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Hu M, Shi L, Yi W, Li F, Yan S. Identification of genomic diversity and selection signatures in Luxi cattle using whole-genome sequencing data. Anim Biosci 2024; 37:461-470. [PMID: 38271971 PMCID: PMC10915192 DOI: 10.5713/ab.23.0304] [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: 08/15/2023] [Revised: 10/13/2023] [Accepted: 11/28/2023] [Indexed: 01/27/2024] Open
Abstract
OBJECTIVE The objective of this study was to investigate the genetic diversity, population structure and whole-genome selection signatures of Luxi cattle to reveal its genomic characteristics in terms of meat and carcass traits, skeletal muscle development, body size, and other traits. METHODS To further analyze the genomic characteristics of Luxi cattle, this study sequenced the whole-genome of 16 individuals from the core conservation farm in Shandong region, and collected 174 published genomes of cattle for conjoint analysis. Furthermore, three different statistics (pi, Fst, and XP-EHH) were used to detect potential positive selection signatures related to selection in Luxi cattle. Moreover, gene ontology and Kyoto encyclopedia of genes and genomes pathway enrichment analyses were performed to reveal the potential biological function of candidate genes harbored in selected regions. RESULTS The results showed that Luxi cattle had high genomic diversity and low inbreeding levels. Using three complementary methods (pi, Fst, and XP-EHH) to detect the signatures of selection in the Luxi cattle genome, there were 2,941, 2,221 and 1,304 potentially selected genes identified, respectively. Furthermore, there were 45 genes annotated in common overlapping genomic regions covered 0.723 Mb, including PLAG1 zinc finger (PLAG1), dedicator of cytokinesis 3 (DOCK3), ephrin A2 (EFNA2), DAZ associated protein 1 (DAZAP1), Ral GTPase activating protein catalytic subunit alpha 1 (RALGAPA1), mediator complex subunit 13 (MED13), and decaprenyl diphosphate synthase subunit 2 (PDSS2), most of which were enriched in pathways related to muscle growth and differentiation and immunity. CONCLUSION In this study, we provided a series of genes associated with important economic traits were found in positive selection regions, and a scientific basis for the scientific conservation and genetic improvement of Luxi cattle.
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Affiliation(s)
- Mingyue Hu
- Department of Animal Science, Jilin University, Changchun 130062,
China
| | - Lulu Shi
- Department of Animal Science, Jilin University, Changchun 130062,
China
| | - Wenfeng Yi
- Department of Animal Science, Jilin University, Changchun 130062,
China
| | - Feng Li
- Shandong Binzhou Animal Science & Veterinary Medicine Academy, Binzhou, 256600,
China
| | - Shouqing Yan
- Department of Animal Science, Jilin University, Changchun 130062,
China
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Jiang C, Zhang J, Song Y, Song X, Wu H, Jiao R, Li L, Zhang G, Wei D. FOXO1 regulates bovine skeletal muscle cells differentiation by targeting MYH3. Int J Biol Macromol 2024; 260:129643. [PMID: 38253149 DOI: 10.1016/j.ijbiomac.2024.129643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 01/03/2024] [Accepted: 01/18/2024] [Indexed: 01/24/2024]
Abstract
The growth and development of bovine skeletal muscle and beef yield is closely intertwined. Our previous research found that forkhead box O1 (FOXO1) plays an important role in the regulation of beef muscle formation, but its specific mechanism is still unknown. In this study, we aimed to clarify the regulatory mechanism of FOXO1 in proliferation and differentiation of bovine skeletal muscle cells (BSMCs). The results showed that interfering with FOXO1 can promote proliferation and the cell G1/S phase of BSMCs by up-regulating the expression of PCNA, CDK1, CDK2, CCNA2, CCNB1, CCND1 and CCNE2. Besides, interfering with FOXO1 inhibited the apoptosis of BSMCs by up-regulating the expression of anti-apoptosis gene BCL2, while simultaneously down-regulating the expression of the pro-apoptosis genes BAD and BAX. Inversely, interfering with FOXO1 can promote the differentiation of BSMCs by up-regulating the expression of myogenic differentiation marker genes MYOD, MYOG, MYF5, MYF6 and MYHC. Furthermore, RNA-seq combined with western bolt, immunofluorescence and chromatin immunoprecipitation analysis showed that FOXO1 could regulate BSMCs differentiation process by influencing PI3K-Akt, Relaxin and TGF-beta signaling pathways, and target MYH3 for transcriptional inhibition. In conclusion, this study provides a basis for studying the role and molecular mechanism of FOXO1 in BSMCs.
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Affiliation(s)
- Chao Jiang
- College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China; Key Laboratory of Ruminant Molecular Cell Breeding, Ningxia Hui Autonomous Region, Yinchuan 750021, China
| | - Jiupan Zhang
- Institute of Animal Science, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan 750021, China
| | - Yaping Song
- College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China; Key Laboratory of Ruminant Molecular Cell Breeding, Ningxia Hui Autonomous Region, Yinchuan 750021, China
| | - Xiaoyu Song
- College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China; Key Laboratory of Ruminant Molecular Cell Breeding, Ningxia Hui Autonomous Region, Yinchuan 750021, China
| | - Hao Wu
- College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China; Key Laboratory of Ruminant Molecular Cell Breeding, Ningxia Hui Autonomous Region, Yinchuan 750021, China
| | - Ruopu Jiao
- College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China; Key Laboratory of Ruminant Molecular Cell Breeding, Ningxia Hui Autonomous Region, Yinchuan 750021, China
| | - Lanlan Li
- College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China; Key Laboratory of Ruminant Molecular Cell Breeding, Ningxia Hui Autonomous Region, Yinchuan 750021, China
| | - Guijie Zhang
- College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China; Key Laboratory of Ruminant Molecular Cell Breeding, Ningxia Hui Autonomous Region, Yinchuan 750021, China
| | - Dawei Wei
- College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China; Key Laboratory of Ruminant Molecular Cell Breeding, Ningxia Hui Autonomous Region, Yinchuan 750021, China.
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Yang X, Li X, Bao Q, Wang Z, He S, Qu X, Tang Y, Song B, Huang J, Yi G. Uncovering Evolutionary Adaptations in Common Warthogs through Genomic Analyses. Genes (Basel) 2024; 15:166. [PMID: 38397156 PMCID: PMC10888464 DOI: 10.3390/genes15020166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 01/15/2024] [Accepted: 01/20/2024] [Indexed: 02/25/2024] Open
Abstract
In the Suidae family, warthogs show significant survival adaptability and trait specificity. This study offers a comparative genomic analysis between the warthog and other Suidae species, including the Luchuan pig, Duroc pig, and Red River hog. By integrating the four genomes with sequences from the other four species, we identified 8868 single-copy orthologous genes. Based on 8868 orthologous protein sequences, phylogenetic assessments highlighted divergence timelines and unique evolutionary branches within suid species. Warthogs exist on different evolutionary branches compared to DRCs and LCs, with a divergence time preceding that of DRC and LC. Contraction and expansion analyses of warthog gene families have been conducted to elucidate the mechanisms of their evolutionary adaptations. Using GO, KEGG, and MGI databases, warthogs showed a preference for expansion in sensory genes and contraction in metabolic genes, underscoring phenotypic diversity and adaptive evolution direction. Associating genes with the QTLdb-pigSS11 database revealed links between gene families and immunity traits. The overlap of olfactory genes in immune-related QTL regions highlighted their importance in evolutionary adaptations. This work highlights the unique evolutionary strategies and adaptive mechanisms of warthogs, guiding future research into the distinct adaptability and disease resistance in pigs, particularly focusing on traits such as resistance to African Swine Fever Virus.
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Affiliation(s)
- Xintong Yang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China; (X.Y.); (X.L.); (Q.B.); (Z.W.); (S.H.); (X.Q.); (Y.T.); (B.S.)
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530005, China;
| | - Xingzheng Li
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China; (X.Y.); (X.L.); (Q.B.); (Z.W.); (S.H.); (X.Q.); (Y.T.); (B.S.)
| | - Qi Bao
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China; (X.Y.); (X.L.); (Q.B.); (Z.W.); (S.H.); (X.Q.); (Y.T.); (B.S.)
| | - Zhen Wang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China; (X.Y.); (X.L.); (Q.B.); (Z.W.); (S.H.); (X.Q.); (Y.T.); (B.S.)
| | - Sang He
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China; (X.Y.); (X.L.); (Q.B.); (Z.W.); (S.H.); (X.Q.); (Y.T.); (B.S.)
| | - Xiaolu Qu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China; (X.Y.); (X.L.); (Q.B.); (Z.W.); (S.H.); (X.Q.); (Y.T.); (B.S.)
| | - Yueting Tang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China; (X.Y.); (X.L.); (Q.B.); (Z.W.); (S.H.); (X.Q.); (Y.T.); (B.S.)
- School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Bangmin Song
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China; (X.Y.); (X.L.); (Q.B.); (Z.W.); (S.H.); (X.Q.); (Y.T.); (B.S.)
- School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Jieping Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530005, China;
| | - Guoqiang Yi
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China; (X.Y.); (X.L.); (Q.B.); (Z.W.); (S.H.); (X.Q.); (Y.T.); (B.S.)
- Kunpeng Institute of Modern Agriculture at Foshan, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Foshan 528226, China
- Bama Yao Autonomous County Rural Revitalization Research Institute, Bama 547500, China
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Tang J, Yang B, Song G, Zhang X, Wang Z, Mo Z, Zan L, Wang H. Effect of bovine myosin heavy chain 3 on proliferation and differentiation of myoblast. Anim Biotechnol 2023; 34:4337-4346. [PMID: 36441630 DOI: 10.1080/10495398.2022.2149549] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The myosin heavy chain 3 (MYH3) gene is an essential gene that affects muscle development. This study aimed to discuss the expression characteristics of the MYH3 gene and its effect on the proliferation and differentiation of bovine myoblasts. Quantitative real time-PCR results display that the expression level of MYH3 was higher in muscle tissue, and the expression increased in the early stage of myoblast differentiation. Interfering with the MYH3 gene in myoblasts resulted in fewer EDU-positive cells and decreased expression of proliferation marker genes. Interference with MYH3 can also affect the differentiation process of myoblasts. Regarding phenotype, myotube differentiation in the interference group was slowed or even stopped. Interference with the expression of MYH3 could significantly reduce the expression of myogenic differentiation marker genes. The above results show that MYH3 is mainly expressed in muscle tissue and is highly expressed in the early stage of differentiation of bovine myoblasts, and interfering with the MYH3 can promote the proliferation and inhibit the differentiation of bovine myoblasts. This study provides a theoretical basis for revealing the regulatory process of bovine myoblast proliferation and differentiation and bovine molecular breeding.
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Affiliation(s)
- Jiayu Tang
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Bohua Yang
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Guibing Song
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Xinyi Zhang
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Zhicong Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Zhaoyi Mo
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Linsen Zan
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
- National Beef Cattle Improvement Center, Yangling, China
| | - Hongbao Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
- National Beef Cattle Improvement Center, Yangling, China
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5
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Ren P, Chen M, Li J, Lin Z, Yang C, Yu C, Zhang D, Liu Y. MYH1F promotes the proliferation and differentiation of chicken skeletal muscle satellite cells into myotubes. Anim Biotechnol 2023; 34:3074-3084. [PMID: 36244007 DOI: 10.1080/10495398.2022.2132953] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
In diploid organisms, interactions between alleles determine phenotypic variation. In previous experiments, only MYH1F was found to show both ASE (spatiotemporal allele-specific expression) and TRD (allelic transmission ratio distortion) characteristics in the pectoral muscle by comparing the genome-wide allele lists of hybrid populations (F1) of meat- and egg- type chickens. In addition, MYH1F is a member of the MYH gene family, which plays an important role in skeletal muscle and non-muscle cells of animals, but the specific expression and function of this gene in chickens are still unknown. Therefore, qRT-PCR was used to detect the expression of MYH1F in different tissues of chicken. Proliferation and differentiation of chicken skeletal muscle satellite cells (SMSCs) have been detected by transfection of MYH1F-specific small interfering RNA (siRNA). The results showed that the expression of MYH1F in chicken skeletal muscle was higher than that in other tissues. Combined with CCK-8 assay, EdU assay, immunofluorescence, and Western blot Assay, it was found that MYH1F knockdown could significantly suppress the proliferation of chicken SMSCs and depress the differentiation and fusion of the cells. These results suggest that MYH1F plays a critical role in myogenesis in poultry, which is of great significance for exploring the regulatory mechanisms of muscle development and improving animal productivity.
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Affiliation(s)
- Peng Ren
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan, China
| | - Meiying Chen
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan, China
| | - Jingjing Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Zhongzhen Lin
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Chaowu Yang
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, Sichuan, China
| | - Chunlin Yu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, Sichuan, China
| | - Donghao Zhang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yiping Liu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
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6
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Zhou F, Wang S, Qin H, Zeng H, Ye J, Yang J, Cai G, Wu Z, Zhang Z. Genome-wide association analysis unveils candidate genes and loci associated with aplasia cutis congenita in pigs. BMC Genomics 2023; 24:701. [PMID: 37990155 PMCID: PMC10664689 DOI: 10.1186/s12864-023-09803-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Accepted: 11/11/2023] [Indexed: 11/23/2023] Open
Abstract
BACKGROUND Aplasia cutis congenita (ACC) is a rare genetic disorder characterized by the localized or widespread absence of skin in humans and animals. Individuals with ACC may experience developmental abnormalities in the skeletal and muscular systems, as well as potential complications. Localized and isolated cases of ACC can be treated through surgical and medical interventions, while extensive cases of ACC may result in neonatal mortality. The presence of ACC in pigs has implications for animal welfare. It contributes to an elevated mortality rate among piglets at birth, leading to substantial economic losses in the pig farming industry. In order to elucidate candidate genetic loci associated with ACC, we performed a Genome-Wide Association Study analysis on 216 Duroc pigs. The primary goal of this study was to identify candidate genes that associated with ACC. RESULTS This study identified nine significant SNPs associated with ACC. Further analysis revealed the presence of two quantitative trait loci, 483 kb (5:18,196,971-18,680,098) on SSC 5 and 159 kb (13:20,713,440-207294431 bp) on SSC13. By annotating candidate genes within a 1 Mb region surrounding the significant SNPs, a total of 11 candidate genes were identified on SSC5 and SSC13, including KRT71, KRT1, KRT4, ITGB7, CSAD, RARG, SP7, PFKL, TRPM2, SUMO3, and TSPEAR. CONCLUSIONS The results of this study further elucidate the potential mechanisms underlying and genetic architecture of ACC and identify reliable candidate genes. These results lay the foundation for treating and understanding ACC in humans.
