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He J, Yu M, Chi C, Du Z, Zheng Y, Chen C, Moawad AS, Song C, Wang X. Insertion of 643bp Retrotransposon Upstream of PPARγ CDS Is Associated with Backfat of Large White Pigs. Animals (Basel) 2023; 13:2355. [PMID: 37508132 PMCID: PMC10376311 DOI: 10.3390/ani13142355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 07/16/2023] [Accepted: 07/17/2023] [Indexed: 07/30/2023] Open
Abstract
PPARs are essential regulators of mammalian fatty acid and lipid metabolism. Although the effects of genetic variations, including single nucleotide polymorphisms (SNPs) in PPARs genes on the phenotype of domestic animals have been investigated, there is limited information on the impact of retrotransposon insertion polymorphisms (RIPs). In this study, a combined comparative genome and polymerase chain reaction (PCR) was used to excavate the RIPs in porcine PPARs. We also investigated the potential effects of retrotransposon insertion on phenotype and expression patterns. This study identified the two RIPs in PPARs genes, namely an ERV in intron 1 of PPARα and a combined retrotransposon in intron 2 of PPARγ, designated as PPARα-ERV-RIP and PPARγ-COM-RIP, respectively. These RIPs exhibited different distribution patterns among Chinese indigenous breeds and Western commercial breeds. Individuals with the PPARα-ERV-RIP+/+ genotype (+/+ indicated homozygous with insertion) among Large White pigs had significantly higher (p < 0.05) corrected backfat thickness compared to those with the other two genotypes. Similarly, those with the PPARγ-COM-RIP-/- genotype had significantly higher (p < 0.05) corrected backfat thickness than those with the other two genotypes in Large White pigs. Moreover, in 30-day-old Sujiang piglets, the PPARγ gene expression in the backfat of those with the PPARγ-COM-RIP-/- genotype (-/- indicated homozygous without insertion) was significantly greater (p < 0.01) than those with other genotypes. The dual luciferase reporter gene assay demonstrated that the combined retrotransposon insertion significantly reduced the activity of the MYC promoter in both C2C12 and 3T3-L1 cells (p < 0.01). Therefore, the combined retrotransposon insertion could function as a repressor to decrease the expression of PPARγ, making PPARγ-COM-RIP a valuable molecular marker for assisted selection of backfat thickness in pig breeding.
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Affiliation(s)
- Jia He
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Miao Yu
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Chenglin Chi
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Zhanyu Du
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Yao Zheng
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Cai Chen
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Ali Shoaib Moawad
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
- Department of Animal Production, Faculty of Agriculture, Kafrelsheikh University, Kafrelsheikh 33516, Egypt
| | - Chengyi Song
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Xiaoyan Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
- International Joint Research Laboratory in Universities of Jiangsu Province of China for Domestic Animal Germplasm Resources and Genetic Improvement, Yangzhou 225009, China
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Liao S, Liu G, Tan B, Qi M, Wu X, Li J, Li X, Zhu C, Huang J, Zhang S, Tang Y, Yin Y. Dietary zero-dimensional fullerene supplementation improves the meat quality, lipid metabolism, muscle fiber characteristics, and antioxidative status in finishing pigs. ANIMAL NUTRITION 2022; 11:171-180. [PMID: 36254219 PMCID: PMC9550521 DOI: 10.1016/j.aninu.2022.06.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 04/27/2022] [Accepted: 06/20/2022] [Indexed: 12/04/2022]
Abstract
With the increasing demand for high-quality pork, more nutritional substances have been studied for the regulation of meat quality. Zero-dimensional fullerenes (C60) can modulate the biological behavior of a variety of cell lines and animals. In this study, we report the biological effects of C60 on finishing pigs at different concentrations. A total of 24 barrows (Duroc × Large White × Landrace), with an average body weight of 21.01 ± 0.98 kg, were divided into 3 groups and each treated daily with C60 (100 or 200 mg per kg feed) or a control diet until the end of the experiment. Our results showed that dietary C60 supplementation improved flesh color, marbling scores, and flavor amino acid contents of longissimus dorsi (LD) of growing-finishing pigs (P < 0.05). C60 improved meat quality by regulating lipid metabolism and muscle fiber morphology by mediating the expression of genes, L-lactic dehydrogenase (LDH), myosin heavy chain (MyHC) IIa, MyHCIIb, peroxisome proliferator-activated receptor γ (PPARγ), and fatty acid transport protein 1 (FATP1) (P < 0.05). Moreover, C60 substantially promoted the mRNA expression of antioxidant enzyme genes (P < 0.05), which also contributed to improving meat quality. These findings have important implications for the application of C60 in the livestock industry, especially for improving the meat quality of fattening pigs.
