Genome-wide identification of quantitative trait loci and candidate genes for seven carcass traits in a four-way intercross porcine population.

Background: Carcass traits are essential economic traits in the commercial pig industry. However, the genetic mechanism of carcass traits is still unclear. In this study, we performed a genome-wide association study (GWAS) based on the specific-locus amplified fragment sequencing (SLAF-seq) to study seven carcass traits on 223 four-way intercross pigs, including dressing percentage (DP), number of ribs (RIB), skin thinkness (ST), carcass straight length (CSL), carcass diagonal length (CDL), loin eye width (LEW), and loin eye thickness (LET).

Identification of potential obese-specific biomarkers and pathways associated with abdominal subcutaneous fat deposition in pig using a comprehensive bioinformatics strategy.

Abdominal subcutaneous fat deposition (ASFD) is not only related to meat quality in the pig industry but also to human health in medicine. It is of great value to elucidate the potential molecular mechanisms of ASFD. The present study aims to identify obese-specific biomarkers and key pathways correlated with ASFD in pigs.

Identification of potential tissue-specific biomarkers involved in pig fat deposition through integrated bioinformatics analysis and machine learning.

Backfat thickness (BT) and intramuscular fat (IMF) content are closely appertained to meat production and quality in pig production. Deposition in subcutaneous adipose (SA) and IMF concerns different genes and regulatory mechanisms. And larger studies with rigorous design should be carried to explore the molecular regulation of fat deposition in different tissues.

Genome-wide single nucleotide polymorphism (SNP) data reveal potential candidate genes for litter traits in a Yorkshire pig population.

The litter trait is one of the most important economic traits, and increasing litter size is of great economic value in the pig industry. However, the molecular mechanisms underlying pig litter traits remain elusive. To identify molecular markers and candidate genes for pig litter traits, a genome-wide association study (GWAS) and selection signature analysis were conducted in a Yorkshire pig population.

Identification of Potential Sex-Specific Biomarkers in Pigs with Low and High Intramuscular Fat Content Using Integrated Bioinformatics and Machine Learning.

Intramuscular fat (IMF) content is a key determinant of pork quality. Controlling the genetic and physiological factors of IMF and the expression patterns of various genes is important for regulating the IMF content and improving meat quality in pig breeding. Growing evidence has suggested the role of genetic factors and breeds in IMF deposition; however, research on the sex factors of IMF deposition is still lacking.

Genome-wide association study reveals genetic loci and candidate genes for meat quality traits in a four-way crossbred pig population.

Meat quality traits (MQTs) have gained more attention from breeders due to their increasing economic value in the commercial pig industry. In this genome-wide association study (GWAS), 223 four-way intercross pigs were genotyped using the specific-locus amplified fragment sequencing (SLAF-seq) and phenotyped for PH at 45 min (PH45), meat color score (MC), marbling score (MA), water loss rate (WL), drip loss (DL) in the longissimus muscle, and cooking loss (CL) in the psoas major muscle. A total of 227, 921 filtered single nucleotide polymorphisms (SNPs) evenly distributed across the entire genome were detected to perform GWAS.

Signatures of selection in indigenous Chinese cattle genomes reveal adaptive genes and genetic variations to cold climate.

Cold climate shapes the genome of animals and drives them to carry sufficient genetic variations to adapt to changes in temperature. However, limited information is available about the genome-wide pattern of adaptations to cold environments in cattle. In the present study, we used 777K SNP genotyping (15 Chinese cattle breeds, 198 individuals) and whole genome resequencing data (54 cattle breeds of the world, 432 individuals) to disentangle divergent selection signatures, especially between the cold-adapted (annual average temperature of habitat, 6.

Genome-Wide Association Study of Growth Traits in a Four-Way Crossbred Pig Population.

Growth traits are crucial economic traits in the commercial pig industry and have a substantial impact on pig production. However, the genetic mechanism of growth traits is not very clear. In this study, we performed a genome-wide association study (GWAS) based on the specific-locus amplified fragment sequencing (SLAF-seq) to analyze ten growth traits on 223 four-way intercross pigs.

Genome-wide association study identifying genetic variants associated with carcass backfat thickness, lean percentage and fat percentage in a four-way crossbred pig population using SLAF-seq technology.

Background: Carcass backfat thickness (BFT), carcass lean percentage (CLP) and carcass fat percentage (CFP) are important to the commercial pig industry. Nevertheless, the genetic architecture of BFT, CLP and CFP is still elusive. Here, we performed a genome-wide association study (GWAS) based on specific-locus amplified fragment sequencing (SLAF-seq) to analyze seven fatness-related traits, including five BFTs, CLP, and CFP on 223 four-way crossbred pigs.

Identification of key sex-specific pathways and genes in the subcutaneous adipose tissue from pigs using WGCNA method.

Background: Adipose tissues (ATs), including visceral ATs (VATs) and subcutaneous ATs (SATs), are crucial for maintaining energy and metabolic homeostasis. SATs have been found to be closely related to obesity and obesity-induced metabolic disease. Some studies have shown a significant association between subcutaneous fat metabolism and sexes.