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Affiliation(s)
- Fuchen Zhou
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, 510642, P.R. China
| | - Shenghui Wang
- Guangdong Wens Breeding Swine Technology Co., Ltd, Guangdong, 527400, P.R. China
| | - Haojun Qin
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, 510642, P.R. China
| | - Haiyu Zeng
- Guangdong Wens Breeding Swine Technology Co., Ltd, Guangdong, 527400, P.R. China
| | - Jian Ye
- Guangdong Wens Breeding Swine Technology Co., Ltd, Guangdong, 527400, P.R. China
| | - Jie Yang
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, 510642, P.R. China
| | - Gengyuan Cai
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, 510642, P.R. China
- Guangdong Wens Breeding Swine Technology Co., Ltd, Guangdong, 527400, P.R. China
| | - Zhenfang Wu
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, 510642, P.R. China.
- Guangdong Wens Breeding Swine Technology Co., Ltd, Guangdong, 527400, P.R. China.
| | - Zebin Zhang
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, 510642, P.R. China.
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Qiu X, Wang HY, Yang ZY, Sun LM, Liu SN, Fan CQ, Zhu F. Uncovering the prominent role of satellite cells in paravertebral muscle development and aging by single-nucleus RNA sequencing. Genes Dis 2023; 10:2597-2613. [PMID: 37554180 PMCID: PMC10404979 DOI: 10.1016/j.gendis.2023.01.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Revised: 11/06/2022] [Accepted: 01/02/2023] [Indexed: 02/05/2023] Open
Abstract
To uncover the role of satellite cells (SCs) in paravertebral muscle development and aging, we constructed a single-nucleus transcriptomic atlas of mouse paravertebral muscle across seven timepoints spanning the embryo (day 16.5) to old (month 24) stages. Eight cell types, including SCs, fast muscle cells, and slow muscle cells, were identified. An energy metabolism-related gene set, TCA CYCLE IN SENESCENCE, was enriched in SCs. Forty-two skeletal muscle disease-related genes were highly expressed in SCs and exhibited similar expression patterns. Among them, Pdha1 was the core gene in the TCA CYCLE IN SENESCENCE; Pgam2, Sod1, and Suclg1 are transcription factors closely associated with skeletal muscle energy metabolism. Transcription factor enrichment analysis of the 42 genes revealed that Myod1 and Mef2a were also highly expressed in SCs, which regulated Pdha1 expression and were associated with skeletal muscle development. These findings hint that energy metabolism may be pivotal in SCs development and aging. Three ligand-receptor pairs of extracellular matrix (ECM)-receptor interactions, Lamc1-Dag1, Lama2-Dag1, and Hspg2-Dag1, may play a vital role in SCs interactions with slow/fast muscle cells and SCs self-renewal. Finally, we built the first database of a skeletal muscle single-cell transcriptome, the Musculoskeletal Cell Atlas (http://www.mskca.tech), which lists 630,040 skeletal muscle cells and provides interactive visualization, a useful resource for revealing skeletal muscle cellular heterogeneity during development and aging. Our study could provide new targets and ideas for developing drugs to inhibit skeletal muscle aging and treat skeletal muscle diseases.
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Affiliation(s)
- Xin Qiu
- Department of Spinal Surgery, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong 518000, China
- Department of Orthopedics and Traumatology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR 999077, China
| | - Hao-Yu Wang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100000, China
- Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, Qingdao, Shandong 266000, China
| | - Zhen-Yu Yang
- Department of Spinal Surgery, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong 518000, China
| | - Li-Ming Sun
- Department of Plastic and Reconstructive Surgery, Xijing Hospital, Forth Military Medical University, Xi'an, Shaanxi 710000, China
| | - Shu-Nan Liu
- Department of Spinal Surgery, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong 518000, China
| | - Chui-Qin Fan
- China Medical University, Shenyang, Liaoning 110000, China
| | - Feng Zhu
- Department of Spinal Surgery, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong 518000, China
- Department of Orthopedics and Traumatology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR 999077, China
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Lee JB, Lim JH, Park HB. Genome-wide association studies to identify quantitative trait loci and positional candidate genes affecting meat quality-related traits in pigs. JOURNAL OF ANIMAL SCIENCE AND TECHNOLOGY 2023; 65:1194-1204. [PMID: 38616878 PMCID: PMC11007289 DOI: 10.5187/jast.2023.e70] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 06/06/2023] [Accepted: 07/11/2023] [Indexed: 04/16/2024]
Abstract
Meat quality comprises a set of key traits such as pH, meat color, water-holding capacity, tenderness and marbling. These traits are complex because they are affected by multiple genetic and environmental factors. The aim of this study was to investigate the molecular genetic basis underlying nine meat quality-related traits in a Yorkshire pig population using a genome-wide association study (GWAS) and subsequent biological pathway analysis. In total, 45,926 single nucleotide polymorphism (SNP) markers from 543 pigs were selected for the GWAS after quality control. Data were analyzed using a genome-wide efficient mixed model association (GEMMA) method. This linear mixed model-based approach identified two quantitative trait loci (QTLs) for meat color (b*) on chromosome 2 (SSC2) and one QTL for shear force on chromosome 8 (SSC8). These QTLs acted additively on the two phenotypes and explained 3.92%-4.57% of the phenotypic variance of the traits of interest. The genes encoding HAUS8 on SSC2 and an lncRNA on SSC8 were identified as positional candidate genes for these QTLs. The results of the biological pathway analysis revealed that positional candidate genes for meat color (b*) were enriched in pathways related to muscle development, muscle growth, intramuscular adipocyte differentiation, and lipid accumulation in muscle, whereas positional candidate genes for shear force were overrepresented in pathways related to cell growth, cell differentiation, and fatty acids synthesis. Further verification of these identified SNPs and genes in other independent populations could provide valuable information for understanding the variations in pork quality-related traits.
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Affiliation(s)
- Jae-Bong Lee
- Korea Zoonosis Research Institute (KoZRI),
Jeonbuk National University, Iksan 54531, Korea
| | - Ji-Hoon Lim
- Department of Animal Resources Science,
Kongju National University, Yesan 32439, Korea
| | - Hee-Bok Park
- Department of Animal Resources Science,
Kongju National University, Yesan 32439, Korea
- Resource Science Research Institute,
Kongju National University, Yesan 32439, Korea
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9
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Zhang T, Li J, Li X, Liu Y. Intermuscular adipose tissue in obesity and related disorders: cellular origins, biological characteristics and regulatory mechanisms. Front Endocrinol (Lausanne) 2023; 14:1280853. [PMID: 37920255 PMCID: PMC10619759 DOI: 10.3389/fendo.2023.1280853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 10/01/2023] [Indexed: 11/04/2023] Open
Abstract
Intermuscular adipose tissue (IMAT) is a unique adipose depot interspersed between muscle fibers (myofibers) or muscle groups. Numerous studies have shown that IMAT is strongly associated with insulin resistance and muscular dysfunction in people with metabolic disease, such as obesity and type 2 diabetes. Moreover, IMAT aggravates obesity-related muscle metabolism disorders via secretory factors. Interestingly, researchers have discovered that intermuscular brown adipocytes in rodent models provide new hope for obesity treatment by acting on energy dissipation, which inspired researchers to explore the underlying regulation of IMAT formation. However, the molecular and cellular properties and regulatory processes of IMAT remain debated. Previous studies have suggested that muscle-derived stem/progenitor cells and other adipose tissue progenitors contribute to the development of IMAT. Adipocytes within IMAT exhibit features that are similar to either white adipocytes or uncoupling protein 1 (UCP1)-positive brown adipocytes. Additionally, given the heterogeneity of skeletal muscle, which comprises myofibers, satellite cells, and resident mesenchymal progenitors, it is plausible that interplay between these cellular components actively participate in the regulation of intermuscular adipogenesis. In this context, we review recent studies associated with IMAT to offer insights into the cellular origins, biological properties, and regulatory mechanisms of IMAT. Our aim is to provide novel ideas for the therapeutic strategy of IMAT and the development of new drugs targeting IMAT-related metabolic diseases.
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Affiliation(s)
- Ting Zhang
- Center of Obesity and Metabolic Diseases, Department of General Surgery, The Third People’s Hospital of Chengdu, Affiliated Hospital of Southwest Jiaotong University & The Second Affiliated Hospital of Chengdu, Chongqing Medical University, Chengdu, China
- Center of Gastrointestinal and Minimally Invasive Surgery, Department of General Surgery, The Third People’s Hospital of Chengdu, Affiliated Hospital of Southwest Jiaotong University & The Second Affiliated Hospital of Chengdu, Chongqing Medical University, Chengdu, China
- Medical Research Center, The Third People’s Hospital of Chengdu, Affiliated Hospital of Southwest Jiaotong University & The Second Affiliated Hospital of Chengdu, Chongqing Medical University, Chengdu, China
| | - Jun Li
- Department of Orthopedics, The Third People’s Hospital of Chengdu, Affiliated Hospital of Southwest Jiaotong University & The Second Affiliated Hospital of Chengdu, Chongqing Medical University, Chengdu, China
| | - Xi Li
- Institute of Life Sciences, Chongqing Medical University, Chongqing, China
| | - Yanjun Liu
- Center of Obesity and Metabolic Diseases, Department of General Surgery, The Third People’s Hospital of Chengdu, Affiliated Hospital of Southwest Jiaotong University & The Second Affiliated Hospital of Chengdu, Chongqing Medical University, Chengdu, China
- Center of Gastrointestinal and Minimally Invasive Surgery, Department of General Surgery, The Third People’s Hospital of Chengdu, Affiliated Hospital of Southwest Jiaotong University & The Second Affiliated Hospital of Chengdu, Chongqing Medical University, Chengdu, China
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10
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Dou L, Liu C, Chen X, Yang Z, Hu G, Zhang M, Sun L, Su L, Zhao L, Jin Y. Supplemental Clostridium butyricum modulates skeletal muscle development and meat quality by shaping the gut microbiota of lambs. Meat Sci 2023; 204:109235. [PMID: 37301103 DOI: 10.1016/j.meatsci.2023.109235] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 05/06/2023] [Accepted: 05/29/2023] [Indexed: 06/12/2023]
Abstract
This study evaluated the contributions of Clostridium butyricum on skeletal muscle development, gastrointestinal flora and meat quality of lambs. Eighteen Dorper (♂) × Small Tailed Han sheep (♀) crossed ewe lambs of similar weight (27.43 ± 1.94 kg; age, 88 ± 5 days) were divided into two dietary treatments. The control group was fed the basal diet (C group), and the probiotic group was supplemented with C. butyricum on the basis of the C group (2.5 × 108 cfu/g, 5 g/day/lamb; P group) for 90 d. The results showed that dietary C. butyricum elevated growth performance, muscle mass, muscle fiber diameter and cross-sectional area, and decreased the shear force value of meat (P < 0.05). Moreover, C. butyricum supplementation accelerated protein synthesis by regulating the gene expression of IGF-1/Akt/mTOR pathway. We identified 54 differentially expressed proteins that regulated skeletal muscle development through different mechanisms by quantitative proteomics. These proteins were associated with ubiquitin-protease, apoptosis, muscle structure, energy metabolism, heat shock, and oxidative stress. The metagenomics sequencing results showed that Petrimonas at the genus level and Prevotella brevis at the species level in the rumen, while Lachnoclostridium, Alloprevotella and Prevotella at the genus level in the feces, were significantly enriched in the P group. Also, butyric acid and valeric acid levels were elevated in both rumen and feces of the P group. Overall, our results support the idea that C. butyricum could change gastrointestinal flora, and affect skeletal muscle development and meat quality of lambs by modulating gut-muscle axis.
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Affiliation(s)
- Lu Dou
- College of Food Science and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China; Integrative Research Base of Beef and Lamb Processing Technology, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Chang Liu
- Inner Mongolia Vocational College of Chemical Engineering, Hohhot 010018, China
| | - Xiaoyu Chen
- College of Food Science and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China; Integrative Research Base of Beef and Lamb Processing Technology, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Zhihao Yang
- College of Food Science and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China; Integrative Research Base of Beef and Lamb Processing Technology, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Guanhua Hu
- College of Food Science and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China; Integrative Research Base of Beef and Lamb Processing Technology, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Min Zhang
- College of Food Science and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China; Integrative Research Base of Beef and Lamb Processing Technology, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Lina Sun
- College of Food Science and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China; Integrative Research Base of Beef and Lamb Processing Technology, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Lin Su
- College of Food Science and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China; Integrative Research Base of Beef and Lamb Processing Technology, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Lihua Zhao
- College of Food Science and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China; Integrative Research Base of Beef and Lamb Processing Technology, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Ye Jin
- College of Food Science and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China; Integrative Research Base of Beef and Lamb Processing Technology, Inner Mongolia Agricultural University, Hohhot 010018, China.
