA sensing and tight junction pathway. ZBP1 at the upstream of cytoplasmic DNA sensing pathway was verified and related to anti-pathogen through RNA interference. Further enrichment analysis using these transcriptome data with cattle large-scale genome-wide association study (GWAS) data confirmed that ZBP1 gene is highly associated with bovine somatic cell score (SCS) trait. Our data shed light on the potential effect of FA through regulating key gene and then protect host cells' defense against S. aureus and MRSA.

Estimates of genomic inbreeding and identification of candidate regions that differ between Chinese indigenous sheep breeds.

BACKGROUND: A run of homozygosity (ROH) is a consecutive tract of homozygous genotypes in an individual that indicates it has inherited the same ancestral haplotype from both parents. Genomic inbreeding can be quantified based on ROH. Genomic regions enriched with ROH may be indicative of selection sweeps and are known as ROH islands. We carried out ROH analyses in five Chinese indigenous sheep breeds; Altay sheep (n = 50 individuals), Large-tailed Han sheep (n = 50), Hulun Buir sheep (n = 150), Short-tailed grassland sheep (n = 150), and Tibetan sheep (n = 50), using genotypes from an Ovine Infinium HD SNP BeadChip. RESULTS: A total of 18,288 ROH were identified. The average number of ROH per individual across the five sheep breeds ranged from 39 (Hulun Buir sheep) to 78 (Large-tailed Han sheep) and the average length of ROH ranged from 0.929 Mb (Hulun Buir sheep) to 2.544 Mb (Large-tailed Han sheep). The effective population size (Ne) of Altay sheep, Large-tailed Han sheep, Hulun Buir sheep, Short-tailed grassland sheep and Tibetan sheep were estimated to be 81, 78, 253, 238 and 70 five generations ago. The highest ROH-based inbreeding estimate (FROH) was 0.0808 in Large-tailed Han sheep, whereas the lowest FROH was 0.0148 in Hulun Buir sheep. Furthermore, the highest proportion of long ROH fragments (> 5 Mb) was observed in the Large-tailed Han sheep breed which indicated recent inbreeding. In total, 49 ROH islands (the top 0.1% of the SNPs most commonly observed in ROH) were identified in the five sheep breeds. Three ROH islands were common to all the five sheep breeds, and were located on OAR2: 12.2-12.3 Mb, OAR12: 78.4-79.1 Mb and OAR13: 53.0-53.6 Mb. Three breed-specific ROH islands were observed in Altay sheep (OAR15: 3.4-3.8 Mb), Large-tailed Han sheep (ORA17: 53.5-53.8 Mb) and Tibetan sheep (ORA5:19.8-20.2 Mb). Collectively, the ROH islands harbored 78 unique genes, including 19 genes that have been documented as having associations with tail types, adaptation, growth, body size, reproduction or immune response. CONCLUSION: Different ROH patterns were observed in five Chinese indigenous sheep breeds, which reflected their different population histories. Large-tailed Han sheep had the highest genomic inbreeding coefficients and the highest proportion of long ROH fragments indicating recent inbreeding. Candidate genes in ROH islands could be used to illustrate the genetic characteristics of these five sheep breeds. Our findings contribute to the understanding of genetic diversity and population demography, and help design and implement breeding and conservation strategies for Chinese sheep.

The landscape of chromatin accessibility in skeletal muscle during embryonic development in pigs.

BACKGROUND: The development of skeletal muscle in pigs during the embryonic stage is precisely regulated by transcriptional mechanisms, which depend on chromatin accessibility. However, how chromatin accessibility plays a regulatory role during embryonic skeletal muscle development in pigs has not been reported. To gain insight into the landscape of chromatin accessibility and the associated genome-wide transcriptome during embryonic muscle development, we performed ATAC-seq and RNA-seq analyses of skeletal muscle from pig embryos at 45, 70 and 100 days post coitus (dpc). RESULTS: In total, 21,638, 35,447 and 60,181 unique regions (or peaks) were found across the embryos at 45 dpc (LW45), 70 dpc (LW70) and 100 dpc (LW100), respectively. More than 91% of the peaks were annotated within - 1 kb to 100 bp of transcription start sites (TSSs). First, widespread increases in specific accessible chromatin regions (ACRs) from embryos at 45 to 100 dpc suggested that the regulatory mechanisms became increasingly complicated during embryonic development. Second, the findings from integrated ATAC-seq and RNA-seq analyses showed that not only the numbers but also the intensities of ACRs could control the expression of associated genes. Moreover, the motif screening of stage-specific ACRs revealed some transcription factors that regulate muscle development-related genes, such as MyoG, Mef2c, and Mef2d. Several potential transcriptional repressors, including E2F6, OTX2 and CTCF, were identified among the genes that exhibited different regulation trends between the ATAC-seq and RNA-seq data. CONCLUSIONS: This work indicates that chromatin accessibility plays an important regulatory role in the embryonic muscle development of pigs and regulates the temporal and spatial expression patterns of key genes in muscle development by influencing the binding of transcription factors. Our results contribute to a better understanding of the regulatory dynamics of genes involved in pig embryonic skeletal muscle development.

