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 post mortem (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. A total of 64 SNPs were identified for six meat quality traits using the mixed linear model (MLM), of which 24 SNPs were located in previously reported QTL regions. The phenotypic variation explained (PVE) by the significant SNPs was from 2.43% to 16.32%. The genomic heritability estimates based on SNP for six meat-quality traits were low to moderate (0.07–0.47) being the lowest for CL and the highest for DL. A total of 30 genes located within 10 kb upstream or downstream of these significant SNPs were found. Furthermore, several candidate genes for MQTs were detected, including pH45 (GRM8), MC (ANKRD6), MA (MACROD2 and ABCG1), WL (TMEM50A), CL (PIP4K2A) and DL (CDYL2, CHL1, ABCA4, ZAG and SLC1A2). This study provided substantial new evidence for several candidate genes to participate in different pork quality traits. The identification of these SNPs and candidate genes provided a basis for molecular marker-assisted breeding and improvement of pork quality traits

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. Using the sequencing data of the conserved population of the Saba pig breed, we demonstrated that the conservation program designed by using the genome-wide SNPs might result in the loss of the genetic diversity of the reproduction trait. We suggested an idea of using phylogenetic tree to select valuable individuals for conservation program based on the genome-wide and trait-specific makers. The selection rule was to make the selected samples to be widely distributed as much as possible in both the genome-wide and trait-specific phylogenetic trees

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. The Bayesian consensus tree revealed a main haplogroup M and twelve minor haplogroups, which suggested a large number of small scale in situ domestication episodes. In particular, haplogroups D1 and D6 represented two highly divergent lineages in the Tibetan highlands and Island Southeastern Asia, respectively. Network analysis of haplogroup M further revealed one main subhaplogroup M1 and two minor subhaplogroups M2 and M3. Intriguingly, M2 was mainly distributed in Southeastern Asia, suggesting for a local origin. Similar with haplogroup D6, M3 was mainly restricted in Island Southeastern Asia. This pattern suggested that Island Southeastern Asia, but not Southeastern Asia, might be the center of domestication of the so-called Pacific clade (M3 and D6 here) described in previous studies. Diversity gradient analysis of major subhaplogroup M1 suggested three local origins in Southeastern Asia, the middle and downstream regions of the Yangtze River, and the Tibetan highlands, respectively. CONCLUSIONS: We identified two new origin centers for domestic pigs in the Tibetan highlands and in the Island Southeastern Asian region

The interaction of digital economy, artificial intelligence and sports industry development --based on China PVAR analysis of provincial panel data

Under the leadership of China's ''dual-carbon'' goal, clarifying the interaction between the digital economy, artificial intelligence, and the sports industry is an important guarantee to promote the structural upgrading of China's sports industry and achieve low-carbon development. Therefore, a panel vector autoregression (PVAR) model is constructed based on the panel data of 15 provinces in China from 2014 to 2020 to investigate the interaction between the three. It is found that (1) every 1-unit increase in the level of digital economy in the lagged period can cause a 0.008-unit increase in the level of AI application in the current period at the 10% significance level, i.e., the digital economy has a short-term and weakly facilitating effect on AI. (2) Every 1 unit of digital economy level in the lagging period can cause 9.539 units of value added to the sports industry at a 1% significance level. That is, the digital economy has a short-term but strong enhancing effect on the development of the sports industry. (3) Their internal driving force mainly drives the development of digital economy and artificial intelligence, and the self-contribution rate is 72.7% and 91.5% respectively. In contrast, the self-driving force of the sports industry is weaker, and the self-contribution rate is only 68.2%. (4) The contribution rate of the digital economy and artificial intelligence to the development of the sports industry is 12.3% and 19.6% respectively, i.e., the sports industry is more affected by the degree of application of artificial intelligence than the level of development of digital economy