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11
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Yin C, Wang Y, Zhou P, Shi H, Ma X, Yin Z, Liu Y. Genomic Scan for Runs of Homozygosity and Selective Signature Analysis to Identify Candidate Genes in Large White Pigs. Int J Mol Sci 2023; 24:12914. [PMID: 37629094 PMCID: PMC10454931 DOI: 10.3390/ijms241612914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 08/09/2023] [Accepted: 08/16/2023] [Indexed: 08/27/2023] Open
Abstract
Large White pigs are extensively utilized in China for their remarkable characteristics of rapid growth and the high proportion of lean meat. The economic traits of pigs, comprising reproductive and meat quality traits, play a vital role in swine production. In this study, 2295 individuals, representing three different genetic backgrounds Large White pig populations were used: 500 from the Canadian line, 295 from the Danish line, and 1500 from the American line. The GeneSeek 50K GGP porcine HD array was employed to genotype the three pig populations. Firstly, genomic selective signature regions were identified using the pairwise fixation index (FST) and locus-specific branch length (LSBL). By applying a top 1% threshold for both parameters, a total of 888 candidate selective windows were identified, harbouring 1571 genes. Secondly, the investigation of regions of homozygosity (ROH) was performed utilizing the PLINK software. In total, 25 genomic regions exhibiting a high frequency of ROHs were detected, leading to the identification of 1216 genes. Finally, the identified potential functional genes from candidate genomic regions were annotated, and several important candidate genes associated with reproductive traits (ADCYAP1, U2, U6, CETN1, Thoc1, Usp14, GREB1L, FGF12) and meat quality traits (MiR-133, PLEKHO1, LPIN2, SHANK2, FLVCR1, MYL4, SFRP1, miR-486, MYH3, STYX) were identified. The findings of this study provide valuable insights into the genetic basis of economic traits in Large White pigs and may have potential use in future pig breeding programs.
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Affiliation(s)
- Chang Yin
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (C.Y.); (Y.W.); (P.Z.); (H.S.); (X.M.)
| | - Yuwei Wang
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (C.Y.); (Y.W.); (P.Z.); (H.S.); (X.M.)
| | - Peng Zhou
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (C.Y.); (Y.W.); (P.Z.); (H.S.); (X.M.)
| | - Haoran Shi
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (C.Y.); (Y.W.); (P.Z.); (H.S.); (X.M.)
| | - Xinyu Ma
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (C.Y.); (Y.W.); (P.Z.); (H.S.); (X.M.)
| | - Zongjun Yin
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China;
| | - Yang Liu
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (C.Y.); (Y.W.); (P.Z.); (H.S.); (X.M.)
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12
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Yue C, Wang J, Shen Y, Zhang J, Liu J, Xiao A, Liu Y, Eer H, Zhang QE. Whole-genome DNA methylation profiling reveals epigenetic signatures in developing muscle in Tan and Hu sheep and their offspring. Front Vet Sci 2023; 10:1186040. [PMID: 37388464 PMCID: PMC10301830 DOI: 10.3389/fvets.2023.1186040] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 05/24/2023] [Indexed: 07/01/2023] Open
Abstract
Introduction The Tan sheep is a popular local breed in China because of its tenderness and flavor. The Hu sheep breed is also famous for its high litter size, and its muscle growth rate is faster than that of Tan sheep. However, the epigenetic mechanism behind these muscle-related phenotypes is unknown. Methods In this study, the longissimus dorsi tissue from 18 6 month-old Tan sheep, Hu sheep, and Tan-Hu F2 generation (6 sheep per population) were collected. After genomic DNA extraction, whole-genome bisulfite sequencing (WGBS) and bioinformatics analysis were performed to construct genome-wide DNA methylome maps for the Tan sheep, Hu sheep and their Tan-Hu F2 generation. Results Distinct genome-wide DNA methylation patterns were observed between Tan sheep and Hu sheep. Moreover, DNA methylated regions were significantly increased in the skeletal muscle from Tan sheep vs. the F2 generation compared to the Hu sheep vs. F2 generation and the Tan sheep vs. Hu sheep. Compared with Hu sheep, the methylation levels of actin alpha 1 (ACTA1), myosin heavy chain 11 (MYH11), Wiskott-Aldrich syndrome protein (WAS), vav guanine nucleotide exchange factor 1 (VAV1), fibronectin 1 (FN1) and Rho-associated protein kinase 2 (ROCK2) genes were markedly distinct in the Tan sheep. Furthermore, Gene Ontology analysis indicated that these genes were involved in myotube differentiation, myotube cell development, smooth muscle cell differentiation and striated muscle cell differentiation. Conclusion The findings from this study, in addition to data from previous research, demonstrated that the ACTA1, MYH11, WAS, VAV1, FN1, and ROCK2 genes may exert regulatory effects on muscle development.
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Affiliation(s)
- Caijuan Yue
- College of Animal Science and Technology, Ningxia University, Yinchuan, Ningxia, China
- Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, Ningxia, China
| | - Jiakang Wang
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Yifei Shen
- Institute of Marxism, China University of Geosciences, Wuhan, Hubei, China
| | - Junli Zhang
- Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, Ningxia, China
| | - Jian Liu
- Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, Ningxia, China
| | - Aiping Xiao
- Animal Husbandry Extension Station, Yinchuan, Ningxia, China
| | - Yisha Liu
- College of Animal Science and Technology, Ningxia University, Yinchuan, Ningxia, China
| | - Hehua Eer
- Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, Ningxia, China
| | - Qiao-e Zhang
- College of Animal Science and Technology, Ningxia University, Yinchuan, Ningxia, China
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13
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Feng L, Si J, Yue J, Zhao M, Qi W, Zhu S, Mo J, Wang L, Lan G, Liang J. The Landscape of Accessible Chromatin and Developmental Transcriptome Maps Reveal a Genetic Mechanism of Skeletal Muscle Development in Pigs. Int J Mol Sci 2023; 24:ijms24076413. [PMID: 37047386 PMCID: PMC10094211 DOI: 10.3390/ijms24076413] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Revised: 03/19/2023] [Accepted: 03/23/2023] [Indexed: 03/30/2023] Open
Abstract
The epigenetic regulation mechanism of porcine skeletal muscle development relies on the openness of chromatin and is also precisely regulated by transcriptional machinery. However, fewer studies have exploited the temporal changes in gene expression and the landscape of accessible chromatin to reveal the underlying molecular mechanisms controlling muscle development. To address this, skeletal muscle biopsy samples were taken from Landrace pigs at days 0 (D0), 60 (D60), 120 (D120), and 180 (D180) after birth and were then analyzed using RNA-seq and ATAC-seq. The RNA-seq analysis identified 8554 effective differential genes, among which ACBD7, TMEM220, and ATP1A2 were identified as key genes related to the development of porcine skeletal muscle. Some potential cis-regulatory elements identified by ATAC-seq analysis contain binding sites for many transcription factors, including SP1 and EGR1, which are also the predicted transcription factors regulating the expression of ACBD7 genes. Moreover, the omics analyses revealed regulatory regions that become ectopically active after birth during porcine skeletal muscle development after birth and identified 151,245, 53,435, 30,494, and 40,911 peaks. The enriched functional elements are related to the cell cycle, muscle development, and lipid metabolism. In summary, comprehensive high-resolution gene expression maps were developed for the transcriptome and accessible chromatin during postnatal skeletal muscle development in pigs.
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Affiliation(s)
- Lingli Feng
- Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, Guangxi University, Nanning 530004, China (G.L.)
| | - Jinglei Si
- Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, Guangxi University, Nanning 530004, China (G.L.)
| | - Jingwei Yue
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100097, China
| | - Mingwei Zhao
- Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, Guangxi University, Nanning 530004, China (G.L.)
| | - Wenjing Qi
- Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, Guangxi University, Nanning 530004, China (G.L.)
| | - Siran Zhu
- Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, Guangxi University, Nanning 530004, China (G.L.)
| | - Jiayuan Mo
- Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, Guangxi University, Nanning 530004, China (G.L.)
| | - Lixian Wang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100097, China
| | - Ganqiu Lan
- Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, Guangxi University, Nanning 530004, China (G.L.)
| | - Jing Liang
- Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, Guangxi University, Nanning 530004, China (G.L.)
- Correspondence:
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14
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Dai H, Chen X, Chen D, Yu B, He J, Chen H, Yan H, Zheng P, Luo Y, Huang Z. Effects of dietary l-theanine supplementation on pork quality and muscle fiber type transformation in finishing pigs. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2023; 103:2106-2115. [PMID: 36460906 DOI: 10.1002/jsfa.12368] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 11/11/2022] [Accepted: 12/03/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND This experiment aimed to investigate effects of dietary l-theanine supplementation on pork quality and muscle fiber type transformation in finishing pigs. In a 30-day experiment, 18 healthy Duroc × Landrace × Yorkshire (DLY) pigs with an average body weight of 86.03 ± 0.83 kg were randomly divided into three groups (a basal diet or a basal diet supplemented with 500 and 1000 ppm l-theanine, respectively), with six duplicates and one pig per replicate. RESULTS The results showed that dietary 1000 ppm l-theanine supplementation significantly reduced (P < 0.05) b*24 h and drip loss. Dietary 1000 ppm l-theanine supplementation significantly increased (P < 0.05) slow myosin heavy chain (MyHC) protein expression and the percentage of slow-twitch fibers, as well as significantly decreased (P < 0.05) fast MyHC protein expression and the percentage of fast-twitch fibers, accompanied by an increase in succinate dehydrogenase (SDH) and malate dehydrogenase (MDH) activities and a decrease in lactate dehydrogenase (LDH) activity. In addition, the adenosine monophosphate (AMP)-activated protein kinase (AMPK) signaling pathway was activated by l-theanine. CONCLUSION Together, this study demonstrated for the first time that dietary supplementation of 1000 ppm l-theanine can improve pork color and drip loss and promote muscle fiber type transformation from fast-twitch to slow-twitch in finishing pigs. © 2022 Society of Chemical Industry.
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Affiliation(s)
- Hanna Dai
- Key Laboratory for Animal Disease-Resistance Nutrition of China Ministry of Education, Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu, Sichuan, P. R. China
| | - Xiaoling Chen
- Key Laboratory for Animal Disease-Resistance Nutrition of China Ministry of Education, Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu, Sichuan, P. R. China
| | - Daiwen Chen
- Key Laboratory for Animal Disease-Resistance Nutrition of China Ministry of Education, Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu, Sichuan, P. R. China
| | - Bing Yu
- Key Laboratory for Animal Disease-Resistance Nutrition of China Ministry of Education, Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu, Sichuan, P. R. China
| | - Jun He
- Key Laboratory for Animal Disease-Resistance Nutrition of China Ministry of Education, Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu, Sichuan, P. R. China
| | - Hong Chen
- College of Food Science, Sichuan Agricultural University, Yaan, Sichuan, P. R. China
| | - Hui Yan
- Key Laboratory for Animal Disease-Resistance Nutrition of China Ministry of Education, Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu, Sichuan, P. R. China
| | - Ping Zheng
- Key Laboratory for Animal Disease-Resistance Nutrition of China Ministry of Education, Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu, Sichuan, P. R. China
| | - Yuheng Luo
- Key Laboratory for Animal Disease-Resistance Nutrition of China Ministry of Education, Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu, Sichuan, P. R. China
| | - Zhiqing Huang
- Key Laboratory for Animal Disease-Resistance Nutrition of China Ministry of Education, Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu, Sichuan, P. R. China
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15
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Effects of the CDC10 ( Septin 7) Gene on the Proliferation and Differentiation of Bovine Intramuscular Preadipocyte and 3T3-L1 Cells. Animals (Basel) 2023; 13:ani13040609. [PMID: 36830396 PMCID: PMC9951720 DOI: 10.3390/ani13040609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 02/01/2023] [Accepted: 02/06/2023] [Indexed: 02/12/2023] Open
Abstract
Intramuscular fat content and marbling affecting meat quality are important economic traits in beef cattle. CDC10 (cell division cycle 10 or Septin 7), a member of the septin family involved in cellular proliferation, was considered as a functional and positional candidate gene for beef marbling. In a previous study, we revealed that the expression levels of CDC10 were also positively correlated with marbling scores in Japanese Black cattle. However, the regulatory mechanism of the CDC10 gene on IMF deposition in cattle remains unclear. In the present study, flow cytometry, EdU proliferation assays, and Oil Red O staining results showed that overexpression of CDC10 could promote the differentiation of bovine intramuscular preadipocyte (BIMP) and 3T3-L1 cells, whereas knockdown of CDC10 resulted in the opposite consequences. Furthermore, quantitative PCR and Western blotting results showed that overexpression of CDC10 could promote the expression levels of adipogenic marker genes PPARγ and C/EBPα at both mRNA and protein levels in BIMP and 3T3-L1 cells, whereas knockdown of CDC10 resulted in the opposite consequences. Our results provide new insights into the regulatory roles of CDC10 in adipocytes in animals.
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16
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Yan S, Pei Y, Li J, Tang Z, Yang Y. Recent Progress on Circular RNAs in the Development of Skeletal Muscle and Adipose Tissues of Farm Animals. Biomolecules 2023; 13:biom13020314. [PMID: 36830683 PMCID: PMC9953704 DOI: 10.3390/biom13020314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 01/15/2023] [Accepted: 01/30/2023] [Indexed: 02/11/2023] Open
Abstract
Circular RNAs (circRNAs) are a highly conserved and specifically expressed novel class of covalently closed non-coding RNAs. CircRNAs can function as miRNA sponges, protein scaffolds, and regulatory factors, and play various roles in development and other biological processes in mammals. With the rapid development of high-throughput sequencing technology, thousands of circRNAs have been discovered in farm animals; some reportedly play vital roles in skeletal muscle and adipose development. These are critical factors affecting meat yield and quality. In this review, we have highlighted the recent advances in circRNA-related studies of skeletal muscle and adipose in farm animals. We have also described the biogenesis, properties, and biological functions of circRNAs. Furthermore, we have comprehensively summarized the functions and regulatory mechanisms of circRNAs in skeletal muscle and adipose development in farm animals and their effects on economic traits such as meat yield and quality. Finally, we propose that circRNAs are putative novel targets to improve meat yield and quality traits during animal breeding.