Revealing New Candidate Genes for Teat Number Relevant Traits in Duroc Pigs Using Genome-Wide Association Studies.

The number of teats is related to the nursing ability of sows. In the present study, we conducted genome-wide association studies (GWAS) for traits related to teat number in Duroc pig population. Two mixed models, one for counted and another for binary phenotypic traits, were employed to analyze seven traits: the right (RTN), left (LTN), and total (TTN) teat numbers; maximum teat number on a side (MAX); left minus right side teat number (LR); the absolute value of LR (ALR); and the presence of symmetry between left and right teat numbers (SLR). We identified 11, 1, 4, 13, and 9 significant SNPs associated with traits RTN, LTN, MAX, TTN, and SLR, respectively. One significant SNP (MARC0038565) was found to be simultaneous associated with RTN, LTN, MAX and TTN. Two annotated genes (VRTN and SYNDIG1L) were located in genomic region around this SNP. Three significant SNPs were shown to be associated with TTN, RTN and MAX traits. Seven significant SNPs were simultaneously detected in two traits of TTN and RTN. Other two SNPs were only identified in TTN. These 13 SNPs were clustered in the genomic region between 96.10-98.09 Mb on chromosome 7. Moreover, nine significant SNPs were shown to be significantly associated with SLR. In total, four and 22 SNPs surpassed genome-wide significance and suggestive significance levels, respectively. Among candidate genes annotated, eight genes have documented association with the teat number relevant traits. Out of them, DPF3 genes on Sus scrofa chromosome (SSC) 7 and the NRP1 gene on SSC 10 were new candidate genes identified in this study. Our findings demonstrate the genetic mechanism of teat number relevant traits and provide a reference to further improve reproductive performances in practical pig breeding programs.

Inadequate spinal cord expansion in intraoperative ultrasound after decompression may predict neurological recovery of degenerative cervical myelopathy.

OBJECTIVE: To compare the neurological recovery between patients with adequate and inadequate immediate spinal cord expansion after sufficient decompression in degenerative cervical myelopathy (DCM). METHODS: Twenty-seven patients subjected to French-door laminoplasty underwent the guidance of intraoperative ultrasound (IOUS) and were prospectively included. The modified Japanese Orthopedic Association (mJOA) score was evaluated before surgery and at 12 months postoperatively. The maximum spinal cord compression (MSCC) after sufficient decompression was calculated on the IOUS image; patients were divided into adequate (MSCC ≥ 0.95) and inadequate (MSCC < 0.95) expansion groups according to the MSCC. The mJOA score, spinal cord hyperechogenicity, age at surgery, symptom duration, occupational rate of the spinal canal, and the minimum anteroposterior diameter of the spinal cord between the two groups were compared. RESULTS: Initially, 2 cases showed residual compression on IOUS; after further decompression, all patients acquired sufficient decompression. All patients achieved improvements in mJOA scores with an average recovery rate of 68.6 ± 20.3%. The recovery rate of the mJOA score of the inadequate expansion group was significantly inferior to that of the adequate expansion group (59.2 ± 21.7% versus 76.2 ± 16.2%, p = 0.028). The spinal cord hyperechogenicity was more common in the inadequate expansion group, while the spinal cord anteroposterior diameter of the inadequate expansion group was significantly smaller than that of the adequate expansion group. CONCLUSIONS: The application of IOUS in French-door laminoplasty could help to confirm sufficient decompression for the treatment of DCM. Inadequate spinal cord expansion after sufficient decompression had the high possibility of predicting less satisfactory neurological recovery of DCM. KEY POINTS: • The intraoperative ultrasound revealed that not all degenerative cervical myelopathy patients acquired adequate spinal cord expansion after sufficient decompression. • Patients who failed to acquire adequate spinal cord expansion commonly combined with spinal cord hyperechogenicity and trended to achieve less satisfactory neurological recovery after surgical decompression. • Inadequate spinal cord expansion after sufficient decompression had the high possibility of predicting less satisfactory neurological recovery of patients with degenerative cervical myelopathy.

