Research

33 pages, 8022 KiB

Open AccessArticle

Changes in Biceps femoris Transcriptome along Growth in Iberian Pigs Fed Different Energy Sources and Comparative Analysis with Duroc Breed

by Rita Benítez, Yolanda Núñez, Miriam Ayuso, Beatriz Isabel, Miguel A. Fernández-Barroso, Eduardo De Mercado, Emilio Gómez-Izquierdo, Juan M. García-Casco, Clemente López-Bote and Cristina Óvilo

Animals 2021, 11(12), 3505; https://doi.org/10.3390/ani11123505 - 08 Dec 2021

Cited by 6 | Viewed by 2757

Abstract

This experiment was conducted to investigate the effects of developmental stage, breed, and diet energy source on the genome-wide expression, meat quality traits, and tissue composition of biceps femoris muscle in growing pure Iberian and Duroc pigs. The study comprised 59 Iberian (IB) [...] Read more.

This experiment was conducted to investigate the effects of developmental stage, breed, and diet energy source on the genome-wide expression, meat quality traits, and tissue composition of biceps femoris muscle in growing pure Iberian and Duroc pigs. The study comprised 59 Iberian (IB) and 19 Duroc (DU) animals, who started the treatment at an average live weight (LW) of 19.9 kg. The animals were kept under identical management conditions and fed two diets with different energy sources (6% high oleic sunflower oil or carbohydrates). Twenty-nine IB animals were slaughtered after seven days of treatment at an average LW of 24.1 kg, and 30 IB animals plus all the DU animals were slaughtered after 47 days at an average LW of 50.7 kg. The main factors affecting the muscle transcriptome were age, with 1832 differentially expressed genes (DEGs), and breed (1055 DEGs), while the effect of diet on the transcriptome was very small. The results indicated transcriptome changes along time in Iberian animals, being especially related to growth and tissue development, extracellular matrix (ECM) composition, and cytoskeleton organization, with DEGs affecting relevant functions and biological pathways, such as myogenesis. The breed also affected functions related to muscle development and cytoskeleton organization, as well as functions related to solute transport and lipid and carbohydrate metabolism. Taking into account the results of the two main comparisons (age and breed effects), we can postulate that the Iberian breed is more precocious than the Duroc breed, regarding myogenesis and muscle development, in the studied growing stage. Full article

(This article belongs to the Special Issue Transcriptomics in Autochthonous Breeds or Populations of Livestock and Aquaculture Species)

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13 pages, 4038 KiB

Open AccessArticle

Transcriptome Analysis of Differentially Expressed mRNA Related to Pigeon Muscle Development

by Hao Ding, Yueyue Lin, Tao Zhang, Lan Chen, Genxi Zhang, Jinyu Wang, Kaizhou Xie and Guojun Dai

Animals 2021, 11(8), 2311; https://doi.org/10.3390/ani11082311 - 05 Aug 2021

Cited by 8 | Viewed by 3393

Abstract

The mechanisms behind the gene expression and regulation that modulate the development and growth of pigeon skeletal muscle remain largely unknown. In this study, we performed gene expression analysis on skeletal muscle samples at different developmental and growth stages using RNA sequencing (RNA−Seq). [...] Read more.

The mechanisms behind the gene expression and regulation that modulate the development and growth of pigeon skeletal muscle remain largely unknown. In this study, we performed gene expression analysis on skeletal muscle samples at different developmental and growth stages using RNA sequencing (RNA−Seq). The differentially expressed genes (DEGs) were identified using edgeR software. Weighted gene co−expression network analysis (WGCNA) was used to identify the gene modules related to the growth and development of pigeon skeletal muscle based on DEGs. A total of 11,311 DEGs were identified. WGCNA aggregated 11,311 DEGs into 12 modules. Black and brown modules were significantly correlated with the 1st and 10th day of skeletal muscle growth, while turquoise and cyan modules were significantly correlated with the 8th and 13th days of skeletal muscle embryonic development. Four mRNA−mRNA regulatory networks corresponding to the four significant modules were constructed and visualised using Cytoscape software. Twenty candidate mRNAs were identified based on their connectivity degrees in the networks, including Abca8b, TCONS−00004461, VWF, OGDH, TGIF1, DKK3, Gfpt1 and RFC5, etc. A KEGG pathway enrichment analysis showed that many pathways were related to the growth and development of pigeon skeletal muscle, including PI3K/AKT/mTOR, AMPK, FAK, and thyroid hormone pathways. Five differentially expressed genes (LAST2, MYPN, DKK3, B4GALT6 and OGDH) in the network were selected, and their expression patterns were quantified by qRT−PCR. The results were consistent with our sequencing results. These findings could enhance our understanding of the gene expression and regulation in the development and growth of pigeon muscle. Full article