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Affiliation(s)
- Simeng Liao
- Laboratory of Animal Nutritional Physiology and Metabolic Process, Key Laboratory of Agro-Ecological Processes in Subtropical Region, National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, 410125, China
- University of Chinese Academy of Sciences, Beijing, 100008, China
| | - Guang Liu
- Laboratory of Animal Nutritional Physiology and Metabolic Process, Key Laboratory of Agro-Ecological Processes in Subtropical Region, National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, 410125, China
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, 410128, China
| | - Bie Tan
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, 410128, China
| | - Ming Qi
- Laboratory of Animal Nutritional Physiology and Metabolic Process, Key Laboratory of Agro-Ecological Processes in Subtropical Region, National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, 410125, China
- University of Chinese Academy of Sciences, Beijing, 100008, China
| | - Xin Wu
- Laboratory of Animal Nutritional Physiology and Metabolic Process, Key Laboratory of Agro-Ecological Processes in Subtropical Region, National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, 410125, China
| | - Jianjun Li
- Laboratory of Animal Nutritional Physiology and Metabolic Process, Key Laboratory of Agro-Ecological Processes in Subtropical Region, National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, 410125, China
| | - Xiaoqing Li
- Xiamen Funano New Material Technology Company, Ltd, Xiamen, 361005, China
| | - Changfeng Zhu
- Xiamen Funano New Material Technology Company, Ltd, Xiamen, 361005, China
| | - Jiamei Huang
- Xiamen Funano New Material Technology Company, Ltd, Xiamen, 361005, China
| | - Shuo Zhang
- Laboratory of Animal Nutritional Physiology and Metabolic Process, Key Laboratory of Agro-Ecological Processes in Subtropical Region, National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, 410125, China
- Yunnan Southwest Agriculture and Animal Husbandry Group, Kunming, 650217, China
| | - Yulong Tang
- Laboratory of Animal Nutritional Physiology and Metabolic Process, Key Laboratory of Agro-Ecological Processes in Subtropical Region, National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, 410125, China
- Corresponding author.
| | - Yulong Yin
- Laboratory of Animal Nutritional Physiology and Metabolic Process, Key Laboratory of Agro-Ecological Processes in Subtropical Region, National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, 410125, China
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, 410128, China
- Corresponding author.
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Solé E, González-Prendes R, Oliinychenko Y, Tor M, Ros-Freixedes R, Estany J, Pena RN. Transcriptome shifts triggered by vitamin A and SCD genotype interaction in Duroc pigs. BMC Genomics 2022; 23:16. [PMID: 34991486 PMCID: PMC8739656 DOI: 10.1186/s12864-021-08244-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 12/08/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The composition of intramuscular fat depends on genetic and environmental factors, including the diet. In pigs, we identified a haplotype of three SNP mutations in the stearoyl-coA desaturase (SCD) gene promoter associated with higher content of monounsaturated fatty acids in intramuscular fat. The second of these three SNPs (rs80912566, C > T) affected a putative retinol response element in the SCD promoter. The effect of dietary vitamin A restriction over intramuscular fat content is controversial as it depends on the pig genetic line and the duration of the restriction. This study aims to investigate changes in the muscle transcriptome in SCD rs80912566 TT and CC pigs fed with and without a vitamin A supplement during the fattening period. RESULTS Vitamin A did not affect carcass traits or intramuscular fat content and fatty acid composition, but we observed an interaction between vitamin A and SCD genotype on the desaturation of fatty acids in muscle. As reported before, the SCD-TT pigs had more monounsaturated fat than the SCD-CC animals. The diet lacking the vitamin A supplement enlarged fatty acid compositional differences between SCD genotypes, partly because vitamin A had a bigger effect on fatty acid desaturation in SCD-CC pigs (positive) than in SCD-TT and SCD-TC animals (negative). The interaction between diet and genotype was also evident at the transcriptome level; the highest number of differentially expressed genes were detected between SCD-TT pigs fed with the two diets. The genes modulated by the diet with the vitamin A supplement belonged to metabolic and signalling pathways related to immunity and inflammation, transport through membrane-bounded vesicles, fat metabolism and transport, reflecting the impact of retinol on a wide range of metabolic processes. CONCLUSIONS Restricting dietary vitamin A during the fattening period did not improve intramuscular fat content despite relevant changes in muscle gene expression, both in coding and non-coding genes. Vitamin A activated general pathways of retinol response in a SCD genotype-dependant manner, which affected the monounsaturated fatty acid content, particularly in SCD-CC pigs.