The complete mitochondrial genome of (Cyprinoidea: Cyprinidae).

We describe the complete mitochondrial genome of the endangered fish . It is a circular molecule of 16,583 bp in size with a D-loop region and contains 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes and 13 protein-coding genes, and all genes show the typical gene arrangement conforming to the vertebrate consensus. The overall base composition of .

Genetic Diversity and Selection Signatures Within Diannan Small-Ear Pigs Revealed by Next-Generation Sequencing.

Genetic characterization of Chinese indigenous pig breeds is essential to promote scientific conservation and sustainable development of pigs. Here, we systematically surveyed the genomes of 75 unrelated Diannan small-ear (DSE) pigs from three diverse regions (Yingjiang County, Jinping County, and Sipsongpanna in Yunnan Province) to describe their population structures, genetic diversity, inbreeding coefficients, and selection signatures. First, these individuals were sequenced and genotyped using the genome reducing and sequencing (GGRS) protocol.

The complete mitochondrial genome of (Teleostei, Siluriformes).

is a key-listed protected indigenous fish species in Nujiang, Yunnan, China. In this study, we firstly reported the complete mitochondrial genome of , which was 16,584 bp in length, containing 13 protein-coding genes, 22 transfer RNAs (tRNAs), 2 ribosomal RNA genes (rRNAs), and a non-coding control region (D-loop). The overall base composition of was 30.

Natural selection on TMPRSS6 associated with the blunted erythropoiesis and improved blood viscosity in Tibetan pigs.

Tibetan pigs, indigenous to Tibetan plateau, are well adapted to hypoxia. So far, there have been not any definitively described genes and functional sites responsible for hypoxia adaptation for the Tibetan pig. The whole genome-wide association studies in human suggested that genetic variations in TMPRSS6 was associated with hemoglobin concentration (HGB) and red cell counts (RBC).

Genome-Wide and Trait-Specific Markers: A Perspective in Designing Conservation Programs.

Nowadays, breed conservation has entered the genomics era and it is imperative to develop novel theory to design the breeding schemes of the conservation populations by using the genomic information. The genome-wide markers have been regarded as a useful strategy to maintain genetic diversity. However, using the genome-wide SNPs to optimize diversity might not be optimal for some specific loci associated with specific-traits.

Gene Co-Expression Network Analysis Unraveling Transcriptional Regulation of High-Altitude Adaptation of Tibetan Pig.

Tibetan pigs have survived at high altitude for millennia and they have a suite of adaptive features to tolerate the hypoxic environment. However, the molecular mechanisms underlying the regulation of hypoxia-adaptive phenotypes have not been completely elucidated. In this study, we analyzed differentially expressed genes (DEGs), biological pathways and constructed co-expression regulation networks using whole-transcriptome microarrays from lung tissues of Tibetan and Duroc pigs both at high and low altitude.

Whole-genome sequencing of six dog breeds from continuous altitudes reveals adaptation to high-altitude hypoxia.

The hypoxic environment imposes severe selective pressure on species living at high altitude. To understand the genetic bases of adaptation to high altitude in dogs, we performed whole-genome sequencing of 60 dogs including five breeds living at continuous altitudes along the Tibetan Plateau from 800 to 5100 m as well as one European breed. More than 150× sequencing coverage for each breed provides us with a comprehensive assessment of the genetic polymorphisms of the dogs, including Tibetan Mastiffs.

The local origin of the Tibetan pig and additional insights into the origin of Asian pigs.

Background: The domestic pig currently indigenous to the Tibetan highlands is supposed to have been introduced during a continuous period of colonization by the ancestors of modern Tibetans. However, there is no direct genetic evidence of either the local origin or exotic migration of the Tibetan pig.

Methods And Findings: We analyzed mtDNA hypervariable segment I (HVI) variation of 218 individuals from seven Tibetan pig populations and 1,737 reported mtDNA sequences from domestic pigs and wild boars across Asia.

[Research and application of animal genetic marker-assisted selection].

With the development of molecular and quantitative genetics and its related subjects, it made a great progress on the research about animal genetic marker-assisted selection (MAS). There were also some successful examples on the application of MAS to animal genetic improvement. The statistical method which using phenotypic, pedigree and genetic marker information to predict individual breeding values has already been developed.

Effects of marker-assisted selection under different initial frequency of QTL favorable allele.

A ten-generation continuous selection experiment on a single trait in a closed population was carried out by stochastic simulation. It assumed that the trait was controlled by polygenes and a single autosomal bi-allelic marked quantitative trait locus (QTL). Individual breeding values were estimated through animal model marker-assisted best linear unbiased prediction (MB-LUP), and breeding animals were selected according to their breeding values.

Primary factors affecting the evaluation accuracy of animal model MBLUP.

Marker-assisted best linear unbiased prediction (MBLUP) is one important method of implementing marker-assisted selection (MAS). The computer stochastic simulation method was used to study the effects of heritability of trait, QTL variance and map distance between two adjacent markers on the evaluation accuracy of animal model MBLUP. With the higher heritability, the smaller QTL variance and the shorter map distance between two adjacent markers, the evaluation accuracy of animal model MBLUP would be increased.