(This article belongs to the Special Issue Transcriptomics in Autochthonous Breeds or Populations of Livestock and Aquaculture Species)

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21 pages, 6645 KiB

Open AccessArticle

Transcriptomic Profiling of Skeletal Muscle Reveals Candidate Genes Influencing Muscle Growth and Associated Lipid Composition in Portuguese Local Pig Breeds

by André Albuquerque, Cristina Óvilo, Yolanda Núñez, Rita Benítez, Adrián López-Garcia, Fabián García, Maria do Rosário Félix, Marta Laranjo, Rui Charneca and José Manuel Martins

Animals 2021, 11(5), 1423; https://doi.org/10.3390/ani11051423 - 16 May 2021

Cited by 16 | Viewed by 3192

Abstract

Gene expression is one of the main factors to influence meat quality by modulating fatty acid metabolism, composition, and deposition rates in muscle tissue. This study aimed to explore the transcriptomics of the Longissimus lumborum muscle in two local pig breeds with distinct [...] Read more.

Gene expression is one of the main factors to influence meat quality by modulating fatty acid metabolism, composition, and deposition rates in muscle tissue. This study aimed to explore the transcriptomics of the Longissimus lumborum muscle in two local pig breeds with distinct genetic background using next-generation sequencing technology and Real-Time qPCR. RNA-seq yielded 49 differentially expressed genes between breeds, 34 overexpressed in the Alentejano (AL) and 15 in the Bísaro (BI) breed. Specific slow type myosin heavy chain components were associated with AL (MYH7) and BI (MYH3) pigs, while an overexpression of MAP3K14 in AL may be associated with their lower loin proportion, induced insulin resistance, and increased inflammatory response via NFkB activation. Overexpression of RUFY1 in AL pigs may explain the higher intramuscular (IMF) content via higher GLUT4 recruitment and consequently higher glucose uptake that can be stored as fat. Several candidate genes for lipid metabolism, excluded in the RNA-seq analysis due to low counts, such as ACLY, ADIPOQ, ELOVL6, LEP and ME1 were identified by qPCR as main gene factors defining the processes that influence meat composition and quality. These results agree with the fatter profile of the AL pig breed and adiponectin resistance can be postulated as responsible for the overexpression of MAP3K14′s coding product NIK, failing to restore insulin sensitivity. Full article

(This article belongs to the Special Issue Transcriptomics in Autochthonous Breeds or Populations of Livestock and Aquaculture Species)

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23 pages, 4564 KiB

Open AccessArticle

Muscle Transcriptome Analysis Reveals Molecular Pathways Related to Oxidative Phosphorylation, Antioxidant Defense, Fatness and Growth in Mangalitsa and Moravka Pigs

by Yolanda Núñez, Čedomir Radović, Radomir Savić, Juan M. García-Casco, Marjeta Čandek-Potokar, Rita Benítez, Dragan Radojković, Miloš Lukić, Marija Gogić, María Muñoz, Luca Fontanesi and Cristina Óvilo

Animals 2021, 11(3), 844; https://doi.org/10.3390/ani11030844 - 16 Mar 2021

Cited by 8 | Viewed by 3226

Abstract

This work was aimed at evaluating loin transcriptome and metabolic pathway differences between the two main Serbian local pig breeds with divergent characteristics regarding muscle growth and fatness, as well as exploring nutrigenomic effects of tannin supplementation in Mangalitsa (MA) pigs. The study [...] Read more.