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Affiliation(s)
- Shanying Yan
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, Key Laboratory of Animal Molecular Design and Precise Breeding of Guangdong Higher Education Institutes, School of Life Science and Engineering, Foshan University, Foshan 528231, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Yangli Pei
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, Key Laboratory of Animal Molecular Design and Precise Breeding of Guangdong Higher Education Institutes, School of Life Science and Engineering, Foshan University, Foshan 528231, China
| | - Jiju Li
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, Key Laboratory of Animal Molecular Design and Precise Breeding of Guangdong Higher Education Institutes, School of Life Science and Engineering, Foshan University, Foshan 528231, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Zhonglin Tang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
- Kunpeng Institute of Modern Agriculture at Foshan, Foshan 528226, China
- Correspondence: (Z.T.); (Y.Y.)
| | - Yalan Yang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
- Kunpeng Institute of Modern Agriculture at Foshan, Foshan 528226, China
- Correspondence: (Z.T.); (Y.Y.)
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17
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Yang M, Zhang R, Liu X, Shi G, Liu H, Wang L, Hou X, Shi L, Wang L, Zhang L. Integrating genome-wide association study with RNA-seq revealed DBI as a good candidate gene for intramuscular fat content in Beijing black pigs. Anim Genet 2023; 54:24-34. [PMID: 36305366 DOI: 10.1111/age.13270] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Revised: 10/04/2022] [Accepted: 10/08/2022] [Indexed: 01/07/2023]
Abstract
Increasing intramuscular fat (IMF) content can enhance the sensory quality of meat, including tenderness, juiciness, flavor, and color. Genome-wide association study and RNA-sequencing (RNA-seq) analysis were used to identify candidate IMF genes in Beijing Black pigs, a popular species among consumers in northern China. Two and three single nucleotide polymorphisms were significantly associated with IMF in SSC13 and SSC15 respectively. Solute carrier family 4 member 7 (SLC4A7) on SSC13 and insulin induced gene 2 (INSIG2), coiled-coil domain containing 93 (CCDC93), and diazepam binding inhibitor acyl-CoA binding protein (DBI) on SSC15 are good candidate genes in this population. Furthermore, RNA-seq analysis was performed between high and low IMF groups, and 534 differentially expressed genes were identified. In addition, based on differentially expressed genes, Kyoto Encyclopedia of Genes and Genomes analysis revealed that peroxisome proliferator-activated receptors and FoxO signaling pathway pathways might contribute to IMF. Moreover, the DBI gene was identified as a candidate for IMF both by genome-wide association study and RNA-seq analysis, suggesting that it might be a crucial candidate gene for influencing IMF in Beijing Black pigs.
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Affiliation(s)
- Man Yang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Run Zhang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiance Liu
- Beijing Heiliu Animal Husbandry Technology Co, Ltd, Beijing, China
| | - Guohua Shi
- Beijing Heiliu Animal Husbandry Technology Co, Ltd, Beijing, China
| | - Hai Liu
- Beijing Heiliu Animal Husbandry Technology Co, Ltd, Beijing, China
| | - Ligang Wang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xinhua Hou
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lijun Shi
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lixian Wang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Longchao Zhang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
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18
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Tan X, He Y, He Y, Yan Z, Chen J, Zhao R, Sui X, Zhang L, Du X, Irwin DM, Zhang S, Li B. Comparative Proteomic Analysis of Glycolytic and Oxidative Muscle in Pigs. Genes (Basel) 2023; 14:genes14020361. [PMID: 36833290 PMCID: PMC9957308 DOI: 10.3390/genes14020361] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Revised: 01/26/2023] [Accepted: 01/28/2023] [Indexed: 01/31/2023] Open
Abstract
The quality of meat is highly correlated with muscle fiber type. However, the mechanisms via which proteins regulate muscle fiber types in pigs are not entirely understood. In the current study, we have performed proteomic profiling of fast/glycolytic biceps femoris (BF) and slow/oxidative soleus (SOL) muscles and identified several candidate differential proteins among these. We performed proteomic analyses based on tandem mass tags (TMTs) and identified a total of 26,228 peptides corresponding to 2667 proteins among the BF and SOL muscle samples. Among these, we found 204 differentially expressed proteins (DEPs) between BF and SOL muscle, with 56 up-regulated and 148 down-regulated DEPs in SOL muscle samples. KEGG and GO enrichment analyses of the DEPs revealed that the DEPs are involved in some GO terms (e.g., actin cytoskeleton, myosin complex, and cytoskeletal parts) and signaling pathways (PI3K-Akt and NF-kappa B signaling pathways) that influence muscle fiber type. A regulatory network of protein-protein interaction (PPI) between these DEPs that regulates muscle fiber types was constructed, which demonstrates how three down-regulated DEPs, including PFKM, GAPDH, and PKM, interact with other proteins to potentially control the glycolytic process. This study offers a new understanding of the molecular mechanisms in glycolytic and oxidative muscles as well as a novel approach for enhancing meat quality by transforming the type of muscle fibers in pigs.
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Affiliation(s)
- Xiaofan Tan
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang 110866, China
| | - Yu He
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang 110866, China
| | - Yuqiao He
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang 110866, China
| | - Zhiwei Yan
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang 110866, China
| | - Jing Chen
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang 110866, China
| | - Ruixue Zhao
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang 110866, China
| | - Xin Sui
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang 110866, China
| | - Lei Zhang
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang 110866, China
| | - Xuehai Du
- Liaoning Provincial Animal Husbandry Development Center, Liaoning Province Agricultural Development Service Center, Shenyang 110032, China
| | - David M. Irwin
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Shuyi Zhang
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang 110866, China
| | - Bojiang Li
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang 110866, China
- Correspondence:
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19
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Vaishnav S, Chauhan A, Ajay A, Saini BL, Kumar S, Kumar A, Bhushan B, Gaur GK. Allelic to genome wide perspectives of swine genetic variation to litter size and its component traits. Mol Biol Rep 2023; 50:3705-3721. [PMID: 36642776 DOI: 10.1007/s11033-022-08168-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 12/01/2022] [Indexed: 01/17/2023]
Abstract
Litter size is a complex and sex limited trait that depends on various biological, managemental and environmental factors. Owing to its low heritability it is inefficaciously selected by traditional methods. However, due to higher heritability of ovulation rate and embryo survival, selection based on component traits of litter size is advocated. QTL analysis and candidate gene approach are among the various supplementary/alternate strategies for selection of litter size. QTL analysis is aimed at identifying genomic regions affecting trait of interest significantly. Candidate gene approach necessitates identification of genes potentially affecting the trait. There are various genes that significantly affect litter size and its component traits viz. ESR, LEP, BF, IGFBP, RBP4, PRLR, CTNNAL1, WNT10B, TCF12, DAZ, and RNF4. These genes affect litter size in a complex interacting manner. Lately, genome wide association study (GWAS) have been utilized to unveil the genetic and biological background of litter traits, and elucidate the genes governing litter size. Favorable SNPs in these genes have been identified and offers a scope for inclusion in selection programs thereby increasing breeding efficiency and profit in pigs. The review provides a comprehensive coverage of investigations carried out globally to unravel the genetic variation in litter size and its component traits in pigs, both at allelic and genome wide level. It offers a current perspective on different strategies including the profiling of candidate genes, QTLs, and genome wide association studies as an aid to efficient selection for litter size and its component traits.
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Affiliation(s)
| | - Anuj Chauhan
- Indian Veterinary Research Institute, Bareilly, India.
| | - Argana Ajay
- Indian Veterinary Research Institute, Bareilly, India
| | | | - Subodh Kumar
- Indian Veterinary Research Institute, Bareilly, India
| | - Amit Kumar
- Indian Veterinary Research Institute, Bareilly, India
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20
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Huang Y, Cai L, Duan Y, Zeng Q, He M, Wu Z, Zou X, Zhou M, Zhang Z, Xiao S, Yang B, Ma J, Huang L. Whole-genome sequence-based association analyses on an eight-breed crossed heterogeneous stock of pigs reveal the genetic basis of skeletal muscle fiber characteristics. Meat Sci 2022; 194:108974. [PMID: 36167013 DOI: 10.1016/j.meatsci.2022.108974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 08/02/2022] [Accepted: 09/05/2022] [Indexed: 10/14/2022]
Abstract
Skeletal muscle fiber characteristics (MFCs) have been extensively studied due to their importance to human health and athletic ability, as well as to the quantity and quality of livestock meat production. Hence, we performed a genome-wide association study (GWAS) on nine muscle fiber traits by using whole genome sequence data in an eight-breed crossed heterogeneous stock pig population. This GWAS revealed 67 quantitative trait loci (QTLs) for these traits. The most significant GWAS signal was detected in the region of Sus scrofa chromosome 12 (SSC12) containing the MYH gene family. Notably, we identified a significant SNP rs322008693 (P = 7.52E-09) as the most likely causal mutation for the total number of muscle fibers (TNMF) QTL on SSC1. The results of EMSA and luciferase assays indicated that the rs322008693 SNP resided in a functional element. These findings provide valuable molecular markers for pig meat production selection as well as for deciphering the genetic mechanisms of the muscle fiber physiology.
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Affiliation(s)
- Yizhong Huang
- State Key Laboratory for Swine Genetics, Breeding and Production Technology, Jiangxi Agricultural University, Nanchang 330045, China
| | - Liping Cai
- State Key Laboratory for Swine Genetics, Breeding and Production Technology, Jiangxi Agricultural University, Nanchang 330045, China
| | - Yanyu Duan
- State Key Laboratory for Swine Genetics, Breeding and Production Technology, Jiangxi Agricultural University, Nanchang 330045, China
| | - Qingjie Zeng
- State Key Laboratory for Swine Genetics, Breeding and Production Technology, Jiangxi Agricultural University, Nanchang 330045, China
| | - Maozhang He
- State Key Laboratory for Swine Genetics, Breeding and Production Technology, Jiangxi Agricultural University, Nanchang 330045, China
| | - Zhongping Wu
- State Key Laboratory for Swine Genetics, Breeding and Production Technology, Jiangxi Agricultural University, Nanchang 330045, China
| | - Xiaoxiao Zou
- State Key Laboratory for Swine Genetics, Breeding and Production Technology, Jiangxi Agricultural University, Nanchang 330045, China
| | - Mengqing Zhou
- State Key Laboratory for Swine Genetics, Breeding and Production Technology, Jiangxi Agricultural University, Nanchang 330045, China
| | - Zhou Zhang
- State Key Laboratory for Swine Genetics, Breeding and Production Technology, Jiangxi Agricultural University, Nanchang 330045, China
| | - Shijun Xiao
- State Key Laboratory for Swine Genetics, Breeding and Production Technology, Jiangxi Agricultural University, Nanchang 330045, China
| | - Bin Yang
- State Key Laboratory for Swine Genetics, Breeding and Production Technology, Jiangxi Agricultural University, Nanchang 330045, China
| | - Junwu Ma
- State Key Laboratory for Swine Genetics, Breeding and Production Technology, Jiangxi Agricultural University, Nanchang 330045, China.
| | - Lusheng Huang
- State Key Laboratory for Swine Genetics, Breeding and Production Technology, Jiangxi Agricultural University, Nanchang 330045, China.
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21
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Vaiman A, Fritz S, Beauvallet C, Boussaha M, Grohs C, Daniel-Carlier N, Relun A, Boichard D, Vilotte JL, Duchesne A. Mutation of the MYH3 gene causes recessive cleft palate in Limousine cattle. GENETICS SELECTION EVOLUTION 2022; 54:71. [PMID: 36309651 PMCID: PMC9617432 DOI: 10.1186/s12711-022-00762-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Accepted: 10/18/2022] [Indexed: 12/03/2022]
Abstract
Background The palate is a structure separating the oral and nasal cavities and its integrity is essential for feeding and breathing. The total or partial opening of the palate is called a cleft palate and is a common malformation in mammals with environmental or hereditary aetiologies. Generally, it compromises life expectancy in the absence of surgical repair. A new form of non-syndromic cleft palate arose recently in Limousine cattle, with animals referred to the French National Observatory of Bovine Abnormalities since 2012. Since the number of affected animals has increased steadily, this study was undertaken to identify the cause of this disease. Results Based on pedigree analysis, occurrence of cleft palate in Limousine cattle was concordant with an autosomal recessive mode of inheritance. Genotyping of 16 affected animals and homozygosity mapping led to the identification of a single disease-associated haplotype on Bos taurus chromosome (BTA)19. The genome of two affected animals was sequenced, and their sequences were compared to the ARS-UCD1.2 reference genome to identify variants. The likely causal variants were compared to the variant database of the 1000 bull genome project and two fully linked mutations in exon 24 of the MYH3 (myosin heavy chain) gene were detected: a 1-bp non-synonymous substitution (BTA19:g.29609623A>G) and a 11-bp frameshift deletion (BTA19:g.29609605-29609615del). These two mutations were specific to the Limousine breed, with an estimated allele frequency of 2.4% and are predicted to be deleterious. The frameshift leads to a premature termination codon. Accordingly, mRNA and protein analyses in muscles from wild-type and affected animals revealed a decrease in MYH3 expression in affected animals, probably due to mRNA decay, as well as an absence of the MYH3 protein in these animals. MYH3 is mostly expressed in muscles, including craniofacial muscles, during embryogenesis, and its absence may impair palate formation. Conclusions We describe a new form of hereditary cleft palate in Limousine cattle. We identified two fully linked and deleterious mutations, ultimately leading to the loss-of-function of the MYH3 protein. The mutations were included on the Illumina EuroG10k v8 and EuroGMD v1 SNP chips and are used to set up a reliable eradication strategy in the French Limousine breed. Supplementary Information The online version contains supplementary material available at 10.1186/s12711-022-00762-2.