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Affiliation(s)
- Emma Solé
- Departament de Ciència Animal, Universitat de Lleida - AGROTECNIO-CERCA Center, Av. Rovira Roure 191, 25197, Lleida, Spain
| | - Rayner González-Prendes
- Departament de Ciència Animal, Universitat de Lleida - AGROTECNIO-CERCA Center, Av. Rovira Roure 191, 25197, Lleida, Spain.,Animal Breeding and Genomics, Wageningen University & Research, 6708PB, Wageningen, The Netherlands
| | | | - Marc Tor
- Departament de Ciència Animal, Universitat de Lleida - AGROTECNIO-CERCA Center, Av. Rovira Roure 191, 25197, Lleida, Spain
| | - Roger Ros-Freixedes
- Departament de Ciència Animal, Universitat de Lleida - AGROTECNIO-CERCA Center, Av. Rovira Roure 191, 25197, Lleida, Spain
| | - Joan Estany
- Departament de Ciència Animal, Universitat de Lleida - AGROTECNIO-CERCA Center, Av. Rovira Roure 191, 25197, Lleida, Spain
| | - Ramona N Pena
- Departament de Ciència Animal, Universitat de Lleida - AGROTECNIO-CERCA Center, Av. Rovira Roure 191, 25197, Lleida, Spain.
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Analysis of long intergenic non-coding RNAs transcriptomic profiling in skeletal muscle growth during porcine embryonic development. Sci Rep 2021; 11:15240. [PMID: 34315913 PMCID: PMC8316452 DOI: 10.1038/s41598-021-94014-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Accepted: 07/05/2021] [Indexed: 11/08/2022] Open
Abstract
Skeletal muscle growth plays a critical role during porcine muscle development stages. Genome-wide transcriptome analysis reveals that long intergenic non-coding RNAs (lincRNAs) are implicated as crucial regulator involving in epigenetic regulation. However, comprehensive analysis of lincRNAs in embryonic muscle development stages remain still elusive. Here, we investigated the transcriptome profiles of Duroc embryonic muscle tissues from days 33, 65, and 90 of gestation using RNA-seq, and 228 putative lincRNAs were identified. Moreover, these lincRNAs exhibit the characteristics of shorter transcripts length, longer exons, less exon numbers and lower expression level compared with protein-coding transcripts. Expression profile analysis showed that a total of 120 lincRNAs and 2638 mRNAs were differentially expressed. In addition, we also performed quantitative trait locus (QTL) mapping analysis for differentially expressed lincRNAs (DE lincRNAs), 113 of 120 DE lincRNAs were localized on 2200 QTLs, we observed many QTLs involved in growth and meat quality traits. Furthermore, we predicted potential target genes of DE lincRNAs in cis or trans regulation. Gene ontology and pathway analysis reveals that potential targets of DE lincRNAs mostly were enriched in the processes and pathways related to tissue development, MAPK signaling pathway, Wnt signaling pathway, TGF-beta signaling pathway and insulin signaling pathway, which involved in skeletal muscle physiological functions. Based on cluster analysis, co-expression network analysis of DE lincRNAs and their potential target genes indicated that DE lincRNAs highly regulated protein-coding genes associated with skeletal muscle development. In this study, many of the DE lincRNAs may play essential roles in pig muscle growth and muscle mass. Our study provides crucial information for further exploring the molecular mechanisms of lincRNAs during skeletal muscle development.
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5
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Mármol-Sánchez E, Luigi-Sierra MG, Castelló A, Guan D, Quintanilla R, Tonda R, Amills M. Variability in porcine microRNA genes and its association with mRNA expression and lipid phenotypes. Genet Sel Evol 2021; 53:43. [PMID: 33947333 PMCID: PMC8097994 DOI: 10.1186/s12711-021-00632-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 04/15/2021] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND Mature microRNAs (miRNAs) play an important role in repressing the expression of a wide range of mRNAs. The presence of polymorphic sites in miRNA genes and their corresponding 3'UTR binding sites can disrupt canonical conserved miRNA-mRNA pairings, and thus modify gene expression patterns. However, to date such polymorphic sites in miRNA genes and their association with gene expression phenotypes and complex traits are poorly characterized in pigs. RESULTS By analyzing whole-genome sequences from 120 pigs and wild boars from Europe and Asia, we identified 285 single nucleotide polymorphisms (SNPs) that map to miRNA loci, and 109,724 SNPs that are located in predicted 7mer-m8 miRNA binding sites within porcine 3'UTR. In porcine miRNA genes, SNP density is reduced compared with their flanking non-miRNA regions. By sequencing the genomes of five Duroc boars, we identified 12 miRNA SNPs that were subsequently genotyped in their offspring (N = 345, Lipgen population). Association analyses of miRNA SNPs with 38 lipid-related traits and hepatic and muscle microarray expression phenotypes recorded in the Lipgen population were performed. The most relevant detected association was between the genotype of the rs319154814 (G/A) SNP located in the apical loop of the ssc-miR-326 hairpin precursor and PPP1CC mRNA levels in the liver (q-value = 0.058). This result was subsequently confirmed by qPCR (P-value = 0.027). The rs319154814 (G/A) genotype was also associated with several fatty acid composition traits. CONCLUSIONS Our findings show a reduced variability of porcine miRNA genes, which is consistent with strong purifying selection, particularly in the seed region that plays a critical role in miRNA binding. Although it is generally assumed that SNPs mapping to the seed region are those with the most pronounced consequences on mRNA expression, we show that a SNP mapping to the apical region of ssc-miR-326 is significantly associated with hepatic mRNA levels of the PPP1CC gene, one of its predicted targets. Although experimental confirmation of such an interaction is reported in humans but not in pigs, this result highlights the need to further investigate the functional effects of miRNA polymorphisms that are located outside the seed region on gene expression in pigs.
