Multi-dimensional annotation of porcine variants using genomic and epigenomic features in pigs.

Background: Investigating the functional impact of genomic variants is essential to uncover the molecular mechanisms behind complex traits. This study compiled a comprehensive dataset of 1,817 whole-genome sequences from diverse pig breeds and populations, capturing the global pig genetic diversity.

Results: Our analyses first revealed 27,167 loss-of-function variants (LoFs), the majority of which also influenced gene expression and splicing, and enriched in genomic regions associated with complex traits in pigs.

Integrating large-scale meta-GWAS and PigGTEx resources to decipher the genetic basis of 232 complex traits in pigs.

Understanding the molecular and cellular mechanisms underlying complex traits in pigs is crucial for enhancing genetic gain via artificial selection and utilizing pigs as models for human disease and biology. Here, we conducted comprehensive genome-wide association studies (GWAS) followed by a cross-breed meta-analysis for 232 complex traits and a within-breed meta-analysis for 12 traits, using 28.3 million imputed sequence variants in 70 328 animals across 14 pig breeds.

Genetic regulation of gene expression across multiple tissues in chickens.

The chicken is a valuable model for understanding fundamental biology and vertebrate evolution and is a major global source of nutrient-dense and lean protein. Despite being the first non-mammalian amniote to have its genome sequenced, a systematic characterization of functional variation on the chicken genome remains lacking. Here, we integrated bulk RNA sequencing (RNA-seq) data from 7,015 samples, single-cell RNA-seq data from 127,598 cells and 2,869 whole-genome sequences to present a pilot atlas of regulatory variants across 28 chicken tissues.

Identified Candidate Genes of Semen Trait in Three Pig Breeds Through Weighted GWAS and Multi-Tissue Transcriptome Analysis.

High-quality semen is an essential factor for the success of artificial insemination, and revealing the genetic structure of pig semen traits helps improve semen quality. This study aimed to identify candidate genes associated with semen traits in three pig breeds (Duroc, Landrace, and Yorkshire) through weighted GWAS and multi-tissue transcriptome analysis. In this study, to identify candidate genes associated with semen traits in Duroc, Landrace, and Yorkshire, we performed weighted GWAS in four traits (sperm motility, sperm progressive motility, sperm abnormality rate, and total sperm count) using 936 pigs and multi-tissue transcriptome analysis using 34 tissues RNA-seq data of 5457 pigs from FarmGTEx.

Identification, Pathogenicity, and Fungicide Sensitivity of Species Associated with Anthracnose on Italian Ryegrass in Southwestern China.

Italian ryegrass ( L.) is widely cultivated as an important forage grass worldwide because of its high nutritional value and good palatability. Anthracnose caused by species was a common and new emerging disease of Italian ryegrass.

Mapping and functional characterization of structural variation in 1060 pig genomes.

Background: Structural variations (SVs) have significant impacts on complex phenotypes by rearranging large amounts of DNA sequence.

Results: We present a comprehensive SV catalog based on the whole-genome sequence of 1060 pigs (Sus scrofa) representing 101 breeds, covering 9.6% of the pig genome.

Evaluating three strategies of genome-wide association analysis for integrating data from multiple populations.

In livestock, genome-wide association studies (GWAS) are usually conducted in a single population (single-GWAS) with limited sample size and detection power. To enhance the detection power of GWAS, meta-analysis of GWAS (meta-GWAS) and mega-analysis of GWAS (mega-GWAS) have been proposed to integrate data from multiple populations at the level of summary statistics or individual data, respectively. However, there is a lack of comparison for these different strategies, which makes it difficult to guide the best practice of GWAS integrating data from multiple study populations.

Exploring the mechanism of artificial selection signature in Chinese indigenous pigs by leveraging multiple bioinformatics database tools.

Background: Chinese indigenous pigs in Yunnan exhibit considerable phenotypic diversity, but their population structure and the biological interpretation of signatures of artificial selection require further investigation. To uncover population genetic diversity, migration events, and artificial selection signatures in Chinese domestic pigs, we sampled 111 Yunnan pigs from four breeds in Yunnan which is considered to be one of the centres of livestock domestication in China, and genotyped them using Illumina Porcine SNP60K BeadChip. We then leveraged multiple bioinformatics database tools to further investigate the signatures and associated complex traits.

PigBiobank: a valuable resource for understanding genetic and biological mechanisms of diverse complex traits in pigs.