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Affiliation(s)
- Anne Vaiman
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
| | - Sébastien Fritz
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
| | - Christian Beauvallet
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
| | - Mekki Boussaha
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
| | - Cécile Grohs
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
| | | | - Anne Relun
- INRAE, Oniris, BIOEPAR, 44300, Nantes, France.,Clinic for Ruminants, Oniris, 44300, Nantes, France
| | - Didier Boichard
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
| | - Jean-Luc Vilotte
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
| | - Amandine Duchesne
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France.
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22
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Chen Q, Li X, Cui J, Xu C, Wei H, Zhao Q, Yao H, You H, Zhang D, Yu H. Effects of Stocking Density on Fatty Acid Metabolism by Skeletal Muscle in Mice. Animals (Basel) 2022; 12:ani12192538. [PMID: 36230279 PMCID: PMC9559694 DOI: 10.3390/ani12192538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Revised: 08/22/2022] [Accepted: 09/18/2022] [Indexed: 11/16/2022] Open
Abstract
Specific pathogen-free (SPF) grade laboratory animals are kept in specific cages for life. The limited space could affect the characterization of colonization and dynamic changes related to gut microorganisms, and affect adipokines, even further affecting the fat synthesis and muscle quality of animals. The objective of this study was to analyze the stocking density on the dynamic distribution of gut microbiota, fat synthesis and muscle quality of SPF grade Kunming mice. Three housing densities were accomplished by raising different mice per cage with the same floor size. Kunming mice were reared at low stocking density (LSD, three mice a group), medium stocking density (MSD, 5 mice a group), and high stocking density (HSD, 10 mice a group) for 12 weeks. The results demonstrated that the stocking density affected intestinal microbial flora composition. We found that compared with the MSD group, the abundance of Lactobacillus in the LSD group and the HSD group decreased, but the abundance of unclassified_Porphyromonadaceae increased. Moreover, fat synthesis and muscle quality were linked to the intestinal microbial flora and stocking density. Compared with the LSD group and the HSD group, the MSD group had a more balanced gut flora, higher fat synthesis and higher muscle quality. Overall, this study demonstrated that stocking density could affect gut microbiota composition, and reasonable stocking density could improve fat synthesis and muscle quality. Our study will provide theoretical support for the suitable stocking density of laboratory animals.
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Affiliation(s)
- Qiuyan Chen
- Center of Animal Experiment, College of Basic Medical Sciences, Jilin University, Changchun 130021, China
- Key Laboratory of Pathobiology, Ministry of Education, Department of Pathophysiology, College of Basic Medical Sciences, Jilin University, Changchun 130021, China
| | - Xiaohui Li
- Center of Animal Experiment, College of Basic Medical Sciences, Jilin University, Changchun 130021, China
| | - Jiarun Cui
- Center of Animal Experiment, College of Basic Medical Sciences, Jilin University, Changchun 130021, China
| | - Caiyun Xu
- Center of Animal Experiment, College of Basic Medical Sciences, Jilin University, Changchun 130021, China
| | - Hongfei Wei
- Center of Animal Experiment, College of Basic Medical Sciences, Jilin University, Changchun 130021, China
| | - Qian Zhao
- Key Laboratory of Pathobiology, Ministry of Education, Department of Pathophysiology, College of Basic Medical Sciences, Jilin University, Changchun 130021, China
| | - Hongli Yao
- Key Laboratory of Pathobiology, Ministry of Education, Department of Pathophysiology, College of Basic Medical Sciences, Jilin University, Changchun 130021, China
| | - Hailong You
- Key Laboratory of Pathobiology, Ministry of Education, Department of Pathophysiology, College of Basic Medical Sciences, Jilin University, Changchun 130021, China
| | - Dawei Zhang
- Center of Animal Experiment, College of Basic Medical Sciences, Jilin University, Changchun 130021, China
- Correspondence: (D.Z.); (H.Y.); Tel.: +86-0-431-8561-9495 (H.Y.)
| | - Huimei Yu
- Center of Animal Experiment, College of Basic Medical Sciences, Jilin University, Changchun 130021, China
- Key Laboratory of Pathobiology, Ministry of Education, Department of Pathophysiology, College of Basic Medical Sciences, Jilin University, Changchun 130021, China
- Correspondence: (D.Z.); (H.Y.); Tel.: +86-0-431-8561-9495 (H.Y.)
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23
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Liu Y, Fu Y, Yang Y, Yi G, Lian J, Xie B, Yao Y, Chen M, Niu Y, Liu L, Wang L, Zhang Y, Fan X, Tang Y, Yuan P, Zhu M, Li Q, Zhang S, Chen Y, Wang B, He J, Lu D, Liachko I, Sullivan ST, Pang B, Chen Y, He X, Li K, Tang Z. Integration of multi-omics data reveals cis-regulatory variants that are associated with phenotypic differentiation of eastern from western pigs. GENETICS SELECTION EVOLUTION 2022; 54:62. [PMID: 36104777 PMCID: PMC9476355 DOI: 10.1186/s12711-022-00754-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 09/02/2022] [Indexed: 11/10/2022]
Abstract
Abstract
Background
The genetic mechanisms that underlie phenotypic differentiation in breeding animals have important implications in evolutionary biology and agriculture. However, the contribution of cis-regulatory variants to pig phenotypes is poorly understood. Therefore, our aim was to elucidate the molecular mechanisms by which non-coding variants cause phenotypic differences in pigs by combining evolutionary biology analyses and functional genomics.
Results
We obtained a high-resolution phased chromosome-scale reference genome with a contig N50 of 18.03 Mb for the Luchuan pig breed (a representative eastern breed) and profiled potential selective sweeps in eastern and western pigs by resequencing the genomes of 234 pigs. Multi-tissue transcriptome and chromatin accessibility analyses of these regions suggest that tissue-specific selection pressure is mediated by promoters and distal cis-regulatory elements. Promoter variants that are associated with increased expression of the lysozyme (LYZ) gene in the small intestine might enhance the immunity of the gastrointestinal tract and roughage tolerance in pigs. In skeletal muscle, an enhancer-modulating single-nucleotide polymorphism that is associated with up-regulation of the expression of the troponin C1, slow skeletal and cardiac type (TNNC1) gene might increase the proportion of slow muscle fibers and affect meat quality.
Conclusions
Our work sheds light on the molecular mechanisms by which non-coding variants shape phenotypic differences in pigs and provides valuable resources and novel perspectives to dissect the role of gene regulatory evolution in animal domestication and breeding.
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24
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Zhu Y, Zhou Z, Huang T, Zhang Z, Li W, Ling Z, Jiang T, Yang J, Yang S, Xiao Y, Charlier C, Georges M, Yang B, Huang L. Mapping and analysis of a spatiotemporal H3K27ac and gene expression spectrum in pigs. SCIENCE CHINA. LIFE SCIENCES 2022; 65:1517-1534. [PMID: 35122624 DOI: 10.1007/s11427-021-2034-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 10/29/2021] [Indexed: 12/12/2022]
Abstract
The limited knowledge of genomic noncoding and regulatory regions has restricted our ability to decipher the genetic mechanisms underlying complex traits in pigs. In this study, we characterized the spatiotemporal landscape of putative enhancers and promoters and their target genes by combining H3K27ac-targeted ChIP-Seq and RNA-Seq in fetal (prenatal days 74-75) and adult (postnatal days 132-150) tissues (brain, liver, heart, muscle and small intestine) sampled from Asian aboriginal Bama Xiang and European highly selected Large White pigs of both sexes. We identified 101,290 H3K27ac peaks, marking 18,521 promoters and 82,769 enhancers, including peaks that were active across all tissues and developmental stages (which could indicate safe harbor locus for exogenous gene insertion) and tissue- and developmental stage-specific peaks (which regulate gene pathways matching tissue- and developmental stage-specific physiological functions). We found that H3K27ac and DNA methylation in the promoter region of the XIST gene may be involved in X chromosome inactivation and demonstrated the utility of the present resource for revealing the regulatory patterns of known causal genes and prioritizing candidate causal variants for complex traits in pigs. In addition, we identified an average of 1,124 super-enhancers per sample and found that they were more likely to show tissue-specific activity than ordinary peaks. We have developed a web browser to improve the accessibility of the results ( http://segtp.jxau.edu.cn/pencode/?genome=susScr11 ).
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Affiliation(s)
- Yaling Zhu
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
- Laboratory Animal Research Center, School of Basic Medical Sciences, Anhui Medical University, Hefei, 230032, China
| | - Zhimin Zhou
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Tao Huang
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Zhen Zhang
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Wanbo Li
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Ziqi Ling
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Tao Jiang
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Jiawen Yang
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Siyu Yang
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Yanyuan Xiao
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Carole Charlier
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
- Unit of Animal Genomics, GIGA-Institute and Faculty of Veterinary Medicine, University of Liege, 4000, Liege, Belgium
| | - Michel Georges
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
- Unit of Animal Genomics, GIGA-Institute and Faculty of Veterinary Medicine, University of Liege, 4000, Liege, Belgium
| | - Bin Yang
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China.
| | - Lusheng Huang
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China.
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25
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Tan X, He Y, Qin Y, Yan Z, Chen J, Zhao R, Zhou S, Irwin DM, Li B, Zhang S. Comparative analysis of differentially abundant proteins between high and low intramuscular fat content groups in donkeys. Front Vet Sci 2022; 9:951168. [PMID: 35967999 PMCID: PMC9364086 DOI: 10.3389/fvets.2022.951168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 07/05/2022] [Indexed: 11/13/2022] Open
Abstract
Intramuscular fat (IMF) is an important regulator that determines meat quality, and its content is closely related to flavor, tenderness, and juiciness. Many studies have used quantitative proteomic analysis to identify proteins associated with meat quality traits in livestock, however, the potential candidate proteins that influence IMF in donkey muscle are not fully understood. In this study, we performed quantitative proteomic analysis, with tandem-mass-tagged (TMT) labeling, with samples from the longissimus dorsi (LD) muscle of the donkey. A total of 585,555 spectra were identified from the six muscle samples used in this study. In total, 20,583 peptides were detected, including 15,279 unique peptides, and 2,540 proteins were identified. We analyzed differentially abundant proteins (DAPs) between LD muscles of donkeys with high (H) and low (L) IMF content. We identified 30 DAPs between the H and L IMF content groups, of which 17 were upregulated and 13 downregulated in the H IMF group. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) functional enrichment analysis of these DAPs revealed many GO terms (e.g., bone morphogenetic protein (BMP) receptor binding) and pathways (e.g., Wnt signaling pathway and Hippo signaling pathway) involved in lipid metabolism and adipogenesis. The construction of protein–protein interaction networks identified 16 DAPs involved in these networks. Our data provide a basis for future investigations into candidate proteins involved in IMF deposition and potential new approaches to improve meat quality in the donkey.
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Affiliation(s)
- Xiaofan Tan
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Yu He
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Yanchun Qin
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Zhiwei Yan
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Jing Chen
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Ruixue Zhao
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Shenglan Zhou
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - David M. Irwin
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Bojiang Li
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
- *Correspondence: Bojiang Li
| | - Shuyi Zhang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
- Shuyi Zhang
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26
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Gong H, Liu W, Wu Z, Zhang M, Sun Y, Ling Z, Xiao S, Ai H, Xin Y, Yang B, Huang L. Evolutionary insights into porcine genomic structural variations based on a novel constructed dataset from 24 worldwide diverse populations. Evol Appl 2022. [DOI: 10.1111/eva.13455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Affiliation(s)
- Huanfa Gong
- State Key Laboratory of Pig Genetic Improvement and Production Technology Jiangxi Agricultural University Nanchang P.R. China
- Key Laboratory of Molecular Animal Nutrition, Ministry of Education, College of Animal Sciences Zhejiang University Hangzhou P.R. China
- Key Laboratory of Animal Nutrition and Feed Science in Eastern China, Ministry of Agriculture, College of Animal Sciences Zhejiang University Hangzhou P.R. China
| | - Weiwei Liu
- State Key Laboratory of Pig Genetic Improvement and Production Technology Jiangxi Agricultural University Nanchang P.R. China
| | - Zhongzi Wu
- State Key Laboratory of Pig Genetic Improvement and Production Technology Jiangxi Agricultural University Nanchang P.R. China
| | - Mingpeng Zhang
- State Key Laboratory of Pig Genetic Improvement and Production Technology Jiangxi Agricultural University Nanchang P.R. China
| | - Yingchun Sun
- State Key Laboratory of Pig Genetic Improvement and Production Technology Jiangxi Agricultural University Nanchang P.R. China
| | - Ziqi Ling
- State Key Laboratory of Pig Genetic Improvement and Production Technology Jiangxi Agricultural University Nanchang P.R. China
| | - Shijun Xiao
- State Key Laboratory of Pig Genetic Improvement and Production Technology Jiangxi Agricultural University Nanchang P.R. China
| | - Huashui Ai
- State Key Laboratory of Pig Genetic Improvement and Production Technology Jiangxi Agricultural University Nanchang P.R. China
| | - Yuyun Xin
- State Key Laboratory of Pig Genetic Improvement and Production Technology Jiangxi Agricultural University Nanchang P.R. China
| | - Bin Yang
- State Key Laboratory of Pig Genetic Improvement and Production Technology Jiangxi Agricultural University Nanchang P.R. China
| | - Lusheng Huang
- State Key Laboratory of Pig Genetic Improvement and Production Technology Jiangxi Agricultural University Nanchang P.R. China
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27
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Zhang L, Li F, Guo Q, Duan Y, Wang W, Yang Y, Yin Y, Gong S, Han M, Yin Y. Balanced branched-chain amino acids modulate meat quality by adjusting muscle fiber type conversion and intramuscular fat deposition in finishing pigs. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2022; 102:3796-3807. [PMID: 34921408 DOI: 10.1002/jsfa.11728] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 12/13/2021] [Accepted: 12/18/2021] [Indexed: 06/14/2023]
Abstract
BACKGROUND Pork is an important food for humans and improving the quality of pork is closely related to human health. This study was designed to investigate the effects of balanced branched-chain amino acid (BCAA)-supplemented protein-restricted diets on meat quality, muscle fiber types, and intramuscular fat (IMF) in finishing pigs. RESULTS The results showed that, compared with the normal protein diet (160 g kg-1 crude protein), the reduced-protein diet (120 g kg-1 crude protein) supplemented with BCAAs to the ratio of 2:1:2 not only had higher average daily gain (P < 0.05) and carcass weight (P < 0.05) but also improved meat tenderness and juiciness by decreasing shear force (P < 0.05) and increasing water-holding capacity (P < 0.05). In particular, this treatment showed higher (P < 0.05) levels of phospho-acetyl-CoA carboxylase (P-ACC) and peroxisome proliferation-activated receptor-γ (PPARγ), and lower (P < 0.05) levels of P-adenosine 5'-monophosphate (AMP)-activated protein kinase (P-AMPK), increasing the composition of IMF and MyHC I (P < 0.05) in the longissimus dorsi muscle (LDM). In terms of health, this group increased eicosapentaenoic acid (EPA) (P < 0.01) and desirable hypocholesterolemic fatty acids (DHFA) (P < 0.05), and decreased atherogenicity (AI) (P < 0.01) and hypercholesterolemic saturated fatty acids (HSFA) (P < 0.05). CONCLUSION Our findings suggest a novel role for a balanced BCAA-supplemented restricted protein (RP) diet in the epigenetic regulation of more tender and healthier pork by increasing IMF deposition and fiber type conversion, providing a cross-regulatory molecular basis for revealing the nutritional regulation network of meat quality. © 2021 Society of Chemical Industry.