Intensity of Intraoperative Spinal Cord Hyperechogenicity as a Novel Potential Predictive Indicator of Neurological Recovery for Degenerative Cervical Myelopathy.

OBJECTIVE: To analyze the correlations between intraoperative ultrasound and MRI metrics of the spinal cord in degenerative cervical myelopathy and identify novel potential predictive ultrasonic indicators of neurological recovery for degenerative cervical myelopathy. MATERIALS AND METHODS: Twenty-two patients who underwent French-door laminoplasty for multilevel degenerative cervical myelopathy were followed up for 12 months. The Japanese Orthopedic Association (JOA) scores were assessed preoperatively and 12 months postoperatively. Maximum spinal cord compression and compression rates were measured and calculated using both intraoperative ultrasound imaging and preoperative T2-weight (T2W) MRI. Signal change rates of the spinal cord on preoperative T2W MRI and gray value ratios of dorsal and ventral spinal cord hyperechogenicity on intraoperative ultrasound imaging were measured and calculated. Correlations between intraoperative ultrasound metrics, MRI metrics, and the recovery rate JOA scores were analyzed using Spearman correlation analysis. RESULTS: The postoperative JOA scores improved significantly, with a mean recovery rate of 65.0 ± 20.3% (p < 0.001). No significant correlations were found between the operative ultrasound metrics and MRI metrics. The gray value ratios of the spinal cord hyperechogenicity was negatively correlated with the recovery rate of JOA scores (ρ = -0.638, p = 0.001), while the ventral and dorsal gray value ratios of spinal cord hyperechogenicity were negatively correlated with the recovery rate of JOA-motor scores (ρ = -0.582, p = 0.004) and JOA-sensory scores (ρ = -0.452, p = 0.035), respectively. The dorsal gray value ratio was significantly higher than the ventral gray value ratio (p < 0.001), while the recovery rate of JOA-motor scores was better than that of JOA-sensory scores at 12 months post-surgery (p = 0.028). CONCLUSION: For degenerative cervical myelopathy, the correlations between intraoperative ultrasound and preoperative T2W MRI metrics were not significant. Gray value ratios of the spinal cord hyperechogenicity and dorsal and ventral spinal cord hyperechogenicity were significantly correlated with neurological recovery at 12 months postoperatively.

Integrated analysis of lncRNAs and mRNAs reveals key trans-target genes associated with ETEC-F4ac adhesion phenotype in porcine small intestine epithelial cells.

BACKGROUND: Long non-coding RNAs (lncRNAs) play crucial roles in gene regulation at the transcriptional and post-transcriptional levels. LncRNAs are belonging to a large class of transcripts with ≥200 nt in length which do not code for proteins, have been widely investigated in various physiological and pathological contexts by high-throughput sequencing techniques and bioinformatics analysis. However, little is known about the regulatory mechanisms by which lncRNAs regulate genes that are associated with Enterotoxigenic Escherichia coli F4 fimbriae (ETEC-F4ac) adhesion phenotype in small intestine epithelial cells of Large White piglets. To address this, we used RNA sequencing to profile lncRNAs and mRNAs of small intestine epithelial cells in Large White piglets differing in their ETEC-F4 adhesion phenotypes and ITGB5 genotypes. Eight male piglets were used in this study and were divided into two groups on the basis of their adhesion phenotype and ITGB5 genotypes, a candidate gene for F4ac receptor. Non-adhesive group (n = 4) with CC genotype and adhesive group (n = 4) with TT genotype. RESULTS: In total, 78 differentially expressed lncRNAs (DE-lncRNA) and 223 differentially expressed mRNAs (log2 |FC| > 1, P < 0.05) were identified in the comparison of non-adhesive vs. adhesive small intestine epithelial cells. Furthermore, cis- and trans-regulatory target genes of DE-lncRNAs were identified, then interaction networks of lncRNAs and their cis- and trans-target differentially expressed genes (DEGs) were constructed separately. A total of 194 cis-targets were involved in the lncRNAs-cis genes interaction network and 61 trans-targets, were involved in lncRNA-trans gene interaction network that we constructed. We determined that cis-target genes were involved in alcoholism, systemic lupus erythematosus, viral carcinogenesis and malaria. Whereas trans-target DEGs were engaged in three important pathways related to the ETEC-F4 adhesion phenotype namely cGMP-PKG signaling pathway, focal adhesion, and adherens junction. The trans-target DEGs which directly involved in these pathways are KCNMB1 in cGMP-PKG signaling pathway, GRB2 in focal adhesion pathway and ACTN4 in focal adhesion and adherens junction pathways. CONCLUSION: The findings of the current study provides an insight into biological functions and epigenetic regulatory mechanism of lncRNAs on porcine small intestine epithelial cells adhesion to ETEC-F4-ac and piglets' diarrhea susceptibility/resistance.

