Genotype data of Chenghua pigs and Neijiang pigs.

The genotype datasets of 21 Chenghua pigs and 49 Neijiang pigs.</p

Genotype data of Tibetan pigs

The genotype datasets of high-altitude and low-altitude Tibetan pigs. After removing duplicates, 149 samples were remaining.</p

Dynamic microRNAome profiles in the developing porcine liver

<p>Increasing evidence suggests that micro (mi)RNAs play important roles in various biological process. To evaluate the roles of miRNA in the porcine liver, we investigated the dynamic profiles of microRNAomes using liver tissue from pigs during the embryonic period (embryonic day 90), weaning stage (postnatal day 30), and adult stage (7 years old). A total of 186 unique miRNAs were differentially expressed during liver development. We also identified that 17, 13, and 6 miRNAs were specifically abundant at embryonic day 90, postnatal day 30, and at 7 years, respectively. Besides regulating basic cellular roles in development, miRNAs expressed at the three developmental stages also participated in regulating “embryonic liver development,” “early hepatic growth and generating a functioning liver,” and “energy metabolic processes,” respectively. Our study indicates that miRNAs are extensively involved in liver development, and provides a valuable resource for the further elucidation of miRNA regulatory roles during liver development.</p> <p>miRNAs are extensively involved in liver development, especially for these stage-enriched miRNAs.</p

Transcriptomic profiling in muscle and adipose tissue identifies genes related to growth and lipid deposition

<div><p>Growth performance and meat quality are important traits for the pig industry and consumers. Adipose tissue is the main site at which fat storage and fatty acid synthesis occur. Therefore, we combined high-throughput transcriptomic sequencing in adipose and muscle tissues with the quantification of corresponding phenotypic features using seven Chinese indigenous pig breeds and one Western commercial breed (Yorkshire). We obtained data on 101 phenotypic traits, from which principal component analysis distinguished two groups: one associated with the Chinese breeds and one with Yorkshire. The numbers of differentially expressed genes between all Chinese breeds and Yorkshire were shown to be 673 and 1056 in adipose and muscle tissues, respectively. Functional enrichment analysis revealed that these genes are associated with biological functions and canonical pathways related to oxidoreductase activity, immune response, and metabolic process. Weighted gene coexpression network analysis found more coexpression modules significantly correlated with the measured phenotypic traits in adipose than in muscle, indicating that adipose regulates meat and carcass quality. Using the combination of differential expression, QTL information, gene significance, and module hub genes, we identified a large number of candidate genes potentially related to economically important traits in pig, which should help us improve meat production and quality.</p></div

Adipose modules AM19 and AM9 are significantly correlated with the fat and lean meat phenotypic traits.

<p>(A) The expression and eigengene values of modules AM19 and AM9 have opposite correlations with the phenotypic traits. Each row in the heatmaps was normalized, with red denoting a higher Z score of the expression (measured using RPKM) or the phenotypic measurements, and blue denoting a lower one. In the expression section, each row represents one gene. Eig_AM19 and Eig_AM9 represent the module eigengenes of AM19 and AM9, respectively. Each column represents one individual pig. FGR: feed/gain ratio, BFP: back waist fat percentage, IMF: intramuscular fat content, BLMP: back waist lean meat percentage, CLMP: carcass lean meat percentage, BBP: back waist bone percentage. (B) Gene significance of back waist fat percentage is positively correlated with the module membership in AM19. Red denotes upregulation in Chinese breeds. (C) Gene significance of back waist lean meat percentage is positively correlated with module membership in AM9. (D) The network of the top 30 genes with the highest module membership in module AM19; only the edges with topological overlap above a threshold of 0.05 are displayed. The rectangle represents the DEGs between Chinese breeds and Yorkshire. (E) The network in module AM9 with the same criteria as those in D. The coexpression networks reflect the degree of topological overlap (the size of the vertex), the DEGs (the red color of the vertex), and the QTL association (the blue color of the label).</p

Higher correlation between adipose modules and traits than for muscle modules.

