ABSTRACT
BACKGROUND: The Shaziling pig (Sus scrofa) is a well-known indigenous breed in China. One of its main advantages over European breeds is its high meat quality. However, little genetic information is available for the Shaziling pig. To screen for differentially expressed genes and proteins that might be responsible for the meat quality, the longissimus dorsi muscles from Shaziling and Yorkshire pig breeds were investigated using an integrative analysis of transcriptomics and proteomics, involving high-throughput sequencing, the two-dimensional gel electrophoresis, and mass spectrometry. RESULTS: Sequencing produced 79,320 unigenes by de novo assembly, and 488 differentially expressed genes in the longissimus dorsi muscle of Shaziling pig compared with the Yorkshire breed were identified. Gene Ontology term enrichment of biological functions and Kyoto Encyclopedia of Genes and Genomes analysis showed that the gene products were mainly involved in metabolism, protein binding, and regulation of skeletal muscle development. At the protein level, 23 differentially expressed proteins were identified, which were potentially associated with fatty acid metabolism, the glycolytic pathway, and skeletal muscle growth. Eight differentially expressed genes were confirmed by real-time PCR. These results give an insight into the mechanisms underlying the formation of skeletal muscle in the Shaziling pig. CONCLUSIONS: Certain differentially expressed genes and proteins are involved in fatty acid metabolism, intramuscular fat deposition, and skeletal muscle growth in the Shaziling pig. These results provide candidate genes for improving meat quality and will promote further transcriptomic research in Shaziling pigs.
Subject(s)
Gene Expression Profiling , Muscle, Skeletal/metabolism , Proteomics , Animals , Male , Molecular Sequence Annotation , Muscle, Skeletal/growth & development , RNA, Messenger/genetics , RNA, Messenger/metabolism , Species Specificity , SwineABSTRACT
Sandu black pig is one of the native breed in Guizhou province in China. The total length of mitochondrial genome of Sandu black pig is 16,741 bp. Mitochondrial genome contains a major non-coding control region (D-Loop region), 2 ribosomal RNA genes, 13 protein-coding genes (PCGs) and 22 transfer RNA genes. This is the first report of the complete mitochondrial genome sequence about Sandu black pig. The mitochondrial genome data of Sandu black pig presented is useful novel markers for further studying the population genetics of sus scrofa.
Subject(s)
Genome, Mitochondrial/genetics , Sus scrofa/genetics , Animals , Genetics, Population , Open Reading Frames/genetics , RNA, Ribosomal/genetics , RNA, Transfer/genetics , Sus scrofa/classificationABSTRACT
In the present study, the ear tissue of an adult Laiwu Black pig is from the Shandong province of China. The complete mitochondrial genome of Laiwu Black pig was determined by polymerase chain reaction (PCR). The complete mitochondrial genome is 16,710 bp, and it contains 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, a control region (D-loop), with the genome organization and gene order being identical to that of the typical vertebrates.
Subject(s)
Genome, Mitochondrial/physiology , Sus scrofa/genetics , Animals , Base Sequence , Mitochondrial Proteins/genetics , Molecular Sequence Data , RNA/genetics , RNA, Mitochondrial , RNA, Ribosomal/genetics , RNA, Transfer/geneticsABSTRACT
Rongchang pig is one of the native breeds in Sichuan province in China. The total length of mitochondrial genome of Rongchang pig is 16,710 bp, including 34.67% A, 26.18% C, 25.82% T and 13.33% G, and in the order A > C > T > G. Mitochondrial genome contains a major non-coding control region (D-Loop region), 2 ribosomal RNA genes, 13 protein-coding genes (PCGs) and 22 transfer RNA genes. This is the first report of the complete mitochondrial genome sequence about Rongchang pig. The mitochondrial genome of Rongchang pig subsequently provides an important information in genetic mechanism and the evolution genomes.
Subject(s)
Genome, Mitochondrial , Sequence Analysis, DNA/methods , Sus scrofa/genetics , Animals , Base Composition , Gene Order , Genome Size , Mitochondria/geneticsABSTRACT
In this study, the complete mitochondrial genome sequence of Diannan small-ear pig in Yunnan Province was firstly reported, which was determined through polymerase chain reaction (PCR) method. The total length of mitochondrial genome of Diannan small-ear pig was 16720 bp, including 34.77% A, 26.18% C, 25.81% T and 13.24% G, and in the order A > C > T > G. Mitochondrial genome contained a major non-coding control region (D-Loop region), 2 ribosomal RNA genes, 13 protein-coding genes (PCGs) and 22 transfer RNA genes. The mitochondrial genome of Diannan small-ear pig provides an important data set for the study on genetic mechanism.
