Integrative transcriptomics and proteomics analysis of longissimus dorsi muscles of Canadian double-muscled Large White pigs

Genome-Wide Association Study of Conformation Traits in Brazilian Holstein Cattle

The linear conformation of animals exerts an influence on health, reproduction, production, and welfare, in addition to longevity, which directly affects the profitability of milk-producing farms. The objectives of this study were (1) to perform genome-wide association studies (GWASs) of conformation traits, namely the Rump, Feet and Legs, Mammary System, Dairy Strength, and Final Classification traits, and (2) to identify genes and related pathways involved in physiological processes associated with conformation traits in Brazilian Holstein cattle. Phenotypic and genotypic data from 2339 Holstein animals distributed across the states of Rio Grande do Sul, Paraná, São Paulo, and Minas Gerais were used. The genotypic data were obtained with a 100 K SNP marker panel. The single-step genome-wide association study (ssGWAS) method was employed in the analyses. Genes close to a significant SNP were identified in an interval of 100 kb up- and downstream using the Ensembl database available in the BioMart tool. The DAVID database was used to identify the main metabolic pathways and the STRING program was employed to create the gene regulatory network. In total, 36 significant SNPs were found on 15 chromosomes; 27 of these SNPs were linked to genes that may influence the traits studied. Fourteen genes most closely related to the studied traits were identified, as well as four genes that showed interactions in important metabolic pathways such as myogenesis, adipogenesis, and angiogenesis. Among the total genes, four were associated with myogenesis (TMOD2, TMOD3, CCND2, and CTBP2), three with angiogenesis (FGF23, FGF1, and SCG3), and four with adipogenesis and body size and development (C5H12orf4, CCND2, EMILIN1, and FGF6). These results contribute to a better understanding of the biological mechanisms underlying phenotypic variability in conformation traits in Brazilian Holstein cattle.

Integrated Omics analysis of pig muscle metabolism under the effects of dietary Chlorella vulgaris and exogenous enzymes

Monogastric feeding is dependent on costly conventional feedstuffs. Microalgae such as Chlorella vulgaris are a sustainable alternative; however, its recalcitrant cell wall hinders monogastric digestion. Carbohydrate Active Enzyme (CAZyme) supplementation is a possible solution. The objective of this work was to evaluate the effect of 5% dietary C. vulgaris (CV) and enzymatic supplementation (CV + R-Rovabio® Excel AP; CV + M-four CAZyme mix) on muscle transcriptome and proteome of finishing pigs, in an integrated approach. Control pigs increased the abundance of contractile apparatus (MYH1, MYH2, MYH4) and energy metabolism (CKMT1, NDUFS3) proteins, demonstrating increased nutrient availability. They had increased expression of SCD, characteristic of increased glucose availability, via the activation of SREBP-1c and ChREBP. CV and CV + R pigs upregulated proteolytic and apoptotic genes (BAX, DDA1), whilst increasing the abundance of glucose (UQCRFS1) and fatty acid catabolism (ACADS) proteins. CV + R pigs upregulated ACOT8 and SIRT3 genes as a response to reduced nutrient availability, maintaining energy homeostasis. The cell wall specific CAZyme mix, CV + M, was able to comparatively reduce Omics alterations in the muscle, thereby reducing endogenous nutrient catabolism compared to the CV + R and CV.

Differences in the Loin Tenderness of Iberian Pigs Explained through Dissimilarities in Their Transcriptome Expression Profile

Simple Summary

The Iberian pig is the most representative autochthonous breed of the Mediterranean region with unique genetic and phenotypic characteristics. The breed has been successfully preserved by its high-quality meat and high-priced products. Tenderness is one of the most relevant meat quality traits, and meat tenderization is influenced by genetic and environmental effects such as pre-slaughter handling and post-mortem conditions. Tenderness could be included in Iberian pig breeding programs, mainly focused on the improvement of premium-cuts percentage, in order to avoid the meat quality decline. A better biological understanding of this trait is needed. In the current study, we analyze the transcriptome of pigs divergent for Warner–Bratzler shear force through RNA-seq technique for the identification, characterization and quantification of candidate genes involved in biological pathways, networks and functions affecting meat tenderness.

Abstract

Tenderness is one of the most important meat quality traits and it can be measured through shear force with the Warner–Bratzler test. In the current study, we use the RNA-seq technique to analyze the transcriptome of Longissimus dorsi (LD) muscle in two groups of Iberian pigs (Tough and Tender) divergent for shear force breeding values. We identified 200 annotated differentially expressed genes (DEGs) and 245 newly predicted isoforms. The RNAseq expression results of 10 genes were validated with quantitative PCR (qPCR). Functional analyses showed an enrichment of DE genes in biological processes related to proteolysis (CTSC, RHOD, MYH8, ACTC1, GADD45B, CASQ2, CHRNA9 and ANKRD1), skeletal muscle tissue development (ANKRD1, DMD, FOS and MSTN), lipid metabolism (FABP3 and PPARGC1A) and collagen metabolism (COL14A1). The upstream analysis revealed a total of 11 transcription regulatory factors that could regulate the expression of some DEGs. Among them, IGF1, VGLL3 and PPARG can be highlighted since they regulate the expression of genes involved in biological pathways that could affect tenderness. The experiment revealed a set of candidate genes and regulatory factors suggestive to search polymorphisms that could be incorporated in a breeding program for improving meat tenderness.