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Affiliation(s)
- Lingyu Zhang
- Hunan Provincial Key Laboratory of Animal Nutritional Physiology and Metabolic Process; Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences; Hunan Provincial Engineering Research Center for Healthy Livestock and Poultry Production; National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production; Scientific Observing and Experimental Station of Animal Nutrition and Feed Science in South-Central, Ministry of Agriculture, Changsha, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Fengna Li
- Hunan Provincial Key Laboratory of Animal Nutritional Physiology and Metabolic Process; Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences; Hunan Provincial Engineering Research Center for Healthy Livestock and Poultry Production; National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production; Scientific Observing and Experimental Station of Animal Nutrition and Feed Science in South-Central, Ministry of Agriculture, Changsha, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Qiuping Guo
- Hunan Provincial Key Laboratory of Animal Nutritional Physiology and Metabolic Process; Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences; Hunan Provincial Engineering Research Center for Healthy Livestock and Poultry Production; National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production; Scientific Observing and Experimental Station of Animal Nutrition and Feed Science in South-Central, Ministry of Agriculture, Changsha, China
| | - Yehui Duan
- Hunan Provincial Key Laboratory of Animal Nutritional Physiology and Metabolic Process; Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences; Hunan Provincial Engineering Research Center for Healthy Livestock and Poultry Production; National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production; Scientific Observing and Experimental Station of Animal Nutrition and Feed Science in South-Central, Ministry of Agriculture, Changsha, China
| | - Wenlong Wang
- Hunan Provincial Key Laboratory of Animal Nutritional Physiology and Metabolic Process; Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences; Hunan Provincial Engineering Research Center for Healthy Livestock and Poultry Production; National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production; Scientific Observing and Experimental Station of Animal Nutrition and Feed Science in South-Central, Ministry of Agriculture, Changsha, China
| | - Yuhuan Yang
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
| | - Yunju Yin
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
| | - Saiming Gong
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
| | - Mengmeng Han
- Hunan Provincial Key Laboratory of Animal Nutritional Physiology and Metabolic Process; Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences; Hunan Provincial Engineering Research Center for Healthy Livestock and Poultry Production; National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production; Scientific Observing and Experimental Station of Animal Nutrition and Feed Science in South-Central, Ministry of Agriculture, Changsha, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yulong Yin
- Hunan Provincial Key Laboratory of Animal Nutritional Physiology and Metabolic Process; Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences; Hunan Provincial Engineering Research Center for Healthy Livestock and Poultry Production; National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production; Scientific Observing and Experimental Station of Animal Nutrition and Feed Science in South-Central, Ministry of Agriculture, Changsha, China
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28
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Wei D, Raza SHA, Wang X, Khan R, Lei Z, Zhang G, Zhang J, Luoreng Z, Ma Y, Alamoudi MO, Aloufi BH, Alshammari AM, Abd El-Aziz AH, Alhomrani M, Alamri AS. Tissue Expression Analysis, Cloning, and Characterization of the 5'-Regulatory Region of the Bovine LATS1 Gene. Front Vet Sci 2022; 9:853819. [PMID: 35692290 PMCID: PMC9185948 DOI: 10.3389/fvets.2022.853819] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 04/19/2022] [Indexed: 11/29/2022] Open
Abstract
As a member of the large tumor suppressor (LATS) gene family, LATS1 plays an important role in regulating muscle growth and development. In this study, we determined the distinct exhibit patterns of tissue expression of bovine LATS1. Further, we determined the functional proximal minimal promoter of bovine LATS1 and identified the key transcription factors in the core promoter region to elucidate its molecular regulation mechanism. The results showed that bovine LATS1 was highly expressed in the longissimus thoracis and upregulation in infancy muscle. An electrophoretic mobility shift assay (EMSA) and chromatin immunoprecipitation (ChIP) assay in combination with site-directed mutation and small interfering RNA (siRNA) interference demonstrated that myogenic differentiation 1 (Myod1) and myocyte enhancer factor 2A (MEF2A) binding in the core promoter region (−298/−123 bp) play important roles in the transcriptional regulation of the bovine LATS1 promoter. Taken together, these interactions provide insight into the regulatory mechanisms of LATS1 transcription in mediating skeletal muscle growth in cattle.
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Affiliation(s)
- Dawei Wei
- School of Agriculture, Ningxia University, Yinchuan, China.,Key Laboratory of Ruminant Molecular Cell Breeding, Ningxia Hui Autonomous Region, Yinchuan, China
| | | | - Xingping Wang
- School of Agriculture, Ningxia University, Yinchuan, China.,Key Laboratory of Ruminant Molecular Cell Breeding, Ningxia Hui Autonomous Region, Yinchuan, China
| | - Rajwali Khan
- Department of Livestock Management, Breeding and Genetics, The University of Agriculture, Peshawar, Pakistan
| | - Zhaoxiong Lei
- School of Agriculture, Ningxia University, Yinchuan, China
| | - Guijie Zhang
- School of Agriculture, Ningxia University, Yinchuan, China.,Key Laboratory of Ruminant Molecular Cell Breeding, Ningxia Hui Autonomous Region, Yinchuan, China
| | - Jiupan Zhang
- Institute of Animal Science, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, China
| | - Zhuoma Luoreng
- School of Agriculture, Ningxia University, Yinchuan, China.,Key Laboratory of Ruminant Molecular Cell Breeding, Ningxia Hui Autonomous Region, Yinchuan, China
| | - Yun Ma
- School of Agriculture, Ningxia University, Yinchuan, China.,Key Laboratory of Ruminant Molecular Cell Breeding, Ningxia Hui Autonomous Region, Yinchuan, China
| | - Muna O Alamoudi
- Department of Biology, College of Science, University of Hail, Hail, Saudi Arabia
| | - Bandar Hamad Aloufi
- Department of Biology, College of Science, University of Hail, Hail, Saudi Arabia
| | | | - Ayman Hassan Abd El-Aziz
- Animal Husbandry and Animal Wealth Development Department, Faculty of Veterinary Medicine, Damanhour University, Damanhour, Egypt
| | - Majid Alhomrani
- Department of Clinical Laboratories Sciences, The Faculty of Applied Medical Sciences, Taif University, Taif, Saudi Arabia.,Centre of Biomedical Sciences Research (CBSR), Deanship of Scientific Research, Taif University, Taif, Saudi Arabia
| | - Abdulhakeem S Alamri
- Department of Clinical Laboratories Sciences, The Faculty of Applied Medical Sciences, Taif University, Taif, Saudi Arabia.,Centre of Biomedical Sciences Research (CBSR), Deanship of Scientific Research, Taif University, Taif, Saudi Arabia
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29
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Kang YJ, Han SH, Kim SG, Kim SY, Kim HA, Yoo JH, Shin MC, Yang BC, Lee JH, Cho IC. The MYH3 gene variant (g.-1805_-1810, ACGT) affects endophenotypes of myoglobin oxidation-reduction states in porcine muscles. Anim Genet 2022; 53:532-533. [PMID: 35698290 DOI: 10.1111/age.13226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 05/19/2022] [Accepted: 05/20/2022] [Indexed: 11/28/2022]
Affiliation(s)
- Yong-Jun Kang
- Subtropical Livestock Research Institute, National Institute of Animal Science, Rural Development Administration, Jeju, Korea
| | - Sang-Hyun Han
- Habitat Conservation Division, Korean National Park Research Institute, Korea National Park Service, Yongju, Korea
| | - Sang-Geum Kim
- Subtropical Livestock Research Institute, National Institute of Animal Science, Rural Development Administration, Jeju, Korea
| | - Su-Yeon Kim
- Subtropical Livestock Research Institute, National Institute of Animal Science, Rural Development Administration, Jeju, Korea
| | - Hyeon-Ah Kim
- Subtropical Livestock Research Institute, National Institute of Animal Science, Rural Development Administration, Jeju, Korea
| | - Ji-Hyun Yoo
- Subtropical Livestock Research Institute, National Institute of Animal Science, Rural Development Administration, Jeju, Korea
| | - Moon-Cheol Shin
- Subtropical Livestock Research Institute, National Institute of Animal Science, Rural Development Administration, Jeju, Korea
| | - Byoung-Chul Yang
- Subtropical Livestock Research Institute, National Institute of Animal Science, Rural Development Administration, Jeju, Korea
| | - Jun Heon Lee
- Division of Animal and Dairy Science, Chungnam National University, Daejeon, Korea
| | - In-Cheol Cho
- Subtropical Livestock Research Institute, National Institute of Animal Science, Rural Development Administration, Jeju, Korea
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30
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Liu H, Hou L, Zhou W, Wang B, Han P, Gao C, Niu P, Zhang Z, Li Q, Huang R, Li P. Genome-Wide Association Study and FST Analysis Reveal Four Quantitative Trait Loci and Six Candidate Genes for Meat Color in Pigs. Front Genet 2022; 13:768710. [PMID: 35464836 PMCID: PMC9023761 DOI: 10.3389/fgene.2022.768710] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 01/24/2022] [Indexed: 12/12/2022] Open
Abstract
Meat color is the primary criterion by which consumers evaluate meat quality. However, there are a few candidate genes and molecular markers of meat color that were reported for pig molecular breeding. The purpose of the present study is to identify the candidate genes affecting meat color and provide the theoretical basis for meat color molecular breeding. A total of 306 Suhuai pigs were slaughtered, and meat color was evaluated at 45 min and 24 h after slaughter by CIELAB color space. All individuals were genotyped using GeneSeek GGP-Porcine 80K SNP BeadChip. The genomic estimated breeding values (GEBVs), heritability, and genetic correlation of meat color were calculated by DMU software. The genome-wide association studies (GWASs) and the fixation index (FST) tests were performed to identify SNPs related to meat color, and the candidate genes within 1 Mb upstream and downstream of significant SNPs were screened by functional enrichment analysis. The heritability of L* 45 min, L* 24 h, a* 45 min, a* 24 h, b* 45 min, and b* 24 h was 0.20, 0.16, 0.30, 0.13, 0.29, and 0.22, respectively. The genetic correlation between a* (a* 45 min and a* 24 h) and L* (L* 45 min and L* 24 h) is strong, whereas the genetic correlation between b* 45 min and b* 24 h is weak. Forty-nine significant SNPs associated with meat color were identified through GWAS and FST tests. Among these SNPs, 34 SNPs were associated with L* 45 min within a 5-Mb region on Sus scrofa chromosome 11 (SSC11); 22 SNPs were associated with a* 45 min within a 14.72-Mb region on SSC16; six SNPs were associated with b* 45 min within a 4.22-Mb region on SSC13; 11 SNPs were associated with b* 24 h within a 2.12-Mb region on SSC3. These regions did not overlap with meat color–associated QTLs reported previously. Moreover, six candidate genes (HOMER1, PIK3CG, PIK3CA, VCAN, FABP3, and FKBP1B), functionally related to muscle development, phosphatidylinositol phosphorylation, and lipid binding, were detected around these significant SNPs. Taken together, our results provide a set of potential molecular markers for the genetic improvement of meat color in pigs.