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Affiliation(s)
- Emilio Mármol-Sánchez
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - María Gracia Luigi-Sierra
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Anna Castelló
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain.,Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain
| | - Dailu Guan
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Raquel Quintanilla
- Animal Breeding and Genetics Program, Institute for Research and Technology in Food and Agriculture (IRTA), Torre Marimon, 08140, Caldes de Montbui, Spain
| | - Raul Tonda
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Marcel Amills
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain. .,Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain.
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6
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Fu Y, Wang L, Tang Z, Yin D, Xu J, Fan Y, Li X, Zhao S, Liu X. An integration analysis based on genomic, transcriptomic and QTX information reveals credible candidate genes for fat-related traits in pigs. Anim Genet 2020; 51:683-693. [PMID: 32557818 DOI: 10.1111/age.12971] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Revised: 05/15/2020] [Accepted: 05/23/2020] [Indexed: 12/27/2022]
Abstract
Meat quality improvement is of great interest to researchers in pig breeding and many researchers have identified abundant associated quantitative trait loci, genes and polymorphisms (QTXs) for fat-related traits. However, it is challenging to determine credible candidate genes from a mass of associations. The efficiency of identification of credible candidate genes in these QTXs is restricted by limited integration analyses of data from multiple omics. In this study, we constructed a 'candidate gene map' of fat-related traits in pigs based on published literature and the latest genome. In total, 6,861 QTXs, which covered 9,323 genes on the pig genome, were used. Combining the QTX hotspots and pathway analysis, we identified 180 candidate genes that may regulate the fat-related traits, and choose PNPLA2, PPARG, SREBF1, ACACA, PPARD and PPARA as credible candidate genes. In addition, we discussed the importance of incorporating transcriptome data and genomic data in causal gene identification, and the multi-omics information can effectively improve the credibility of identified candidate genes.
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Affiliation(s)
- Y Fu
- School of Computer Science and Technology, Wuhan University of Technology, Wuhan, Hubei, 430070, China.,Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture and College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - L Wang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture and College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Z Tang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture and College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - D Yin
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture and College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - J Xu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture and College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Y Fan
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture and College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - X Li
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture and College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - S Zhao
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture and College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - X Liu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture and College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
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Wang Y, Zhang W, Wu X, Wu C, Qian L, Wang L, Zhang X, Yang M, Li D, Ding J, Wang C, Yin Z, Ding Y. Transcriptomic comparison of liver tissue between Anqing six-end-white pigs and Yorkshire pigs based on RNA sequencing. Genome 2020; 63:203-214. [DOI: 10.1139/gen-2019-0105] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Chinese indigenous pig and Western commercial pig breeds show different patterns of lipid metabolism, fat deposition, and fatty acid composition; for these reasons, they have become vitally important models of energy metabolism and obesity in humans. To compare the mechanisms underlying lipid metabolism between Yorkshire pigs (lean type) and Anqing six-end-white pigs (obese type), the liver transcriptomes of six castrated boars with a body weight of approximately 100 kg (three Yorkshire and three Anqing) were analyzed by RNA-seq. The total number of reads produced for each liver sample ranged from 47.05 to 62.6 million. Among 362 differentially expressed genes, 142 were up-regulated and 220 were down-regulated in Anqing six-end-white pigs. Based on these data, 79 GO terms were significantly enriched. The top 10 (the 10 with lowest corrected P-value) significantly enriched GO terms were identified, including lipid metabolic process and carboxylic acid metabolic process. Pathway analysis revealed three significantly enriched KEGG pathways including PPAR signaling pathway, steroid hormone biosynthesis, and retinol metabolism. Based on protein–protein interaction networks, multiple genes responsible for lipid metabolism were identified, such as PCK1, PPARA, and CYP7A1, and these were considered promising candidate genes that could affect porcine liver lipid metabolism and fat deposition. Our results provide abundant transcriptomic information that will be useful for animal breeding and biomedical research.