Proteomic analyses of sheep (ovis aries) embryonic skeletal muscle

The growth and development of embryonic skeletal muscle plays a crucial role in sheep muscle mass. But proteomic analyses for embryonic skeletal development in sheep had been little involved in the past research. In this study, we explored differential abundance proteins during embryonic skeletal muscle development by the tandem mass tags (TMT) and performed a protein profile analyses in the longissimus dorsi of Chinese merino sheep at embryonic ages Day85 (D85N), Day105 (D105N) and Day135 (D135N). 5,520 proteins in sheep embryonic skeletal muscle were identified, and 1,316 of them were differential abundance (fold change ≥1.5 and p-value < 0.05). After the KEGG enrichment analyses, these differential abundance proteins were significant enriched in the protein binding, muscle contraction and energy metabolism pathways. After validation of the protein quantification with the parallel reaction monitoring (PRM), 41% (16/39) significant abundance proteins were validated, which was similar to the results of protein quantification with TMT. All results indicated that D85N to D105N was the stage of embryonic muscle fibers proliferation, while D105N to D135N was the stage of their hypertrophy. These findings provided a deeper understanding of the function and rules of proteins in different phases of sheep embryonic skeletal muscle growth and development.

TMT-labeled quantitative proteomic analyses on the longissimus dorsi to identify the proteins underlying intramuscular fat content in pigs

The Laiwu pig is famous for its excessively extremely high level of intramuscular fat content (IMF), however, the exact regulatory mechanism underlying intramuscular fat deposition in skeletal muscle is still unknown. As an economically important trait in pigs, IMF is controlled by multiple genes and biological pathways. In this study, we performed an integrated transcriptome-assisted TMT-labeled quantitative proteomic analysis of the longissimus dorsi (LD) muscle in Laiwu pigs at the fastest IMF deposition stage and identified 5074 unique proteins and 52 differentially abundant proteins (DAPs) (>1.5-fold cutoff, p < .05). These DAPs were hierarchically clustered in the LD muscle over two developmental stages from 120 d to 240 d. A comparison between transcriptomic (mRNA) and proteomic data revealed two differentially expressed genes corresponding to the DAPs. Changes in the levels of the nine proteins were further analyzed using RT-qPCR and parallel reaction monitoring (PRM). The proteins identified in this study could serve as candidates for elucidating the molecular mechanism of IMF deposition in pigs. SIGNIFICANCE: The intramuscular fat content (IMF) refers to the amount of fat within muscles and plays an important role in meat quality by affecting meat quality-related traits, such as tenderness, juiciness and flavor. Using the integrated transcriptome-assisted TMT-labeled quantitative proteomic approach to characterize changes in the proteomic profile of the longissimus dorsi muscle, we identified differentially abundant proteins, such as ALDH1B1, OTX2, AnxA6 and Zfp512, that are associated with intramuscular fat deposition and fat biosynthesis in pigs. These proteins could serve as candidates for elucidating the molecular mechanism of IMF deposition in pigs.

Transcriptomics Analysis on Excellent Meat Quality Traits of Skeletal Muscles of the Chinese Indigenous Min Pig Compared with the Large White Breed

The Min pig (Sus scrofa) is a well-known indigenous breed in China. One of its main advantages over European breeds is its high meat quality. Additionally, different cuts of pig also show some different traits of meat quality. To explore the underlying mechanism responsible for the differences of meat quality between different breeds or cuts, the longissimus dorsi muscle (LM) and the biceps femoris muscle (BF) from Min and Large White pigs were investigated using transcriptome analysis. The gene expression profiling identified 1371 differentially expressed genes (DEGs) between LM muscles from Min and Large White pigs, and 114 DEGs between LM and BF muscles from the same Min pigs. Gene Ontology (GO) enrichment of biological functions and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that the gene products were mainly involved in the IRS1/Akt/FoxO1 signaling pathway, adenosine 5′-monophosphate-activated protein kinase (AMPK) cascade effects, lipid metabolism and amino acid metabolism pathway. Such pathways contributed to fatty acid metabolism, intramuscular fat deposition, and skeletal muscle growth in Min pig. These results give an insight into the mechanisms underlying the formation of skeletal muscle and provide candidate genes for improving meat quality. It will contribute to improving meat quality of pigs through molecular breeding.

Global protein expression analysis of molecular markers of DS-1-47, a component of implantation-promoting traditional chinese medicine

This study investigated the molecular markers of DS-1-47, a component of an implantation- promoting traditional Chinese medicine consisting of Astragalus mongholicus, Atractylodes macrocephala, Scutellaria baicalensis and Dipsacales, in an attempt to clarify the molecular mechanism and action targets of DS-1-47. Controlled ovarian stimulation (COS) method was used to establish the implantation dysfunction models of mice. Animals were divided into normal pregnant group, COS model group and DS-1-47 group. Laser capture microdissection-double dimensional electrophoresis-mass spectrum (LCM-DE-MS) was used to analyze the uterine protein molecules that were possibly involved in the promotion of implantation. Twenty-three proteins in DS-1-47 group were significantly changed as compared to those in COS model group, with 7 proteins down-regulated and 16 proteins up-regulated. Except for some constituent proteins, the down-regulated proteins included collagen α-1 (VI) chain, keratin 7, keratin 14, myosin regulatory light chain 12B, myosin light polypeptide 9, heat shock protein β-7, and C-U-editing enzyme APOBEC-2; the up-regulated proteins included apolipoprotein A-I, calcium regulated protein-3, proliferating cell nuclear antigen, L-xylulose reductase, and calcium binding protein. These 23 proteins that were regulated by DS-1-47 represented a broad diversity of molecule functions. The down-regulated proteins were associated with stress and immune response, and those up-regulated proteins were related to proliferation. It was suggested that these proteins were important in regulating the uterine environment for the blastocyst implantation. By identification of DS-1-47 markers, proteomic analysis coupled with functional assays is demonstrated to be a promising approach to better understand the molecular mechanism of traditional Chinese medicine.