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Affiliation(s)
- Hang Liu
- Institute of Swine Science, Nanjing Agricultural University, Nanjing, China
- Huaian Academy, Nanjing Agricultural University, Huaian, China
- Hangzhou Academy of Agricultural Sciences, Hangzhou, China
| | - Liming Hou
- Institute of Swine Science, Nanjing Agricultural University, Nanjing, China
- Huaian Academy, Nanjing Agricultural University, Huaian, China
| | - Wuduo Zhou
- Institute of Swine Science, Nanjing Agricultural University, Nanjing, China
| | - Binbin Wang
- Institute of Swine Science, Nanjing Agricultural University, Nanjing, China
- Huaian Academy, Nanjing Agricultural University, Huaian, China
| | - Pingping Han
- Institute of Swine Science, Nanjing Agricultural University, Nanjing, China
| | - Chen Gao
- Institute of Swine Science, Nanjing Agricultural University, Nanjing, China
- Huaian Academy, Nanjing Agricultural University, Huaian, China
| | - Peipei Niu
- Huaian Academy, Nanjing Agricultural University, Huaian, China
| | - Zongping Zhang
- Huaian Academy, Nanjing Agricultural University, Huaian, China
| | - Qiang Li
- Huaiyin Pig Breeding Farm of Huaian City, Huaian, China
| | - Ruihua Huang
- Institute of Swine Science, Nanjing Agricultural University, Nanjing, China
- Huaian Academy, Nanjing Agricultural University, Huaian, China
| | - Pinghua Li
- Institute of Swine Science, Nanjing Agricultural University, Nanjing, China
- Huaian Academy, Nanjing Agricultural University, Huaian, China
- *Correspondence: Pinghua Li,
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31
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Xu J, Jiang AM, Zhang C, Zheng Y, Zhang T, Zhou L. Potential of eight mutations for marker-assisted breeding in Chinese Lulai black pigs. CANADIAN JOURNAL OF ANIMAL SCIENCE 2022. [DOI: 10.1139/cjas-2021-0108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Molecular marker-assisted selection (MAS) provides an efficient tool for pig breeding. In this study, according to the literature, we selected eight effective or causal mutations from eight functional genes, including five causal mutations in PHKG1 (rs330928088), MUC13 (rs319699771), IGF2 (g.3072G>A), VRTN (g.20311_20312ins291) and MYH3 (XM_013981330.2:g.-1805_-1810del) genes, and three effective mutations in LIPE (rs328830166), LEPR (rs45435518) and MC4R (rs81219178) genes, to investigate the potential breeding effect of them in 418 Lulai pigs. The linear model was used to analyze the association between mutations and intramuscular fat (IMF) content, average backfat thickness (ABT) and muscle moisture percent (MMP). The results revealed that among the four effective mutations, only the mutation in the LEPR gene, which affect IMF deposition, was significantly associated with IMF content. However, the other molecular markers were not significantly associated with the affected traits reported in previous studies, and these mutations are ineffective for MAS in the Lulai black pig population. Therefore, causal mutations in PHKG1, IGF2 and VRTN genes, and an effective mutation in LEPR gene could be used as effective breeding makers for MAS in Lulai pigs. These results can provide helpful information for further breeding in Lulai black pigs.
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Affiliation(s)
- Jing Xu
- Qingdao Agricultural University, 98431, Qingdao, China, 266109
| | - Ai mei Jiang
- Jiaozhou City Bureau of Agriculture and Rural Affairs, Qingdao, China
| | | | | | - Tingrong Zhang
- Qingdao Agricultural University, 98431, Qingdao, China, 266109
| | - Lisheng Zhou
- Qingdao Agricultural University, 98431, Qingdao, China, 266109
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32
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Dietary lycopene supplementation improves meat quality, antioxidant capacity and skeletal muscle fiber type transformation in finishing pigs. ANIMAL NUTRITION (ZHONGGUO XU MU SHOU YI XUE HUI) 2022; 8:256-264. [PMID: 34988307 PMCID: PMC8688882 DOI: 10.1016/j.aninu.2021.06.012] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 06/04/2021] [Accepted: 06/18/2021] [Indexed: 01/08/2023]
Abstract
This study aimed to investigate effects of dietary lycopene supplementation on meat quality, antioxidant ability and muscle fiber type transformation in finishing pigs. In a 70-day experiment, 18 Duroc × Landrace × Yorkshire barrows were randomly allocated to 3 dietary treatments including a basal diet supplemented with 0, 100 and 200 mg/kg lycopene, respectively. Each dietary treatment had 6 replicates with one pig each. Results showed that dietary 200 mg/kg lycopene supplementation increased muscle redness a∗ value, intramuscular fat and crude protein contents, and decreased muscle lightness L∗ and yellowness b∗ values (P < 0.05), suggesting that addition of 200 mg/kg lycopene to the diet of finishing pigs improved color, nutritional value and juiciness of pork after slaughter. Results also showed that dietary lycopene supplementation enhanced antioxidant capacity of finishing pigs (P < 0.05). Moreover, dietary supplementation of 200 mg/kg lycopene significantly increased slow myosin heavy chain (MyHC) protein level and slow-twitch fiber percentage, and decreased fast MyHC protein level and fast-twitch fiber percentage (P < 0.05), suggesting that the addition of 200 mg/kg lycopene to the diet of finishing pigs promoted muscle fiber type conversion from fast-twitch to slow-twitch. Together, we provide the first evidence that dietary 200 mg/kg lycopene supplementation improves meat quality, enhances antioxidant capacity and promotes muscle fiber type transformation from fast-twitch to slow-twitch in finishing pigs.
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33
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Salavati M, Woolley SA, Cortés Araya Y, Halstead MM, Stenhouse C, Johnsson M, Ashworth CJ, Archibald AL, Donadeu FX, Hassan MA, Clark EL. Profiling of open chromatin in developing pig (Sus scrofa) muscle to identify regulatory regions. G3 (BETHESDA, MD.) 2022; 12:6460335. [PMID: 34897420 PMCID: PMC9210303 DOI: 10.1093/g3journal/jkab424] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 12/03/2021] [Indexed: 06/14/2023]
Abstract
There is very little information about how the genome is regulated in domestic pigs (Sus scrofa). This lack of knowledge hinders efforts to define and predict the effects of genetic variants in pig breeding programs. To address this knowledge gap, we need to identify regulatory sequences in the pig genome starting with regions of open chromatin. We used the "Improved Protocol for the Assay for Transposase-Accessible Chromatin (Omni-ATAC-Seq)" to identify putative regulatory regions in flash-frozen semitendinosus muscle from 24 male piglets. We collected samples from the smallest-, average-, and largest-sized male piglets from each litter through five developmental time points. Of the 4661 ATAC-Seq peaks identified that represent regions of open chromatin, >50% were within 1 kb of known transcription start sites. Differential read count analysis revealed 377 ATAC-Seq defined genomic regions where chromatin accessibility differed significantly across developmental time points. We found regions of open chromatin associated with downregulation of genes involved in muscle development that were present in small-sized fetal piglets but absent in large-sized fetal piglets at day 90 of gestation. The dataset that we have generated provides a resource for studies of genome regulation in pigs and contributes valuable functional annotation information to filter genetic variants for use in genomic selection in pig breeding programs.
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Affiliation(s)
- Mazdak Salavati
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh EH25 9RG, UK
- Centre for Tropical Livestock Genetics and Health (CTLGH), Roslin Institute, University of Edinburgh, Edinburgh EH25 9RG, UK
| | - Shernae A Woolley
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh EH25 9RG, UK
| | - Yennifer Cortés Araya
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh EH25 9RG, UK
| | - Michelle M Halstead
- Department of Animal Science, University of California Davis, Davis, CA 95616, USA
| | - Claire Stenhouse
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh EH25 9RG, UK
- Department of Animal Science, Texas A&M University, College Station, TX 77843, USA
| | - Martin Johnsson
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh EH25 9RG, UK
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala 750 07, Sweden
| | - Cheryl J Ashworth
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh EH25 9RG, UK
| | - Alan L Archibald
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh EH25 9RG, UK
| | - Francesc X Donadeu
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh EH25 9RG, UK
| | - Musa A Hassan
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh EH25 9RG, UK
- Centre for Tropical Livestock Genetics and Health (CTLGH), Roslin Institute, University of Edinburgh, Edinburgh EH25 9RG, UK
| | - Emily L Clark
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh EH25 9RG, UK
- Centre for Tropical Livestock Genetics and Health (CTLGH), Roslin Institute, University of Edinburgh, Edinburgh EH25 9RG, UK
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34
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Hao D, Wang X, Yang Y, Thomsen B, Holm LE, Qu K, Huang B, Chen H. Integrated Analysis of mRNA and MicroRNA Co-expressed Network for the Differentiation of Bovine Skeletal Muscle Cells After Polyphenol Resveratrol Treatment. Front Vet Sci 2022; 8:777477. [PMID: 35036414 PMCID: PMC8759604 DOI: 10.3389/fvets.2021.777477] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 11/15/2021] [Indexed: 01/01/2023] Open
Abstract
Resveratrol (RSV) has been confirmed to benefit human health. Resveratrol supplemented in the feeds of animals improved pork, chicken, and duck meat qualities. In this study, we identified differentially expressed (DE) messenger RNAs (mRNAs) (n = 3,856) and microRNAs (miRNAs) (n = 93) for the weighted gene co-expression network analysis (WGCNA) to investigate the co-expressed DE mRNAs and DE miRNAs in the primary bovine myoblasts after RSV treatment. The mRNA results indicated that RSV treatments had high correlations with turquoise module (0.91, P-value = 0.01) and blue module (0.93, P-value < 0.01), while only the turquoise module (0.96, P-value < 0.01) was highly correlated with the treatment status using miRNA data. After biological enrichment analysis, the 2,579 DE genes in the turquoise module were significantly enriched in the Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. The top two GO terms were actin filament-based process (GO:0030029) and actin cytoskeleton organization (GO:0030036). The top two KEGG pathways were regulation of actin cytoskeleton (bta04810) and tight junction (bta04530). Then, we constructed the DE mRNA co-expression and DE miRNA co-expression networks in the turquoise module and the mRNA–miRNA targeting networks based on their co-expressions in the key module. In summary, the RSV-induced miRNAs participated in the co-expression networks that could affect mRNA expressions to regulate the primary myoblast differentiation. Our study provided a better understanding of the roles of RSV in inducing miRNA and of the characteristics of DE miRNAs in the key co-expressed module in regulation of mRNAs and revealed new candidate regulatory miRNAs and genes for the beef quality traits.
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Affiliation(s)
- Dan Hao
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, Yangling, China.,Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Xiao Wang
- Konge Larsen ApS, Kongens Lyngby, Denmark
| | - Yu Yang
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, Yangling, China
| | - Bo Thomsen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Lars-Erik Holm
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Kaixing Qu
- Academy of Science and Technology, Chuxiong Normal University, Chuxiong, China
| | - Bizhi Huang
- Yunnan Academy of Grassland and Animal Science, Kunming, China
| | - Hong Chen
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, Yangling, China.,College of Animal Science, Xinjiang Agricultural University, Urumqi, China
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35
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Ding R, Zhuang Z, Qiu Y, Ruan D, Wu J, Ye J, Cao L, Zhou S, Zheng E, Huang W, Wu Z, Yang J. Identify known and novel candidate genes associated with backfat thickness in Duroc pigs by large-scale genome-wide association analysis. J Anim Sci 2022; 100:6509022. [PMID: 35034121 PMCID: PMC8867564 DOI: 10.1093/jas/skac012] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 01/14/2022] [Indexed: 01/18/2023] Open
Abstract
Backfat thickness (BFT) is complex and economically important traits in the pig industry, since it reflects fat deposition and can be used to measure the carcass lean meat percentage in pigs. In this study, all 6,550 pigs were genotyped using the Geneseek Porcine 50K SNP Chip to identify SNPs related to BFT and to search for candidate genes through genome-wide association analysis in two Duroc populations. In total, 80 SNPs, including 39 significant and 41 suggestive SNPs, and 6 QTLs were identified significantly associated with the BFT. In addition, 9 candidate genes, including a proven major gene MC4R, 3 important candidate genes (RYR1, HMGA1, and NUDT3) which were previously described as related to BFT, and 5 novel candidate genes (SIRT2, NKAIN2, AMH, SORCS1, and SORCS3) were found based on their potential functional roles in BFT. The functions of candidate genes and gene set enrichment analysis indicate that most important pathways are related to energy homeostasis and adipogenesis. Finally, our data suggest that most of the candidate genes can be directly used for genetic improvement through molecular markers, except that the MC4R gene has an antagonistic effect on growth rate and carcass lean meat percentage in breeding. Our results will advance our understanding of the complex genetic architecture of BFT traits and laid the foundation for additional genetic studies to increase carcass lean meat percentage of pig through marker-assisted selection and/or genomic selection.
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Affiliation(s)
- Rongrong Ding
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, 510642, P. R. China,Guangdong Wens Breeding Swine Technology Co., Ltd., Guangdong, 527400, P. R. China
| | - Zhanwei Zhuang
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, 510642, P. R. China
| | - Yibin Qiu
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, 510642, P. R. China
| | - Donglin Ruan
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, 510642, P. R. China
| | - Jie Wu
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, 510642, P. R. China
| | - Jian Ye
- Guangdong Wens Breeding Swine Technology Co., Ltd., Guangdong, 527400, P. R. China
| | - Lu Cao
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, 510642, P. R. China
| | - Shenping Zhou
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, 510642, P. R. China
| | - Enqin Zheng
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, 510642, P. R. China,Lingnan Guangdong Laboratory of Modern Agriculture, Guangzhou, 510642, P. R. China
| | - Wen Huang
- Department of Animal Science, Michigan State University, East Lansing, MI, USA
| | - Zhenfang Wu
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, 510642, P. R. China,Guangdong Wens Breeding Swine Technology Co., Ltd., Guangdong, 527400, P. R. China,Lingnan Guangdong Laboratory of Modern Agriculture, Guangzhou, 510642, P. R. China
| | - Jie Yang
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, 510642, P. R. China,Lingnan Guangdong Laboratory of Modern Agriculture, Guangzhou, 510642, P. R. China,Corresponding authors:
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36
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Zhao L, Zhou L, Hao X, Wang L, Han F, Liu L, Duan X, Guo F, He J, Liu N. Identification and Characterization of Circular RNAs in Association With the Deposition of Intramuscular Fat in Aohan Fine-Wool Sheep. Front Genet 2021; 12:759747. [PMID: 34938314 PMCID: PMC8685527 DOI: 10.3389/fgene.2021.759747] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 11/02/2021] [Indexed: 01/20/2023] Open
Abstract
Aohan fine-wool sheep (AFWS) is a high-quality fine-wool sheep breed that supplies wool and meat. Research is needed on the molecular mechanism behind intramuscular fat (IMF) deposition that greatly improves mutton quality. The widely expressed non-coding RNA is physiologically used in roles such as competitive endogenous RNA (ceRNA) that includes circular RNAs (circRNAs). Although circRNAs were studied in many fields, little research was devoted to IMF in sheep. We used the longissimus dorsi muscle of 2 and 12-month-old AWFS as research material to identify circRNAs related to IMF deposition in these sheep by RNA-seq screening for differentially expressed circRNAs in the two age groups. A total of 11,565 candidate circRNAs were identified, of which the 104 differentially expressed circRNAs in the two age groups were analyzed. Enrichment analysis was performed using Gene Ontology and the Kyoto Encyclopedia of Genes and Genomes. The enriched pathways included lipid transport (GO:0006869), negative regulation of canonical Wnt signaling pathway (GO:0090090), fat digestion and absorption (ko04975), and sphingolipid metabolism (ko00600). The differentially expressed circRNAs included ciRNA455, circRNA9086, circRNA7445, circRNA4557, and others. The source genes involved in these pathways might regulate IMF deposition. We used the TargetScan and miRanda software for interaction analysis, and a network diagram of circRNA-miRNA interactions was created. CircRNA455-miR-127, circRNA455-miR-29a, circRNA455-miR-103, circRNA4557-mir149-5p, and circRNA2440-mir-23a might be involved in the IMF deposition process. The targeting relationship of circRNA4557-miR-149-5p was verified by a dual-luciferase reporter assay. The RT-qPCR results of seven randomly selected circRNAs were consistent with the sequencing results. This study provides additional information on circRNA regulation of IMF deposition in AFWS and is a useful resource for future research on this sheep breed.