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Affiliation(s)
- Yuanlang Wang
- Anhui Provincial Laboratory of Local Animal Genetic Resource Conservation and Bio-Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Wei Zhang
- Anhui Provincial Laboratory of Local Animal Genetic Resource Conservation and Bio-Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Xudong Wu
- Anhui Provincial Laboratory of Local Animal Genetic Resource Conservation and Bio-Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Chaodong Wu
- Anhui Provincial Laboratory of Local Animal Genetic Resource Conservation and Bio-Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Li Qian
- Anhui Provincial Laboratory of Local Animal Genetic Resource Conservation and Bio-Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Li Wang
- Anhui Provincial Laboratory of Local Animal Genetic Resource Conservation and Bio-Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Xiaodong Zhang
- Anhui Provincial Laboratory of Local Animal Genetic Resource Conservation and Bio-Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Min Yang
- Anhui Provincial Laboratory of Local Animal Genetic Resource Conservation and Bio-Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Dengtao Li
- Anhui Provincial Laboratory of Local Animal Genetic Resource Conservation and Bio-Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Jian Ding
- Anhui Provincial Laboratory of Local Animal Genetic Resource Conservation and Bio-Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Chonglong Wang
- Key Laboratory of Pig Molecular Quantitative Genetics of Anhui Academy of Agricultural Sciences, Anhui Provincial Key Laboratory of Livestock and Poultry Product Safety Engineering, Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei, Anhui 230031, China
| | - Zongjun Yin
- Anhui Provincial Laboratory of Local Animal Genetic Resource Conservation and Bio-Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Yueyun Ding
- Anhui Provincial Laboratory of Local Animal Genetic Resource Conservation and Bio-Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui 230036, China
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8
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Stachowiak M, Szczerbal I, Flisikowski K. Investigation of allele-specific expression of genes involved in adipogenesis and lipid metabolism suggests complex regulatory mechanisms of PPARGC1A expression in porcine fat tissues. BMC Genet 2018; 19:107. [PMID: 30497374 PMCID: PMC6267897 DOI: 10.1186/s12863-018-0696-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 11/19/2018] [Indexed: 02/06/2023] Open
Abstract
Background The expression of genes involved in regulating adipogenesis and lipid metabolism may affect economically important fatness traits in pigs. Allele-specific expression (ASE) reflects imbalance between allelic transcript levels and can be used to identify underlying cis-regulatory elements. ASE has not yet been intensively studied in pigs. The aim of this investigation was to analyze the differential allelic expression of four genes, PPARA, PPARG, SREBF1, and PPARGC1A, which are involved in the regulation of fat deposition in porcine subcutaneous and visceral fat and longissimus dorsi muscle. Results Quantification of allelic proportions by pyrosequencing revealed that both alleles of PPARG and SREBF1 are expressed at similar levels. PPARGC1A showed the greatest ASE imbalance in fat deposits in Polish Large White (PLW), Polish Landrace and Pietrain pigs; and PPARA in PLW pigs. Significant deviations of mean PPARGC1A allelic transcript ratio between cDNA and genomic DNA were detected in all tissues, with the most pronounced difference (p < 0.001) in visceral fat of PLW pigs. To search for potential cis-regulatory elements affecting ASE in the PPARGC1A gene we analyzed the effects of four SNPs (rs337351686, rs340650517, rs336405906 and rs345224049) in the promoter region, but none were associated with ASE in the breeds studied. DNA methylation analysis revealed significant CpG methylation differences between samples showing balanced (allelic transcript ratio ≈1) and imbalanced allelic expression for CpG site at the genomic position in chromosome 8 (SSC8): 18527678 in visceral fat (p = 0.017) and two CpG sites (SSC8:18525215, p = 0.030; SSC8:18525237, p = 0.031) in subcutaneous fat. Conclusions Our analysis of differential allelic expression suggests that PPARGC1A is subjected to cis-regulation in porcine fat tissues. Further studies are necessary to identify other regulatory elements localized outside the PPARGC1A proximal promoter region. Electronic supplementary material The online version of this article (10.1186/s12863-018-0696-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Monika Stachowiak
- Department of Genetics and Animal Breeding, Poznan University of Life Sciences, Wolynska 33, 60-637, Poznan, Poland.