Subject(s)
Genome, Mitochondrial , Sequence Analysis, DNA/methods , Sus scrofa/genetics , Animals , Base Composition , Gene Order , Genome Size , Mitochondria/geneticsABSTRACT
In this study, the total length of mitochondrial genome of Duroc pig is 16,731 bp, including 34.66% A, 26.27% C, 25.74% T and 13.33% G. Mitochondrial genome contains a major non-coding control region (D-Loop region), 2 ribosomal RNA genes, 13 protein-coding genes (PCGs) and 22 transfer RNA genes. ND2 selects ATT as the initiation codon, and ATA is chose as an initiation codon in ND3 and ND5, the nonstandard start codon is GTG in ND4L and the rest protein common start codon is ATG. The mitochondrial genome of Duroc pig provides an important data in genetic mechanism, which plays an important role in the three-way crossbred pigs.
Subject(s)
Genome, Mitochondrial , Sus scrofa/genetics , Animals , Base Pairing/genetics , Base Sequence , Codon/genetics , DNA, Mitochondrial/genetics , Open Reading Frames/geneticsABSTRACT
The complete mitochondrial nucleotide sequence of the Bama miniature pig was sequenced in this study. This sequence is homologous to that of the other vertebrate mitochondrial genome. The mitochondrial genome of the Bama miniature pig is 16,711 bp and contains 37 genes including 22 tRNA genes, 13 protein-coding genes (PCGs), 2 ribosomal RNA genes and 1 control region (D-loop). The 13 PCGs initiated with ATN as start codon and terminated with TAA, TA or T as stop codon. The DNA sequence in the Bama miniature pig D-loop region contains the repeat motif (-TACACGTGCG-) and 5'nucleotide of the first repeat is at the position 796 bp.
Subject(s)
Genome, Mitochondrial/genetics , Sequence Analysis, DNA , Swine, Miniature/genetics , Swine/genetics , Animals , Genes, rRNA , Molecular Sequence Annotation , Molecular Sequence Data , Open Reading Frames/genetics , RNA, Transfer/geneticsABSTRACT
In the present study, we sequenced the complete mitochondrial genome of Wuzhishan pig, which was 16,741 bp in size and had a nucleotide composition in A and T (60.46%). The genome consisted of a major non-coding control region (D-loop region) and 37 genes, including 2 ribosomal RNA (rRNA) genes, 13 protein-coding genes (PCGs), and 22 transfer RNA (tRNA) genes. The genes in the mitochondrial genomes of Wuzhishan pig used three kinds of initiation codons (ATA, ATG, and GTG) and four kinds of termination codons (TAA, AGA, TAG, and an incomplete termination codons T-). The complete mitochondrial genome sequence of Wuzhishan pig provides an important data set for further study on genetic mechanism.
Subject(s)
Genome, Mitochondrial/genetics , Sequence Analysis, DNA , Sus scrofa/genetics , Animals , Codon , Genes, rRNA , Molecular Sequence Annotation , Molecular Sequence Data , Open Reading Frames/genetics , RNA, Transfer/geneticsABSTRACT
In this study, the complete mitochondrial genome sequence of the Shaziling pig was reported in Human Province, which was determined through PCR-based method. The total length of the mitogenome is 16,690 bp. It contains the typical structure, including 2 ribosomal RNA genes, 13 protein-coding genes, 22 transfer RNA genes and 1 non-coding control region (D-loop region) as that of most other vertebrates. The overall composition of the mitogenome was estimated to be 34.67% for A, 25.84% for T, 26.17% for C and 13.32% for G, with an A + T (60.51%)-rich feature in the Shaziling pig. All the protein initiation codons are ATG, except for ND2, ND3 and ND5 are ATA, ND4L is GTG, ND6 is TTA. The complete mitochondrial genome sequence of the Shaziling pig in Human Province provides an important data set for the study in genetic mechanism.
Subject(s)
DNA, Mitochondrial/chemistry , Genome, Mitochondrial , Swine/genetics , Animals , Base Sequence , Genes, Mitochondrial , Genome Size , Molecular Sequence Data , Sequence Analysis, DNAABSTRACT
In this work, we reported the complete mitochondrial genome sequence of the Ningxiang pig (Human Province), which was determined through PCR-based method. The total length of the mitogenome is 16,690 bp. The overall composition of the mitogenome was estimated to be 34.70% for A, 25.81% for T, 26.18% for C, 13.30% for G, respectively, indicating that an A + T(60.52%)-rich feature occurs in the Ningxiang pig. It contains the typical structure, including 2 ribosomal RNA genes, 13 protein-coding genes, 22 transfer RNA genes and 1 non-coding control region (D-loop region). The arrangement of these genes was the same as that found in the Landrace pig. All the protein initiation codons are ATG, except for ND2. ND3 and ND5 are ATA, ND4L is GTG. The complete mitochondrial genome sequence of the Ningxiang pig in Human Province provides an important data for further study about genetic mechanism.