To fully unlock the potential of pigs as both agricultural species for animal-based protein food and biomedical models for human biology and disease, a comprehensive understanding of molecular and cellular mechanisms underlying various complex phenotypes in pigs and how the findings can be translated to other species, especially humans, are urgently needed. Here, within the Farm animal Genotype-Tissue Expression (FarmGTEx) project, we build the PigBiobank (http://pigbiobank.farmgtex.

High Diversity of Species Associated with Leaf Spot on Italian Ryegrass in Southwestern China: Six New Records and Three New Species.

Italian ryegrass is widely cultivated for the production of forage, hay, and silage because of its high nutritional value and good palatability. Leaf spots caused by fungi pose a serious threat to forage crops. In order to expand the knowledge of fungi causing leaf spots in ryegrass () in Sichuan, Yunnan, Chongqing, and Guizhou of southwestern China, a comprehensive survey was undertaken from 2015 to 2022.

Evaluation of Performance Tradeoffs When Using Mechanically Swept 1-D Linear Arrays for 3-D DCE-US.

Dynamic contrast-enhanced ultrasound imaging (DCE-US) may be used to characterize tumor vascular perfusion using metrics derived from time-amplitude curves (TACs). The 3-D DCE-US enables generation of 3-D parametric maps of TAC metrics that may inform on how perfusion varies across the entire tumor. The aim of this work was to understand the effect of low temporal sampling (i.

Evaluation of six machine learning classification algorithms in pig breed identification using SNPs array data.

Breed identification utilizing multiple information sources and methods is widely applicated in the field of animal genetics and breeding. Simultaneously, with the development of artificial intelligence, the integration of high-throughput genomic data and machine learning techniques is increasingly used for breed identification. In this context, we used 654 individuals from 15 pig breeds, evaluating the performance of machine learning and stacking ensemble learning classifiers, as well as the function of feature selection and anomaly detection in different scenarios.

Meta-analysis of genome-wide association studies uncovers shared candidate genes across breeds for pig fatness trait.

Background: Average backfat thickness (BFT) is a critical complex trait in pig and an important indicator for fat deposition and lean rate. Usually, genome-wide association study (GWAS) was used to discover quantitative trait loci (QTLs) of BFT in a single population. However, the power of GWAS is limited by sample size in a single population.

Insights into the architecture of human-induced polygenic selection in Duroc pigs.

Background: As one of the most utilized commercial composite boar lines, Duroc pigs have been introduced to China and undergone strongly human-induced selection over the past decades. However, the efficiencies and limitations of previous breeding of Chinese Duroc pigs are largely understudied. The objective of this study was to uncover directional polygenic selection in the Duroc pig genome, and investigate points overlooked in the past breeding process.

Differences in the Characteristics and Pathogenicity of Species Associated with Seeds of Italian Ryegrass.

is a genus of pathogens that cause leaf damage and a common seedborne fungus of Italian ryegrass ( Lam.). To elucidate the main seedborne species, 36 seed samples of Italian ryegrass were collected; in total, 113 strains, representing 12.

A Nude Mouse Model of Orthotopic Liver Transplantation of Human Hepatocellular Carcinoma HCCLM3 Cell Xenografts and the Use of Imaging to Evaluate Tumor Progression.

BACKGROUND This study aimed to develop a nude mouse model of orthotopic liver transplantation of HCCLM3 human hepatocellular carcinoma (HCC) cell xenografts and the use of imaging and histology to evaluate tumor development and progression. MATERIAL AND METHODS HCCLM3 cells were injected subcutaneously into 25 healthy male athymic BALB/c (nu/nu) nude mice. The tumors that developed were transplanted into the liver of a new set of nude mice.

Effect of dry heat treatment with xanthan on waxy rice starch.

Waxy rice starch was impregnated with xanthan and heat-treated in a dry state. The effects on the pasting and rheological properties of the treated starch-xanthan mixture were evaluated. Swelling of the granule was restricted, and a continuous rise of the viscosity during pasting was provided for the treated sample.

Effect of polysaccharides on the gelatinization properties of cornstarch dispersions.

Konjac glucomannan (KG, neutral), carboxymethylcellulose (CMC, negatively charged), and chitosan (positively charged) were added to cornstarch dispersions to study the effect of polysaccharide-starch interactions on starch gelatinization properties. Pasting and retrogradation properties were measured with a rheometer and DSC. Swelling properties of the starch granules were determined by solubility index, swelling power, and particle size distribution.