This work was aimed at evaluating loin transcriptome and metabolic pathway differences between the two main Serbian local pig breeds with divergent characteristics regarding muscle growth and fatness, as well as exploring nutrigenomic effects of tannin supplementation in Mangalitsa (MA) pigs. The study comprised 24 Mangalitsa and 10 Moravka (MO) males, which were kept under identical management conditions. Mangalitsa animals were divided in two nutritional groups (n = 12) receiving a standard (control) or tannin–supplemented diet (1.5%; MAT). Moravka pigs were fed the standard mixture. All animals were slaughtered at a similar age; 120 kg of average live weight (LW) and loin tissue was used for RNA-seq analysis. Results showed 306 differentially expressed genes (DEGs) according to breed, enriched in genes involved in growth, lipid metabolism, protein metabolism and muscle development, such as PDK4, FABP4, MYOD1 and STAT3, as well as a relevant number of genes involved in mitochondrial respiratory activity (MT-NDs, NDUFAs among others). Oxidative phosphorylation was the most significantly affected pathway, activated in Mangalitsa muscle, revealing the basis of a different muscle metabolism. Also, many other relevant pathways were affected by breed and involved in oxidative stress response, fat accumulation and development of skeletal muscle. Results also allowed the identification of potential regulators and causal networks such as those controlled by FLCN, PPARGC1A or PRKAB1 with relevant regulatory roles on DEGs involved in mitochondrial and lipid metabolism, or IL3 and TRAF2 potentially controlling DEGs involved in muscle development. The Tannin effect on transcriptome was small, with only 23 DEGs, but included interesting ones involved in lipid deposition such as PPARGC1B. The results indicate a significant effect of the breed on muscle tissue gene expression, affecting relevant biological pathways and allowing the identification of strong regulatory candidate genes to underlie the gene expression and phenotypic differences between the compared groups. Full article

(This article belongs to the Special Issue Transcriptomics in Autochthonous Breeds or Populations of Livestock and Aquaculture Species)

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14 pages, 524 KiB

Open AccessArticle

Comparative Transcriptome Profile between Iberian Pig Varieties Provides New Insights into Their Distinct Fat Deposition and Fatty Acids Content

by Ana Villaplana-Velasco, Jose Luis Noguera, Ramona Natacha Pena, Maria Ballester, Lourdes Muñoz, Elena González, Juan Florencio Tejeda and Noelia Ibáñez-Escriche

Animals 2021, 11(3), 627; https://doi.org/10.3390/ani11030627 - 27 Feb 2021

Cited by 8 | Viewed by 2467

Abstract

The high deposition of intramuscular fat and the content of oleic fatty acid are characteristic of the Iberian pig. These two parameters present great variability and are differentiated amongst the varieties that make up the Iberian pig population. Although previous studies generated evidence [...] Read more.

The high deposition of intramuscular fat and the content of oleic fatty acid are characteristic of the Iberian pig. These two parameters present great variability and are differentiated amongst the varieties that make up the Iberian pig population. Although previous studies generated evidence for causal genes and polymorphisms associated to the adipogenic potential of the Iberian pig, there is little information about how genetic expression influences this trait’s variability. The aim of this study was to analyses the expression profile between two varieties of Iberian pig (Torbiscal and Retinto) and their reciprocal crosses differentiated in their intramuscular fat (IMF) content and fatty acid (FA) composition in the Longissimus thoracis muscle using an RNA-seq approach. Our results corroborate that the Retinto variety is the fattiest amongst all studied varieties as its upregulated genes, such as FABP3 and FABP5, SLC27A1 and VEGFA among others, contribute to increasing adiposity. In its turn, Torbiscal pigs showed an upregulation of genes associated with the inhibition of fat deposition such as ADIPOQ and CPT1A. Further genetic variation analysis in these Iberian varieties showed relevant associations for SNP located within the differentially expressed genes with IMF and FA content. Thus, the differences found in the genetic architecture and the muscle transcriptome of these Iberian varieties might explain the variability in their fat content and composition and hence, their meat quality. Full article

(This article belongs to the Special Issue Transcriptomics in Autochthonous Breeds or Populations of Livestock and Aquaculture Species)

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25 pages, 1473 KiB

Open AccessArticle

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

by Miguel Ángel Fernández-Barroso, Carmen Caraballo, Luis Silió, Carmen Rodríguez, Yolanda Nuñez, Fernando Sánchez-Esquiliche, Gema Matos, Juan María García-Casco and María Muñoz

Animals 2020, 10(9), 1715; https://doi.org/10.3390/ani10091715 - 22 Sep 2020

Cited by 10 | Viewed by 3936

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 [...] Read more.