Subject(s)
DNA, Mitochondrial/chemistry , Genome, Mitochondrial , Swine/genetics , Animals , Base Composition , Base Sequence , Genes, Mitochondrial , Genome Size , Molecular Sequence Data , Sequence Analysis, DNAABSTRACT
Daweizi pig is one of the famous native breed in China. In this work we reported the complete mitochondrial genome sequence of the Daweizi pig in Human Province for the first time. The total length of the mitogenome is 16,690 bp, with the base composition of 34.68% for A, 25.80% for T, 26.21% for C, 13.31% for G and an A + T (60.48%)-rich feature occurs in the Daweizi pig. It is made up of two ribosomal RNA genes, 13 protein-coding genes, 22 transfer RNA genes and one non-coding control region (D-loop region). The arrangement of these genes was the same as that found in the Landrace pig. The complete mitochondrial genome sequence of the Daweizi pig provides an important data set for further study on the germplasm resources.
Subject(s)
DNA, Mitochondrial/chemistry , Genome, Mitochondrial , Swine/genetics , Animals , Base Composition , Base Sequence , Genes, Mitochondrial , Genome Size , Molecular Sequence Data , Sequence Analysis, DNAABSTRACT
Duroc (â) × [Landrace (â) × Yorshire (â)] (D × LY) pig is the popular hybrid pigs in order to make the most use of the heterosis in the world. In this study, the complete nucleotide sequence of D × LY pig mitochondrial genome was determined for the first time. Sequence analysis showed that the genome structure was in accordance with other pig breeds. It contained 22 tRNA genes, 2 ribosomal RNA genes, 13 protein-coding genes and 1 control region (D-loop region). The complete mitochondrial genome sequence of the D × LY pig provides an important data set for further study in genetic mechanism.
Subject(s)
Genome, Mitochondrial , Mitochondria/genetics , Swine/genetics , Animals , Base Composition , Female , Inbreeding , Male , Molecular Sequence Data , Sequence Analysis, DNAABSTRACT
The complete mitochondrial genome sequence of Qianshao spotted pig was first determined in this study. The mitogenome (16,700 bp) consists of 22 tRNA genes, 2 ribosomal RNA genes, 13 protein-coding genes and 1 control region (D-loop region). The complete mitochondrial genome sequence of the Qianshao spotted pig enriches data resource for further study in genetic mechanism.
Subject(s)
DNA, Mitochondrial/analysis , Genome, Mitochondrial , Swine/genetics , Animals , DNA, Mitochondrial/genetics , Molecular Sequence Data , Open Reading Frames/genetics , RNA, Transfer/genetics , Sequence Analysis, DNA , Swine/classificationABSTRACT
Taoyuan Black pig is the native breed of Hunan province in China. In this study, the complete nucleotide sequence of Taoyuan Black pig mitochondrial genome was first determined. Sequence analysis showed that the genome structure was in accordance with other pig breeds. It contained 22 tRNA genes, 2 ribosomal RNA genes, 13 protein-coding genes and 1 control region (D-loop region). The complete mitochondrial genome sequence of the Taoyuan Black pig provides an important data set for further study on genetic mechanism.
Subject(s)
Genome, Mitochondrial , Genomics , Swine/genetics , Animals , Base Composition , Codon , Genes, Mitochondrial , Genomics/methods , Molecular Sequence Data , Open Reading Frames , Sequence Analysis, DNAABSTRACT
Diacylgycerol acyltransferase2 (DGAT2) is an important enzyme in many organisms. DGAT2 catalyzes the final step of triacylglycerol (TAG) biosynthesis by converting diacylgycerol (DAG) and fatty acyl-coenzyme A (CoA) into TAG. This enzyme is encoded by both DGAT2 and DGAT1 genes. This paper reviews the discovery of the DGAT2 gene, its structure, chromosomal location and biological effect. The relationship between its genetic polymorphisms and animal performance traits is also discussed. The review ends with future prospects.
Subject(s)
Diacylglycerol O-Acyltransferase/genetics , Diacylglycerol O-Acyltransferase/physiology , Animals , Diacylglycerol O-Acyltransferase/metabolism , Humans , Polymorphism, Genetic/genetics , Triglycerides/metabolismABSTRACT
Diacylgycerol Acyltransferase (DGAT) plays an important role in the formation of lipid in different tissues of biological body. DGAT catalyzes the final step in triacylglycerol (TAG) biosynthesis by converting diacylgycerol (DAG) and fatty acyl-coenzyme A (CoA) into triacylglycerol. This enzyme is coded by both DGAT1 and DGAT2. DGAT1 belongs to the gene family of cholesterol acyltransferase (ACAT). DGAT2 belongs to the gene family of monoacylgycerol acyltransferases (MGAT1). This paper reviewed the structure, location on chromosome and biological effect of DGAT-related genes. The relationship between polymorphism and performance of animal was also discussed.
