Revealing genes related teat number traits via genetic variation in Yorkshire pigs based on whole-genome sequencing.

Background: Teat number is one of the most important indicators to evaluate the lactation performance of sows, and increasing the teat number has become an important method to improve the economic efficiency of farms. Therefore, it is particularly important to deeply analyze the genetic mechanism of teat number traits in pigs. In this study, we detected Single Nucleotide Ploymorphism (SNP), Insertion-Deletion (InDel) and Structural variant (SV) by high-coverage whole-genome resequencing data, and selected teat number at birth and functional teat number as two types of teat number traits for genome-wide association study (GWAS) to reveal candidate genes associated with pig teat number traits.

Phosphate-Induced Acidic Microenvironment for Improved Contaminant Removal during FeS Oxygenation.

The coexistence of mackinawite (FeS) and phosphate is widely observed in natural systems. However, the underlying mechanism regarding how phosphate influences the environmental behavior of FeS, especially during the FeS oxygenation in aquatic systems, remains in its fancy. This study for the first time reported that the presence of phosphate, even at a low concentration of 0.

Heterosis formation mechanism, prediction methods, and their application and prospect in pig production.

Heterosis is the phenomenon that the hybrid offspring outperform two-parent population. Hybridisation has been widely used in plant and animal production as it effectively improves the growth and developmental performance, reproductive performance and disease resistance of the offspring. Hybridization can effectively improve the growth and development performance, reproductive performance and disease resistance of offspring, so it is widely used in animal and plant production.

Multi-omic characterization of allele-specific regulatory variation in hybrid pigs.

Hybrid mapping is a powerful approach to efficiently identify and characterize genes regulated through mechanisms in cis. In this study, using reciprocal crosses of the phenotypically divergent Duroc and Lulai pig breeds, we perform a comprehensive multi-omic characterization of regulatory variation across the brain, liver, muscle, and placenta through four developmental stages. We produce one of the largest multi-omic datasets in pigs to date, including 16 whole genome sequenced individuals, as well as 48 whole genome bisulfite sequencing, 168 ATAC-Seq and 168 RNA-Seq samples.

Discriminating the Active Ru Species Towards the Selective Generation of Singlet Oxygen from Peroxymonosulfate: Nanoparticles Surpass Single-Atom Catalysts.

Singlet oxygen (O) is an exceptional reactive oxygen species in advanced oxidation processes for environmental remediation. Despite single-atom catalysts (SACs) representing the promising candidate for the selective generation of O from peroxymonosulfate (PMS), the necessity to meticulously regulate the coordination environment of metal centers poses a significant challenge in the precisely-controlled synthetic method. Another dilemma to SACs is their high surface free energy, which results in an inherent tendency for the surface migration and aggregation of metal atoms.

Identification of Candidate Genes for Economically Important Carcass Cutting in Commercial Pigs through GWAS.

During the process of pork production, the carcasses of pigs are divided and sold, which provides better economic benefits and market competitiveness for pork production than selling the carcass as a whole. Due to the significant cost of post-slaughter phenotypic measurement, the genetic architecture of tenderloin weight (TLNW) and rib weight (RIBW)-important components of pig carcass economic value-remain unknown. In this study, we conducted genome-wide association studies (GWAS) for TLNW and RIBW traits in a population of 431 Duroc × Landrace × Yorkshire (DLY) pigs.

Ferrous ion enhanced Fenton-like degradation of emerging contaminants by sulfidated nanosized zero-valent iron with pH insensitivity.

In this study, the performance and mechanism of the integrated sulfidated nanosized zero-valent iron and ferrous ions (S-nZVI/Fe) system for oxygen activation to remove emerging contaminants (ECs) were comprehensively explored. The S-nZVI/Fe system exhibited a 2.4-8.

A pan-cancer analysis identifies SOAT1 as an immunological and prognostic biomarker.

Sterol o-acyltransferase1 (SOAT1) is an enzyme that regulates lipid metabolism. Nevertheless, the predictive value of SOAT1 regarding immune responses in cancer is not fully understood. Herein, we aimed to expound the predictive value and the potential biological functions of SOAT1 in pan-cancer.

The SWine IMputation (SWIM) haplotype reference panel enables nucleotide resolution genetic mapping in pigs.

Genetic mapping to identify genes and alleles associated with or causing economically important quantitative trait variation in livestock animals such as pigs is a major goal in animal genetic improvement. Despite recent advances in high-throughput genotyping technologies, the resolution of genetic mapping in pigs remains poor due in part to the low density of genotyped variant sites. In this study, we overcame this limitation by developing a reference haplotype panel for pigs based on 2259 whole genome-sequenced animals representing 44 pig breeds.