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. Full article

(This article belongs to the Special Issue Transcriptomics in Autochthonous Breeds or Populations of Livestock and Aquaculture Species)

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12 pages, 1818 KiB

Open AccessArticle

Meta-Transcriptomic Analysis of RNAseq Data Reveals Pacu and Loach Fish with Unusually High Levels of Myoglobin Expression in Skeletal Muscles

by Rui-Yi Chen, Bui Thi Ngoc Hieu, Gilbert Audira, Bao Lou, Ming-Der Lin and Chung-Der Hsiao

Animals 2020, 10(7), 1130; https://doi.org/10.3390/ani10071130 - 03 Jul 2020

Cited by 2 | Viewed by 2712

Abstract

Oxygen-binding proteins, such as myoglobin, hemoglobin, neuroglobin, and cytoglobin, play a role in oxygen binding and delivery to tissues. In icefish, the loss of myoglobin and hemoglobin genes has been reported to be an adaptive evolution event. This interesting finding prompted us to [...] Read more.

Oxygen-binding proteins, such as myoglobin, hemoglobin, neuroglobin, and cytoglobin, play a role in oxygen binding and delivery to tissues. In icefish, the loss of myoglobin and hemoglobin genes has been reported to be an adaptive evolution event. This interesting finding prompted us to exam oxygen-binding protein expression in diverse fish species. Taking advantage of substantial RNAseq data deposited in the NCBI (National Center for Biotechnology Information) database, we adopted a meta-transcriptomic approach to explore and compare four oxygen-binding protein gene expression levels in the skeletal muscle of 25 diverse fish species for the first time. RNAseq data were downloaded from the NCBI Sequence Read Archive (SRA) database, and de novo assembly was performed to generate transcript contigs. The genes encoding oxygen-binding proteins were then identified by the BLAST search, and the relative expression level of oxygen-binding protein genes was normalized by the RPKM (Reads per Kilobase Million) method. By performing expression profiling, hierarchy clustering, and principal component analysis, pacu and loach fish were noticed by their high myoglobin expression levels in skeletal muscle tissues among 25 diverse fish species. In conclusion, we demonstrated that meta-transcriptomic analysis of RNAseq data is an informative approach to compare the oxygen-binding protein expression and putative gene expansion event in fish. Full article

(This article belongs to the Special Issue Transcriptomics in Autochthonous Breeds or Populations of Livestock and Aquaculture Species)

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11 pages, 2006 KiB

Open AccessArticle

Identification of Ovarian Circular RNAs and Differential Expression Analysis between MeiShan and Large White Pigs

by Guoming Liang, Junyu Yan, Jin Guo and Zhonglin Tang

Animals 2020, 10(7), 1114; https://doi.org/10.3390/ani10071114 - 29 Jun 2020

Cited by 16 | Viewed by 2247

Abstract

MeiShan and Large White pigs differ in their female fecundity. However, the mechanisms behind the gene expression and regulation that cause these differences remain unclear. In this study, we profiled circRNAs and identified 5,879 circRNAs from the ovaries of MeiShan and Large White [...] Read more.

MeiShan and Large White pigs differ in their female fecundity. However, the mechanisms behind the gene expression and regulation that cause these differences remain unclear. In this study, we profiled circRNAs and identified 5,879 circRNAs from the ovaries of MeiShan and Large White pigs. Eighty-five circRNAs were differentially expressed between the two pig breeds. Of these, 37 were up-regulated and 48 were down-regulated in MeiShan pigs. Gene ontology enrichment analysis suggested that the differentially expressed circRNA were involved in the hormone-mediated signaling pathway. We verified that circSCIN and its parent gene, scinderin (SCIN), were differentially expressed by reverse transcription and quantitative PCR (RT-qPCR). Luciferase assays demonstrated that circSCIN can target and sponge miR-133 and miR-148a/b. The identification of differentially expressed circRNAs (DECs) and their regulatory functions increased our understanding of the differences in reproductive efficiency between MeiShan and Large White pigs. Full article

(This article belongs to the Special Issue Transcriptomics in Autochthonous Breeds or Populations of Livestock and Aquaculture Species)

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