| | - Izabela Szczerbal
- Department of Genetics and Animal Breeding, Poznan University of Life Sciences, Wolynska 33, 60-637, Poznan, Poland
| | - Krzysztof Flisikowski
- Chair of Livestock Biotechnology, Technical University of Munich, Liesel-Beckmannstr. 1, 85354, Freising, Germany
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Polasik D, Tyra M, Żak G, Terman A. An analysis of MYH7 single nucleotide polymorphism (g.7:75667956G>A) in relation to growth and carcass traits in pigs. JOURNAL OF ANIMAL AND FEED SCIENCES 2018. [DOI: 10.22358/jafs/98929/2018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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10
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Jin CL, Wang Q, Zhang ZM, Xu YL, Yan HC, Li HC, Gao CQ, Wang XQ. Dietary Supplementation with Pioglitazone Hydrochloride and Chromium Methionine Improves Growth Performance, Meat Quality, and Antioxidant Ability in Finishing Pigs. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2018; 66:4345-4351. [PMID: 29682966 DOI: 10.1021/acs.jafc.8b01176] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
This work was designed to investigate the synergistic effects of pioglitazone hydrochloride (PGZ) and chromium methionine (CrMet) on meat quality, muscle fatty acid profile, and antioxidant ability of pigs. Pigs in four groups were fed a basic diet or basic diet supplemented with 15 mg/kg of PGZ, 200 μg/kg of CrMet, or 15 mg/kg of PGZ + 200 μg/kg of CrMet. In comparison to the control group, the average daily feed intake, feed/gain ratio, and serum high-density lipoprotein level decreased in the PGZ + CrMet group. Dietary PGZ + CrMet supplementation increased carcass dressing percentage, intramuscular fat, and marbling score. The percentages of C18:1ω-9c, C18:2ω-6c, C18:3ω-3, and polyunsaturated fatty acid (PUFA) in the longissimus thoracis muscle were increased in the PGZ + CrMet group. Greater superoxide dismutase and glutathione peroxidase activities were observed in the PGZ + CrMet group compared to the control group. Collectively, these findings suggested that feed with PGZ and CrMet improved the growth performance and meat quality, especially for PUFA proportions and antioxidant ability.
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Affiliation(s)
- Cheng-Long Jin
- College of Animal Science , South China Agricultural University/Guangdong Provincial Key Laboratory of Animal Nutrition Control/National Engineering Research Center for Breeding Swine Industry , Guangzhou , Guangdong 510642 , People's Republic of China
| | - Qiang Wang
- College of Animal Science , South China Agricultural University/Guangdong Provincial Key Laboratory of Animal Nutrition Control/National Engineering Research Center for Breeding Swine Industry , Guangzhou , Guangdong 510642 , People's Republic of China
| | - Zong-Ming Zhang
- College of Animal Science , South China Agricultural University/Guangdong Provincial Key Laboratory of Animal Nutrition Control/National Engineering Research Center for Breeding Swine Industry , Guangzhou , Guangdong 510642 , People's Republic of China
| | - Yin-Long Xu
- Guangzhou United Bio-Technology Feed Company, Limited , Guangzhou , Guangdong 510545 , People's Republic of China
| | - Hui-Chao Yan
- College of Animal Science , South China Agricultural University/Guangdong Provincial Key Laboratory of Animal Nutrition Control/National Engineering Research Center for Breeding Swine Industry , Guangzhou , Guangdong 510642 , People's Republic of China
| | - Hai-Chang Li
- Department of Surgery, Davis Heart and Lung Research Institute , The Ohio State University , Columbus , Ohio 43210 , United States
| | - Chun-Qi Gao
- College of Animal Science , South China Agricultural University/Guangdong Provincial Key Laboratory of Animal Nutrition Control/National Engineering Research Center for Breeding Swine Industry , Guangzhou , Guangdong 510642 , People's Republic of China
| | - Xiu-Qi Wang
- College of Animal Science , South China Agricultural University/Guangdong Provincial Key Laboratory of Animal Nutrition Control/National Engineering Research Center for Breeding Swine Industry , Guangzhou , Guangdong 510642 , People's Republic of China
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11
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Yang WC, Guo WL, Zan LS, Wang YN, Tang KQ. Bta-miR-130a regulates the biosynthesis of bovine milk fat by targeting peroxisome proliferator-activated receptor gamma. J Anim Sci 2017; 95:2898-2906. [PMID: 28727095 DOI: 10.2527/jas.2017.1504] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Milk fat determines the quality of milk and is also a main targeted trait in dairy cow breeding. Recent studies have revealed important regulatory roles of microRNAs (miRNA) in milk fat synthesis in the mammary gland. However, the role of miRNA in bovine mammary epithelial cells (BMEC) remains largely unknown. In this study, we found that the overexpression of miR-130a significantly decreased cellular triacylglycerol (TAG) levels and suppressed lipid droplet formation, whereas the inhibition of miR-130a resulted in greater lipid droplet formation and TAG accumulation in BMEC. MiR-130a also significantly affected mRNA expression related to milk fat metabolism. Specifically, the overexpression of miR-130a reduced the mRNA expression of , , , and , whereas the downregulation of miR-130a increased the mRNA expression of , , , , , and . Furthermore, western blot analysis revealed the protein level of PPARG in miR-130a mimic and inhibitor transfection groups to be consistent with the mRNA expression response. Finally, luciferase reporter assays verified that PPARG was the direct target of miR-130a. This study provides the first experimental evidence that miR-130a directly affects TAG synthesis in BMEC by targeting PPARG, suggesting that miR-130a potentially could be used to improve beneficial milk components in dairy cows.