Improving the accuracy of genomic prediction for meat quality traits using whole genome sequence data in pigs.

Background: Pork quality can directly affect customer purchase tendency and meat quality traits have become valuable in modern pork production. However, genetic improvement has been slow due to high phenotyping costs. In this study, whole genome sequence (WGS) data was used to evaluate the prediction accuracy of genomic best linear unbiased prediction (GBLUP) for meat quality in large-scale crossbred commercial pigs.

Identification of candidate genes associated with carcass component weights in commercial crossbred pigs through a combined GWAS approach.

In the pork industry chain, carcass cutting is crucial for enhancing the commercial value of pork carcasses. However, the genetic mechanisms underlying carcass component weights remain poorly understood. Here, we used a combined genome-wide association study (GWAS) approach that integrated single- and multi-locus models to map genetic markers and genes associated with the weights of seven carcass components in Duroc × Landrace × Yorkshire (DLY) pigs.

Tuning FeO for sustainable cathodic heterogeneous electro-Fenton catalysis by acetylated chitosan.

Peroxidase-like catalysts are safe and low-cost candidates to tackle the dilemma in constructing sustainable cathodic heterogeneous electro-Fenton (CHEF) catalysts for water purification, but the elusive structure-property relationship of enzyme-like catalysts constitutes a pressing challenge for the advancement of CHEF processes in practically relevant water and wastewater treatment. Herein, we probe the origins of catalytic efficiency in the CHEF process by artificially tailoring the peroxidase-like activity of FeO through a series of acetylated chitosan-based hydrogels, which serve as ecofriendly alternatives to traditional carbon shells. The optimized acetylated chitosan wrapping FeO hydrogel on the cathode shows an impressive activity and stability in CHEF process, overcoming the complicated and environmentally unfavored procedures in the electro-Fenton-related processes.

Asymmetrically Coordinated CoB N Moieties for Selective Generation of High-Valence Co-Oxo Species via Coupled Electron-Proton Transfer in Fenton-like Reactions.

High-valence metal species generated in peroxymonosulfate (PMS)-based Fenton-like processes are promising candidates for selective degradation of contaminants in water, the formation of which necessitates the cleavage of OH and OO bonds as well as efficient electron transfer. However, the high dissociation energy of OH bond makes its cleavage quite challenging, largely hampering the selective generation of reactive oxygen species. Herein, an asymmetrical configuration characterized by a single cobalt atom coordinated with boron and nitrogen (CoB N ) is established to offer a strong local electric field, upon which the cleavage of OH bond is thermodynamically favored via a promoted coupled electron-proton transfer process, which serves an essential step to further allow OO bond cleavage and efficient electron transfer.

The Genetic Architecture of Meat Quality Traits in a Crossbred Commercial Pig Population.

Meat quality is of importance in consumer acceptance and purchasing tendency of pork. However, the genetic architecture of pork meat quality traits remains elusive. Herein, we conducted genome-wide association studies to detect single nucleotide polymorphisms (SNPs) and genes affecting meat pH and meat color (, lightness; , redness; , yellowness) in 1518 three-way crossbred pigs.

A composite strategy of genome-wide association study and copy number variation analysis for carcass traits in a Duroc pig population.

Background: Carcass traits are important in pig breeding programs for improving pork production. Understanding the genetic variants underlies complex phenotypes can help explain trait variation in pigs. In this study, we integrated a weighted single-step genome-wide association study (wssGWAS) and copy number variation (CNV) analyses to map genetic variations and genes associated with loin muscle area (LMA), loin muscle depth (LMD) and lean meat percentage (LMP) in Duroc pigs.

Capabilities of hepatitis B surface antigen are divergent from hepatitis B virus DNA in delimiting natural history phases of chronic hepatitis B virus infection.

Objective: Quantitative hepatitis B surface antigen (HBsAg) and hepatitis B virus (HBV) DNA in the natural history of chronic HBV infection have not been rationally evaluated. This study aimed to re-characterize quantitative HBsAg and HBV DNA in the natural history phases.

Methods: A total of 595 and 651 hepatitis B e antigen (HBeAg)-positive patients and 485 and 705 HBeAg-negative patients were assigned to the early and late cohorts, respectively.

Identification of Homozygous Regions With Adverse Effects on the Five Economic Traits of Duroc Pigs.

Runs of homozygosity (ROH) are widely used to estimate genomic inbreeding, which is linked to inbreeding depression on phenotypes. However, the adverse effects of specific homozygous regions on phenotypic characteristics are rarely studied in livestock. In this study, the 50 K SNP data of 3,770 S21 Duroc (American origin) and 2,096 S22 Duroc (Canadian origin) pigs were used to investigate the harmful ROH regions on five economic traits.