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. The present study aimed to identify potential sex-specific biomarkers strongly associated with IMF deposition in low- and high-IMF pig populations. The GSE144780 expression dataset of IMF deposition-related genes were obtained from the Gene Expression Omnibus. Initially, differentially expressed genes (DEGs) were detected in male and female low-IMF (162 DEGs, including 64 up- and 98 down-regulated genes) and high-IMF pigs (202 DEGs, including 147 up- and 55 down-regulated genes). Moreover, hub genes were screened via PPI network construction. Furthermore, hub genes were screened for potential sex-specific biomarkers using the least absolute shrinkage and selection operator machine learning algorithm, and sex-specific biomarkers in low-IMF (troponin I (TNNI1), myosin light chain 9(MYL9), and serpin family C member 1(SERPINC1)) and high-IMF pigs (CD4 molecule (CD4), CD2 molecule (CD2), and amine oxidase copper-containing 2(AOC2)) were identified, and then verified by quantitative real-time PCR (qRT-PCR) in semimembranosus muscles. Additionally, the gene set enrichment analysis and single-sample gene set enrichment analysis of hallmark gene sets were collectively performed on the identified biomarkers. Finally, the transcription factor-biomarker and lncRNA-miRNA-mRNA (biomarker) networks were predicted. The identified potential sex-specific biomarkers may provide new insights into the molecular mechanisms of IMF deposition and the beneficial foundation for improving meat quality in pig breeding

Enhanced Visualization of Hematoxylin and Eosin Stained Pathological Characteristics by Phasor Approach

The phasor approach to fluorescence lifetime imaging microscopy (FLIM) is used to identify different types of tissues from hematoxylin and eosin (H&E) stained basal cell carcinoma (BCC) sections. The results suggest that working directly on the phasor space with the clustering assignment achieves immunofluorescence like simultaneous five or six-color imaging by using multiplexed fluorescence lifetimes of H&E. The phase approach is of particular effectiveness for enhanced visualization of the abnormal morphology of a suspected nidus. Moreover, the phasor approach to H&E FLIM data can determine the actual paths or the infiltrating trajectories of basophils and immune cells associated with the preneoplastic or neoplastic skin lesions. The integration of the phasor approach with routine histology proved its available value for skin cancer prevention and early detection. We therefore believe that the phasor analysis of H&E tissue sections is an enhanced visualization tool with the potential to simplify the preparation process of special staining and serve as color contrast aided imaging in clinical pathological examination

The Seepage Evolution Characteristics in Undisturbed Loess under Dynamic Preferential Flow: New Insights from X-ray Computed Tomography

Preferential flow is widely developed in varieties of voids (such as macropores and fissures) in loess areas, affecting slope hydrology and stability and even leading to geological disasters. However, the model of seepage evolution with dynamic preferential flow is not clear, which obstructs the disclosure of the mechanism of landslides induced by the preferential flow. This study aimed to capture the seepage and occurrence status of water in loess voids, explain the variability characteristics of the loess pore structure, and reveal the seepage evolution model of dynamic preferential flow. Preferential infiltration experiments were conducted by combining X-ray computed tomography (X-ray CT) nondestructive detection with contrast techniques under dynamic seepage conditions. Three-dimensional (3D) visualized reconstruction, digital image correlation (DIC), image processing, and quantitative analyses were performed in AVIZO 2019.1, including two-dimensional (2D) and 3D characteristics of preferential flow distribution and macropore changing, dynamic variation of the porosity, pore number, volume, dip angle, and connectivity. Results showed that (1) preferential flow exists under saturated and unsaturated conditions in loess with strong uniformity and anisotropy; (2) preferential flow not only migrates into existing connected macropores, but also connects the original isolated pores into channels and forms larger percolation groups of contrast medium under the gradually increased high pressure; (3) the seepage develops with the evolution model of ‘preferential flow–piston flow–preferential piston mixture flow–piston flow’ in the dynamic process. The new insights into the characteristics of the seepage evolution in undisturbed loess under dynamic preferential flow will enrich the understanding of loess seepage and provided an important reference for future research on the slope instability of the loess induced by preferential flow