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12
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Shen B, Pan Q, Yang Y, Gao Y, Liu X, Li W, Han Y, Yuan X, Qu Y, Zhao Z. miR-224 Affects Mammary Epithelial Cell Apoptosis and Triglyceride Production by Downregulating ACADM and ALDH2 Genes. DNA Cell Biol 2016; 36:26-33. [PMID: 27918674 DOI: 10.1089/dna.2016.3540] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
MicroRNAs (miRNAs) are small noncoding RNA molecules that involve in various biological functions by regulating the expressions of target genes. In recent years, many researchers have demonstrated that miR-224 played an important role in regulating lipid metabolism. Therefore, in this study, the target genes of miR-224 were verified and the regulatory role of miR-224 was confirmed in lipid metabolism. In this study, bioinformatics methods were used for primarily predicting the target gene of miR-224 and dual-luciferase reporter system was used for further verify the relationship between miR-224 and its target gene. Then, the miR-224 mimics, miR-224 inhibitor, and miRNA-ShNC were transfected into mammary epithelial cells (MECs), respectively, and the expression of miR-224 and its target genes was detected by quantitative real-time polymerase chain reaction and Western blot. Furthermore, the triglyceride production and cell apoptosis were detected by triglyceride mensuration reagent kit using flow cytometry. The results showed that ACADM and ALDH2 were predicted to be the target genes of miR-224, primarily by bioinformatics analysis. We founded that miR-224 could recognize with ACADM-3'UTR and ALDH2-3'UTR, indicating that the target sites existed in 3'UTR of ACADM and ALDH2. And then, the expressions of miR-224 had negative trend with the levels of ACADM and ALDH2, suggesting that miR-224 could downregulate the expressions of ACADM and ALDH2. Finally, the triglyceride production decreased and apoptosis rate increased after the overexpression of miR-224 in MECs. The above results indicated that miR-224 regulating target genes in lipid metabolism might be used as a new pathway for better breeding.
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Affiliation(s)
- Binglei Shen
- 1 College of Animal Science, Heilongjiang Bayi Agricultural University , Daqing, People's Republic of China
| | - Qiqi Pan
- 1 College of Animal Science, Heilongjiang Bayi Agricultural University , Daqing, People's Republic of China
| | - Yuwei Yang
- 2 College of Animal Science, Jilin University , Changchun, Jilin, People's Republic of China
| | - Yan Gao
- 1 College of Animal Science, Heilongjiang Bayi Agricultural University , Daqing, People's Republic of China
| | - Xin Liu
- 2 College of Animal Science, Jilin University , Changchun, Jilin, People's Republic of China
| | - Wei Li
- 1 College of Animal Science, Heilongjiang Bayi Agricultural University , Daqing, People's Republic of China
| | - Yunsheng Han
- 1 College of Animal Science, Heilongjiang Bayi Agricultural University , Daqing, People's Republic of China
| | - Xue Yuan
- 1 College of Animal Science, Heilongjiang Bayi Agricultural University , Daqing, People's Republic of China
| | - Yongli Qu
- 1 College of Animal Science, Heilongjiang Bayi Agricultural University , Daqing, People's Republic of China
| | - Zhihui Zhao
- 2 College of Animal Science, Jilin University , Changchun, Jilin, People's Republic of China
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Juszczuk-Kubiak E, Bujko K, Grześ M, Cymer M, Wicińska K, Szostak A, Pierzchała M. Study of bovine gene: the temporal-spatial expression patterns, polymorphism and association analysis with meat production traits. J Anim Sci 2016; 94:4536-4548. [PMID: 27898947 DOI: 10.2527/jas.2016-0741] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The gene () encodes a transcription factor belonging to the MEF2 family that plays an important role in myogenesis by transcriptional regulation of genes involved in skeletal muscle growth and development. Despite the established importance of the factors in the muscular growth and development, the temporal-spatial expression and biological function of have not been reported in cattle. The aim of this study was to analyze the level of expression in the developing longissimus dorsi muscle (LM) of 4 cattle breeds (Polish Holstein-Friesian [HF], Limousine [LIM], Hereford [HER], Polish Red [PR]), differing in terms of meat production and utility type, at 6, 9, and 12 mo of age. The genetic polymorphism and expression patterns in 6 tissues (heart, spleen, liver, semitendinosus muscle [ST], gluteus medius muscle [GM], and LM) were also investigated. The results showed that mRNA was expressed at a high level in adult skeletal and cardiac muscles. Moreover, expression was markedly greater in the GM than in the LM ( 0.05) and ST ( 0.01). An age-dependent and breed-specific comparison of mRNA level in skeletal muscle of HF, LIM, HER, and PR bulls showed that age was significant differentiating factor of transcript/protein abundance in the LM of HER and LIM ( 0.001) compared to HF and PR, for which the differences in mRNA level were not significant ( > 0.05). Regarding the breed effect on the expression, significantly greater mRNA/protein level was noticed in the LM of 9 and 12 mo-old HER than of LIM ( 0.01), HF ( 0.001), and PR ( 0.001). Four novel SNP, namely, (promoter), (exon 7), (exon 8), and (3'UTR), were identified. We found that 3'UTR variant, situated within the seed region of the miR-5187-3p and miR-6931-5p binding sites, was associated with the level of mRNA/protein in LM of 12-mo-old HF bulls. In addition, we observed a significant association between some carcass quality traits, including meat and carcass fatness quality traits, and various 3'UTR genotypes in the investigated population of HF cattle. Our finding provides new evidence of the significant role in the postnatal muscle growth and development in cattle, and indicates that can be a promising molecular marker for carcass quality-related traits in adult cattle.