Runs of Homozygosity Uncover Potential Functional-Altering Mutation Associated With Body Weight and Length in Two Duroc Pig Lines.

Runs of homozygosity (ROH) are widely used to investigate genetic diversity, demographic history, and positive selection signatures of livestock. Commercial breeds provide excellent materials to reveal the landscape of ROH shaped during the intense selection process. Here, we used the GeneSeek Porcine 50K single-nucleotide polymorphism (SNP) Chip data of 3,770 American Duroc (AD) and 2,096 Canadian Duroc (CD) pigs to analyze the genome-wide ROH.

Genome-Wide Association Analysis Reveals Genetic Loci and Candidate Genes for Chest, Abdominal, and Waist Circumferences in Two Duroc Pig Populations.

Chest circumference (CC), abdominal circumference (AC), and waist circumference (WC) are regarded as important indicators for improving economic traits because they can reflect the growth and physiological status in pigs. However, the genetic architecture of CC, AC, and WC is still elusive. Here, we performed single-trait and multi-trait genome-wide association studies (GWASs) for CC, AC, and WC in 2,206 American origin Duroc (AOD) and 2,082 Canadian origin Duroc (COD) pigs.

Assessment of Heterozygosity and Genome-Wide Analysis of Heterozygosity Regions in Two Duroc Pig Populations.

Heterozygosity can effectively reflect the diverse models of population structure and demographic history. However, the genomic distribution of heterozygotes and the correlation between regions of heterozygosity (runs of heterozygosity, ROHet) and phenotypes are largely understudied in livestock. The objective of this study was to identify ROHet in the Duroc pig genome, and investigate the relationships between ROHet and eight important economic traits.

Identify known and novel candidate genes associated with backfat thickness in Duroc pigs by large-scale genome-wide association analysis.

Backfat thickness (BFT) is complex and economically important traits in the pig industry, since it reflects fat deposition and can be used to measure the carcass lean meat percentage in pigs. In this study, all 6,550 pigs were genotyped using the Geneseek Porcine 50K SNP Chip to identify SNPs related to BFT and to search for candidate genes through genome-wide association analysis in two Duroc populations. In total, 80 SNPs, including 39 significant and 41 suggestive SNPs, and 6 QTLs were identified significantly associated with the BFT.

Genome-Wide Detection of Genetic Loci and Candidate Genes for Body Conformation Traits in Duroc × Landrace × Yorkshire Crossbred Pigs.

The Duroc × (Landrace × Yorkshire) hybrid pigs (DLY) are the most popular commercial pigs, providing consumers with the largest source of pork. In order to gain more insights into the genetic architecture of economically important traits in pigs, we performed a genome-wide association study (GWAS) using the GeneSeek Porcine 50 K SNP Chip to map the genetic markers and genes associated with body conformation traits (BCT) in 311 DLY pigs. The quantitative traits analyzed included body weight (BW), carcass length (CL), body length (BL), body height (BH), and body mass index (BMI).

A Novel Non-invasive Model Based on GPR for the Prediction of Liver Fibrosis in Patients With Chronic Hepatitis B.

Some controversy remains regarding conventional serum indices for the evaluation of liver fibrosis. Therefore, we aimed to combine the existing index with other serum parameters to discriminate liver fibrosis stages in patients with chronic hepatitis B (CHB). A total of 1,622 treatment-naïve CHB patients were divided into training ( = 1,211) and validation ( = 451) cohorts.

and in gut microbiota lessened in chronic liver diseases and hepatocellular carcinoma patients: a pilot study.

The gut microbiota system plays a vital role in liver diseases. This study aimed to address the diversity of gut microbiota and its correlations with clinical parameters in healthy individuals, chronic liver disease (CLD), and hepatocellular carcinoma (HCC) patients. Fecal specimens of nine healthy individuals, 11 CLD, and 21 HCC were collected.

Genomic Analyses Revealed the Genetic Difference and Potential Selection Genes of Growth Traits in Two Duroc Lines.

Duroc pigs are famous for their high growth rate, feed conversion efficiency, and lean meat percentage. Given that they have been subjected to artificial selection and breeding in multiple countries, various lines with obvious differences in production performance have formed. In this study, we genotyped 3,770 American Duroc (AD) pigs and 2,098 Canadian Duroc (CD) pigs using the GeneSeek Porcine SNP50 Beadchip to dissect the genetic differences and potential selection genes of growth traits in these two Duroc pig lines.