<p>(A) The distribution of Pearson’s correlation between the module eigengene and traits for adipose and muscle tissues. (B) The module eigengene significance of adipose tissue. The displayed traits and modules have at least Pearson’s correlation <i>r</i>>0.7 and <i>P</i><0.01. Cell color represents the correlation (red, positive correlation; blue, negative correlation, according to the color legend). Two numbers in each cell show the correlation level (upper) and correlation significance (lower in the parentheses). Rows represent traits and columns represent coexpression modules. (C) The module eigengene significance of muscle tissue. The displayed traits and modules have at least Pearson’s correlation <i>r</i>>0.5 and <i>P</i><0.01. The cell color, numbers in each cell, and X and Y axes have the same meanings as those in B. (D) The enriched Gene Ontology biological processes for the selected modules in adipose and muscle tissues. The height of the bar corresponding to the minus log10-transformed adjusted <i>P</i> value. A: adipose, M: muscle.</p

Lactation-Related MicroRNA Expression Profiles of Porcine Breast Milk Exosomes

<div><p>Breast milk is the primary source of nutrition for newborns, and is rich in immunological components. MicroRNAs (miRNAs) are present in various body fluids and are selectively packaged inside the exosomes, a type of membrane vesicles, secreted by most cell types. These exosomal miRNAs could be actively delivered into recipient cells, and could regulate target gene expression and recipient cell function. Here, we analyzed the lactation-related miRNA expression profiles in porcine milk exosomes across the entire lactation period (newborn to 28 days after birth) by a deep sequencing. We found that immune-related miRNAs are present and enriched in breast milk exosomes (<em>p</em><10⁻¹⁶, <em>χ</em>² test) and are generally resistant to relatively harsh conditions. Notably, these exosomal miRNAs are present in higher numbers in the colostrums than in mature milk. It was higher in the serum of colostrum-only fed piglets compared with the mature milk-only fed piglets. These immune-related miRNA-loaded exosomes in breast milk may be transferred into the infant body via the digestive tract. These observations are a prelude to in-depth investigations of the essential roles of breast milk in the development of the infant’s immune system.</p> </div

Modules significantly correlated with phenotypic traits that were also significantly enriched for DEGs.

<p>Modules significantly correlated with phenotypic traits that were also significantly enriched for DEGs.</p

Consistent expression levels between Chinese indigenous breeds and the YY breed.

<p>(A) The numbers of DEGs between all pairs of samples. The numbers indicate the genes that were upregulated for the samples on the y-axis and downregulated on the x-axis. The darker the red, the greater the number of DEGs. A: adipose tissue; M: <i>longissimus dorsi</i> muscle tissue. (B) Venn diagram summarizing the number of DEGs shared among tissues. (C) Comparisons of the expression level between the DEGs that were highly expressed in YY and in Chinese breeds for the two tissues. The ratio is calculated based on the average RPKM of the replicates. Red indicates the genes expressed more highly in Chinese breeds and blue indicates those expressed more highly in YY. (D) The selected enriched biological processes in the Gene Ontology gene sets for the upregulated genes in the two tissues from Chinese breeds and the YY breed.</p

Lactation-related miRNA expression profiles.

<p>(A) Distribution of lactation-related pre-miRNAs. Out of 1,527 pre-miRNAs deposited in miRBase 18.0, 84 (5.50%) pre-miRNAs have been designated as immunopathology-related pre-miRNAs, based on annotation in the Pathway Central database (SABiosciences, MD, USA). These immune-related pre-miRNAs are enriched in each milk exosomal miRNA library. <i>χ</i>² test (**<i>p</i><10⁻¹⁶): Numbers of immunopathology-related miRNAs and others detected in milk exosomes compared with the total entries in miRBase 18.0. The three biological replicates at 0 days are denoted by 0d-1, -2 and -3, respectively. (B) Hierarchical clustering and heat map matrix of pairwise Spearman correlations of the counts of 234 unique miRNAs between eight exosomal miRNA libraries. (C) Top 10 unique miRNAs with the highest expression levels in milk exosomal miRNA libraries. Plot of the unique miRNAs versus their % in total counts of all unique miRNAs for each library. The dashed vertical lines represent the accumulative % of the top 10 unique miRNAs in total counts of all unique miRNAs. Seven miRNAs that are present in the top 10 miRNAs in all six libraries are connected by lines.</p