Comparative Study of Single-Trait and Multi-Trait Genomic Prediction Models.

Conventional genomic selection models trait individually, neglecting complex trait interactions. Multi-trait models address this by considering genetic correlations, thus improving breeding value accuracy. Despite their theoretical benefits, quantifying these models' breeding advantages across genetic backgrounds is essential.

mRNA expression profiles in muscle-derived extracellular vesicles of Large White and wild boar piglets reveal their potential roles in immunity and muscle phenotype.

Introduction: Extracellular vesicles (EVs) known for their pivotal role in intercellular communication through RNA delivery, hold paramount implications for understanding muscle phenotypic variations in diverse pig breeds.

Methods: In this study, we compared the mRNA expression profiles of muscles and muscle-derived extracellular vesicles (M-EVs), and also examined the diversity of enriched genes in M-EVs between weaned wild boars and commercial Large White pigs with respect to their numbers and biological functions.

Results: The results of the study showed that the variation in the expression profiles of mRNAs between muscles and M-EVs was much greater than the variability between the respective breeds.

The utilization of N-acetylgalactosamine and its effect on the metabolism of amino acids in Erysipelotrichaceae strain.

Background: The metabolism of gut microbiota produces bioactive metabolites that modulate host physiology and promote self-growth. Erysipelotrichaceae is one of the most common anaerobic microorganism families in the gut, which has been discovered to play a vital role in host metabolic disorders and inflammatory diseases. Our previous study found that N-acetylgalactosamine (GalNAc) in caecal content of pigs significantly affected the abundance of Erysipelotrichaceae strains.

Whole-genome sequences restore the original classification of dabbling ducks (genus Anas).

Anas, is a genus of dabbling ducks and encompasses a considerable number of species, among which some are the progenitors of domestic ducks. However, the taxonomic position of the Anas genus remains uncertain because several of its species, initially categorized as Anas based on morphological characteristics, were subsequently reclassified and grouped with the South American genus Tachyeres, primarily based on analysis of their mitochondrial gene sequences. Here, we constructed a phylogenetic tree using nine of our recently assembled Anas genomes, two Tachyeres genomes, and one Cairina genome that are publicly available.

Exploration of Genome-Wide Recombination Rate Variation Patterns at Different Scales in Pigs.

Meiotic recombination is a prevalent process in eukaryotic sexual reproduction organisms that plays key roles in genetic diversity, breed selection, and species evolution. However, the recombination events differ across breeds and even within breeds. In this study, we initially computed large-scale population recombination rates of both sexes using approximately 52 K SNP genotypes in a total of 3279 pigs from four different Chinese and Western breeds.

Omics-based construction of regulatory variants can be applied to help decipher pig liver-related traits.

Genetic variants can influence complex traits by altering gene expression through changes to regulatory elements. However, the genetic variants that affect the activity of regulatory elements in pigs are largely unknown, and the extent to which these variants influence gene expression and contribute to the understanding of complex phenotypes remains unclear. Here, we annotate 90,991 high-quality regulatory elements using acetylation of histone H3 on lysine 27 (H3K27ac) ChIP-seq of 292 pig livers.

IgA nephropathy: gut microbiome regulates the production of hypoglycosilated IgA1 via the TLR4 signaling pathway.

Background: Immunoglobulin A nephropathy (IgAN) is a major cause of primary glomerulonephritis characterized by mesangial deposits of galactose-deficient IgA1 (Gd-IgA1). Toll-like receptors (TLRs), particularly TLR4, are involved in the pathogenesis of IgAN. The role of gut microbiota on IgAN patients was recently investigated.

Phenotypic correlations of carpal gland diverticular number with production traits and its genome-wide association analysis in multiple pig populations.

Pig carpal glands play crucial roles in territorial recognition, reproductive behavior, and information exchange; however, their effects on production traits and underlying genetic mechanisms remain unclear. In this study, 1028 pigs from six populations were counted for the carpal gland diverticular numbers (CGDNs) on the left (CGDN) and right (CGDN) legs, and their carcass and meat quality traits were assessed. The CGDNs were significantly different among the populations, and Licha Black pigs had a lower CGDN than the Bama Xiang breed.

Single-cell profiling of the pig cecum at various developmental stages.

The gastrointestinal tract is essential for food digestion, nutrient absorption, waste elimination, and microbial defense. Single-cell transcriptome profiling of the intestinal tract has greatly enriched our understanding of cellular diversity, functional heterogeneity, and their importance in intestinal tract development and disease. Although such profiling has been extensively conducted in humans and mice, the single-cell gene expression landscape of the pig cecum remains unexplored.

[Activation of intestinal mucosal TLR4/NF-κB pathway is associated with renal damage in mice with pseudo-sterile IgA nephropathy].

Objective To investigate the effect of intestinal mucosal Toll-like receptor 4/nuclear factor κB (TLR4/NF-κB) signaling pathway on renal damage in pseudo-sterile IgA nephropathy (IgAN) mice. Methods C57BL/6 mice were randomly divided into experimental group (pseudosterile mouse model group), control group (IgAN mouse model group), pseudosterile mouse blank group, and normal mouse blank group. Pseudosterile mice were established by intragastric administration of quadruple antibiotics once a day for 14 days.

Dominance is common in mammals and is associated with trans-acting gene expression and alternative splicing.

Background: Dominance and other non-additive genetic effects arise from the interaction between alleles, and historically these phenomena play a major role in quantitative genetics. However, most genome-wide association studies (GWAS) assume alleles act additively.

Results: We systematically investigate both dominance-here representing any non-additive within-locus interaction-and additivity across 574 physiological and gene expression traits in three mammalian stocks: F2 intercross pigs, rat heterogeneous stock, and mice heterogeneous stock.

Characterization of the pig lower respiratory tract antibiotic resistome.

Respiratory diseases and its treatments are highly concerned in both the pig industry and human health. However, the composition and distribution of antibiotic resistance genes (ARGs) in swine lower respiratory tract microbiome remain unknown. The relationships of ARGs with mobile genetic elements (MGEs) and lung health are unclear.

Employing pigs to decipher the host genetic effect on gut microbiome: advantages, challenges, and perspectives.

The gut microbiota is a complex and diverse ecosystem comprised of trillions of microbes and plays an essential role in host's immunity, metabolism, and even behaviors. Environmental and host factors drive the huge variations in the gut microbiome among individuals. Here, we summarize accumulated evidences about host genetic effect on the gut microbial compositions with emphases on the correlation between host genetic kinship and the similarity of microbial compositions, heritability estimates of microbial taxa, and identification of genomic variants associated with the gut microbiome in pigs as well as in humans.

Genetic architecture for skeletal muscle glycolytic potential in Chinese Erhualian pigs revealed by a genome-wide association study using 1.4M SNP array.

Muscle glycolytic potential (GP) is a key factor affecting multiple meat quality traits. It is calculated based on the contents of residual glycogen and glucose (RG), glucose-6-phosphate (G6P), and lactate (LAT) contents in muscle. However, the genetic mechanism of glycolytic metabolism in skeletal muscle of pigs remains poorly understood.