Estimation of inbreeding and identification of regions under heavy selection based on runs of homozygosity in a Large White pig population.

BACKGROUND: Runs of homozygosity (ROHs) are homozygous segments of the genome where the two haplotypes inherited from the parents are identical. The current availability of genotypes for a very large number of single nucleotide polymorphisms (SNPs) is leading to more accurate characterization of ROHs in the whole genome. Here, we investigated the occurrence and distribution of ROHs in 3,692 Large White pigs and compared estimates of inbreeding coefficients calculated based on ROHs (F ROH), homozygosity (F HOM), genomic relationship matrix (F GRM) and pedigree (F PED). Furthermore, we identified genomic regions with high ROH frequencies and annotated their candidate genes. RESULTS: In total, 176,182 ROHs were identified from 3,569 animals, and all individuals displayed at least one ROH longer than 1 Mb. The ROHs identified were unevenly distributed on the autosomes. The highest and lowest coverages of Sus scrofa chromosomes (SSC) by ROH were on SSC14 and SSC13, respectively. The highest pairwise correlation among the different inbreeding coefficient estimates was 0.95 between F ROH_total and F HOM, while the lowest was - 0.083 between F GRM and F PED. The correlations between F PED and F ROH using four classes of ROH lengths ranged from 0.18 to 0.37 and increased with increasing ROH length, except for ROH > 10 Mb. Twelve ROH islands were located on four chromosomes (SSC1, 4, 6 and 14). These ROH islands harboured genes associated with reproduction, muscular development, fat deposition and adaptation, such as SIRT1, MYPN, SETDB1 and PSMD4. CONCLUSION: F ROH can be used to accurately assess individual inbreeding levels compared to other inbreeding coefficient estimators. In the absence of pedigree records, F ROH can provide an alternative to inbreeding estimates. Our findings can be used not only to effectively increase the response to selection by appropriately managing the rate of inbreeding and minimizing the negative effects of inbreeding depression but also to help detect genomic regions with an effect on traits under selection.

Genomic Scan for Selection Signature Reveals Fat Deposition in Chinese Indigenous Sheep with Extreme Tail Types.

It is a unique feature that fat can be deposited in sheep tails and rumps. To elucidate the genetic mechanism underlying this trait, we collected 120 individuals from three Chinese indigenous sheep breeds with extreme tail types, namely large fat-tailed sheep (n = 40), Altay sheep (n = 40), and Tibetan sheep (n = 40), and genotyped them using the Ovine Infinium HD SNP BeadChip. Then genomic scan for selection signatures was performed using the hapFLK. In total, we identified 25 genomic regions exhibiting evidence of having been under selection. Bioinformatic analysis of the genomic regions showed that selection signatures related to multiple candidate genes had a demonstrated role in phenotypic variation. Nine genes have documented association with sheep tail types, including WDR92, TBX12, WARS2, BMP2, VEGFA, PDGFD, HOXA10, ALX4, and ETAA1. Moreover, a number of genes were of particular interest, including RXFP2 associated with the presence/absence and morphology of horns; MITF involved in coat color; LIN52 and SYNDIG1L related to the number of teats; MSRB3 gene associated with ear sizes; LTBP2 considered as a positional candidate genes for number of ribs; JAZF1 regulating lipid metabolism; PGRMC2, SPAG17, TSHR, GTF2A1, and LARP1B implicated with reproductive traits. Our findings provide insights into fat tail formation and a reference for carrying out molecular breeding and conservation in sheep.