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Stachowiak M, Szczerbal I, Switonski M. Genetics of Adiposity in Large Animal Models for Human Obesity-Studies on Pigs and Dogs. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2016; 140:233-70. [PMID: 27288831 DOI: 10.1016/bs.pmbts.2016.01.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The role of domestic mammals in the development of human biomedical sciences has been widely documented. Among these model species the pig and dog are of special importance. Both are useful for studies on the etiology of human obesity. Genome sequences of both species are known and advanced genetic tools [eg, microarray SNP for genome wide association studies (GWAS), next generation sequencing (NGS), etc.] are commonly used in such studies. In the domestic pig the accumulation of adipose tissue is an important trait, which influences meat quality and fattening efficiency. Numerous quantitative trait loci (QTLs) for pig fatness traits were identified, while gene polymorphisms associated with these traits were also described. The situation is different in dog population. Generally, excessive accumulation of adipose tissue is considered, similar to humans, as a complex disease. However, research on the genetic background of canine obesity is still in its infancy. Between-breed differences in terms of adipose tissue accumulation are well known in both animal species. In this review we show recent advances of studies on adipose tissue accumulation in pigs and dogs, and their potential importance for studies on human obesity.
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Affiliation(s)
- M Stachowiak
- Department of Genetics, Animal Breeding, Poznań University of Life Sciences, Poznań, Poland
| | - I Szczerbal
- Department of Genetics, Animal Breeding, Poznań University of Life Sciences, Poznań, Poland
| | - M Switonski
- Department of Genetics, Animal Breeding, Poznań University of Life Sciences, Poznań, Poland.
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Zhang YR, Gui LS, Li YK, Jiang BJ, Wang HC, Zhang YY, Zan LS. Molecular Characterization of Bovine SMO Gene and Effects of Its Genetic Variations on Body Size Traits in Qinchuan Cattle (Bos taurus). Int J Mol Sci 2015. [PMID: 26225956 PMCID: PMC4581179 DOI: 10.3390/ijms160816966] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Smoothened (Smo)-mediated Hedgehog (Hh) signaling pathway governs the patterning, morphogenesis and growth of many different regions within animal body plans. This study evaluated the effects of genetic variations of the bovine SMO gene on economically important body size traits in Chinese Qinchuan cattle. Altogether, eight single nucleotide polymorphisms (SNPs: 1-8) were identified and genotyped via direct sequencing covering most of the coding region and 3'UTR of the bovine SMO gene. Both the p.698Ser.>Ser. synonymous mutation resulted from SNP1 and the p.700Ser.>Pro. non-synonymous mutation caused by SNP2 mapped to the intracellular C-terminal tail of bovine Smo protein; the other six SNPs were non-coding variants located in the 3'UTR. The linkage disequilibrium was analyzed, and five haplotypes were discovered in 520 Qinchuan cattle. Association analyses showed that SNP2, SNP3/5, SNP4 and SNP6/7 were significantly associated with some body size traits (p < 0.05) except SNP1/8 (p > 0.05). Meanwhile, cattle with wild-type combined haplotype Hap1/Hap1 had significantly (p < 0.05) greater body length than those with Hap2/Hap2. Our results indicate that variations in the SMO gene could affect body size traits of Qinchuan cattle, and the wild-type haplotype Hap1 together with the wild-type alleles of these detected SNPs in the SMO gene could be used to breed cattle with superior body size traits. Therefore, our results could be helpful for marker-assisted selection in beef cattle breeding programs.
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Affiliation(s)
- Ya-Ran Zhang
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Lin-Sheng Gui
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Yao-Kun Li
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Bi-Jie Jiang
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Hong-Cheng Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Ying-Ying Zhang
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Lin-Sen Zan
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China.
- National Beef Cattle Improvement Center of Northwest A&F University, Yangling 712100, Shaanxi, China.
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