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Affiliation(s)
- Le Zhao
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, China
| | - Lisheng Zhou
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, China
| | - Xiaojing Hao
- Qingdao Animal Husbandry and Veterinary Research Institute, Qingdao, China
| | - Lei Wang
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, China
| | - Fuhui Han
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, China
| | - Lirong Liu
- China Animal Health and Epidemiology Center, Qingdao, China
| | - Xinming Duan
- Nongfayuan Zhejiang Agricultural Development Co. Ltd., Huzhou, China
| | - Feng Guo
- Tongliao Animal Agriculture Development Service Center, Tongliao, China
| | - Jianning He
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, China
| | - Nan Liu
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, China
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Li D, Huang M, Zhuang Z, Ding R, Gu T, Hong L, Zheng E, Li Z, Cai G, Wu Z, Yang J. Genomic Analyses Revealed the Genetic Difference and Potential Selection Genes of Growth Traits in Two Duroc Lines. Front Vet Sci 2021; 8:725367. [PMID: 34557543 PMCID: PMC8453014 DOI: 10.3389/fvets.2021.725367] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 08/03/2021] [Indexed: 01/02/2023] Open
Abstract
Duroc pigs are famous for their high growth rate, feed conversion efficiency, and lean meat percentage. Given that they have been subjected to artificial selection and breeding in multiple countries, various lines with obvious differences in production performance have formed. In this study, we genotyped 3,770 American Duroc (AD) pigs and 2,098 Canadian Duroc (CD) pigs using the GeneSeek Porcine SNP50 Beadchip to dissect the genetic differences and potential selection genes of growth traits in these two Duroc pig lines. Population structure detection showed that there were significant genetic differences between the two Duroc pig lines. Hence, we performed F ST and cross-population extended haplotype homozygosity (XP-EHH) analyses between the two lines. As a result, we identified 38 annotated genes that were significantly enriched in the gland development pathway in the AD line, and 61 annotated genes that were significantly enriched in the immune-related pathway in the CD line. For three growth traits including backfat thickness (BFT), loin muscle depth (LMD), and loin muscle area (LMA), we then performed selection signature detection at 5 and 10% levels within the line and identified different selected regions and a series of candidate genes that are involved in lipid metabolism and skeletal muscle development or repair, such as IRX3, EBF2, WNT10B, TLR2, PITX3, and SGCD. The differences in selected regions and genes between the two lines may be the cause of the differences in growth traits. Our study suggests significant genetic differences between the AD and CD lines, which provide a theoretical basis for selecting different Duroc lines as sires for different needs.
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Affiliation(s)
- Desen Li
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, China
| | - Min Huang
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, China
| | - Zhanwei Zhuang
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, China
| | - Rongrong Ding
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, China
| | - Ting Gu
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, China
| | - Linjun Hong
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, China
| | - Enqin Zheng
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, China
| | - Zicong Li
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, China
| | - Gengyuan Cai
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, China
| | - Zhenfang Wu
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, China.,Lingnan Guangdong Laboratory of Modern Agriculture, Guangzhou, China
| | - Jie Yang
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, China
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Li M, Zhu M, Chai W, Wang Y, Fan D, Lv M, Jiang X, Liu Y, Wei Q, Wang C. Determination of lipid profiles of Dezhou donkey meat using an LC-MS-based lipidomics method. J Food Sci 2021; 86:4511-4521. [PMID: 34535907 DOI: 10.1111/1750-3841.15917] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 08/02/2021] [Accepted: 08/23/2021] [Indexed: 12/17/2022]
Abstract
Intramuscular fat (IMF) is an important factor affecting meat quality, but lipid and metabolic profiles of donkey meat remain unclear. The present study was conducted to investigate lipid characteristics in different parts of Dezhou donkey using lipidomics. The results show that IMF was more abundant in longissimus dorsi muscle (LDM) than rump muscle (RM) and hamstring muscle (HM), and mainly composed of triglycerides (TGs) rich in saturated fatty acid (SFAs) and monounsaturated fatty acid (MUFAs). A total of 1143 lipids belonging to 14 subclasses were identified in donkey meat, of which 73 lipids (23 upregulated and 50 downregulated) including glycerolipids (GLs), glycerophospholipids (GPs) and sphingolipids (SPs) were significantly different and are therefore potential biomarkers in LDM versus RM versus HM analyses (variable importance in projection >1, p < 0.05). Notably, 21 TGs upregulated in LDM were rich in MUFAs at sn-1 and SFAs at 2 and 3 positions of TG. Donkey muscle accumulated far more SFAs at the sn-3 position of TG, while more SFAs were present at the sn-1 positions of phosphatidylcholine (PC) and phosphatidylethanolamine (PE), and the percentages of SFAs at the three positions in TG, PC, and PE in the LDM group were much higher. The abundance of MUFAs at the sn-2 positions of TG, PC, and PE was significantly greater than in sn-1 or 3 positions, and the percentages of 18:1n-9 at the sn-1 and 2 position of TGs in LDM were significantly higher than in RM and HM groups. Polyunsaturated fatty acids (e.g.,18:2n-6, 18:3n-3, and 20:4n-6) tended to occur at the sn-1 position in TG, but at the sn-2 position in PC and PE. Significantly differential lipids were mainly enriched in GP, GL, and SP pathways, all considered key pathways for regulating IMF. The results reveal the components, structures and metabolic pathways of lipid molecules in donkey meat, and provide novel insight into the development of donkey meat products and accurate regulation of IMF. PRACTICAL APPLICATION: Intramuscular fat (IMF) is an important factor affecting meat quality, which is directly related to meat flavor, juiciness, and tenderness, but lipid and metabolic profiles of IMF remain unclear. The current results provide basic information for the development of donkey meat products, and broaden our understanding of the regulation of IMF.
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Affiliation(s)
- Mengmeng Li
- College of Agronomy, Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, Liaocheng University, Liaocheng, China
| | - Mingxia Zhu
- College of Agronomy, Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, Liaocheng University, Liaocheng, China
| | - Wenqiong Chai
- College of Agronomy, Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, Liaocheng University, Liaocheng, China
| | - Yonghui Wang
- College of Agronomy, Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, Liaocheng University, Liaocheng, China
| | - Dongmei Fan
- College of Agronomy, Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, Liaocheng University, Liaocheng, China
| | - Mengqing Lv
- College of Agronomy, Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, Liaocheng University, Liaocheng, China
| | - Xiaojing Jiang
- College of Agronomy, Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, Liaocheng University, Liaocheng, China
| | - Yongxiang Liu
- College of Agronomy, Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, Liaocheng University, Liaocheng, China
| | - Qingxin Wei
- College of Agronomy, Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, Liaocheng University, Liaocheng, China
| | - Changfa Wang
- College of Agronomy, Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, Liaocheng University, Liaocheng, China
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Goda Y, Yamanaka D, Nishi H, Masuda M, Kamei H, Kumano M, Ito K, Katsumata M, Yamanouchi K, Kataoka N, Hakuno F, Takahashi SI. Dietary lysine restriction induces lipid accumulation in skeletal muscle through an increase in serum threonine levels in rats. J Biol Chem 2021; 297:101179. [PMID: 34508782 PMCID: PMC8488598 DOI: 10.1016/j.jbc.2021.101179] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Revised: 08/23/2021] [Accepted: 09/07/2021] [Indexed: 11/02/2022] Open
Abstract
We previously reported that dietary amino acid restriction induces the accumulation of triglycerides (TAG) in the liver of growing rats. However, differences in TAG accumulation in individual cell types or other tissues were not examined. In this study, we show that TAG also accumulates in the muscle and adipose tissues of rats fed a low amino acid (low-AA) diet. In addition, dietary lysine restriction (low-Lys) induces lipid accumulation in muscle and adipose tissues. In adjusting the nitrogen content to that of the control diet, we found that glutamic acid supplementation to the low-AA diet blocked lipid accumulation, but supplementation with the low-Lys diet did not, suggesting that a shortage of nitrogen caused lipids to accumulate in the skeletal muscle in the rats fed a low-AA diet. Serum amino acid measurement revealed that, in rats fed a low-Lys diet, serum lysine levels were decreased, while serum threonine levels were significantly increased compared with the control rats. When the threonine content was restricted in the low-Lys diet, TAG accumulation induced by the low-Lys diet was completely abolished in skeletal muscle. Moreover, in L6 myotubes cultured in medium containing high threonine and low lysine, fatty acid uptake was enhanced compared with that in cells cultured in control medium. These findings suggest that the increased serum threonine in rats fed a low-Lys diet resulted in lipid incorporation into skeletal muscle, leading to the formation of fatty muscle tissue. Collectively, we propose conceptual hypothesis that "amino-acid signal" based on lysine and threonine regulates lipid metabolism.
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Affiliation(s)
- Yuki Goda
- Departments of Animal Sciences and Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Daisuke Yamanaka
- Department of Veterinary Medical Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Hiroki Nishi
- Departments of Animal Sciences and Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Masato Masuda
- Departments of Animal Sciences and Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Hiroyasu Kamei
- Departments of Animal Sciences and Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Mikako Kumano
- Departments of Animal Sciences and Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Koichi Ito
- Department of Veterinary Medical Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Masaya Katsumata
- School of Veterinary Science, Azabu University, Sagamihara, Kanagawa, Japan
| | - Keitaro Yamanouchi
- Department of Veterinary Medical Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Naoyuki Kataoka
- Departments of Animal Sciences and Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Fumihiko Hakuno
- Departments of Animal Sciences and Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan.
| | - Shin-Ichiro Takahashi
- Departments of Animal Sciences and Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan.
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40
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GWAS and Post-GWAS High-Resolution Mapping Analyses Identify Strong Novel Candidate Genes Influencing the Fatty Acid Composition of the Longissimus dorsi Muscle in Pigs. Genes (Basel) 2021; 12:genes12091323. [PMID: 34573305 PMCID: PMC8468772 DOI: 10.3390/genes12091323] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 08/23/2021] [Accepted: 08/25/2021] [Indexed: 12/02/2022] Open
Abstract
Fatty acid (FA) composition is one of the most important parameters for the assessment of meat quality in pigs. The FA composition in pork can also affect human health. Our aim was to identify quantitative trait loci (QTLs) and positional candidate genes affecting the FA profile of the longissimus dorsi muscle in a large F2 intercross between Landrace and Korean native pigs comprising 1105 F2 progeny by genome-wide association studies (GWAS) and post-GWAS high-resolution mapping analyses. We performed GWAS using the PorcineSNP60K BeadChip and a linear mixed model. Four genome-wide significant QTL regions in SSC8, SSC12, SSC14, and SSC16 were detected (p < 2.53 × 10−7). Several co-localizations of QTLs in SSC12 for oleic acid, linoleic acid, arachidonic acid, monounsaturated FAs, polyunsaturated FAs, and the polyunsaturated/saturated FA ratio were observed. To refine the QTL region in SSC12, a linkage and linkage disequilibrium analysis was applied and could narrow down the critical region to a 0.749 Mb region. Of the genes in this region, GAS7, MYH2, and MYH3 were identified as strong novel candidate genes based on further conditional association analyses. These findings provide a novel insight into the genetic basis of FA composition in pork and could contribute to the improvement of pork quality.
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41
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Yang Y, Cheng Z, Zhang W, Hei W, Lu C, Cai C, Zhao Y, Gao P, Guo X, Cao G, Li B. GOT1 regulates adipocyte differentiation by altering NADPH content. Anim Biosci 2021; 35:155-165. [PMID: 34474530 PMCID: PMC8738948 DOI: 10.5713/ab.21.0174] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 07/27/2021] [Indexed: 12/02/2022] Open
Abstract
Objective This study was performed to examine whether the porcine glutamic-oxaloacetic transaminase 1 (GOT1) gene has important functions in regulating adipocyte differentiation. Methods Porcine GOT1 knockout and overexpression vectors were constructed and transfected into the mouse adipogenic 3T3-L1 cells. Lipid droplets levels were measured after 8 days of differentiation. The mechanisms through which GOT1 participated in lipid deposition were examined by measuring the expression of malate dehydrogenase 1 (MDH1) and malic enzyme (ME1) and the cellular nicotinamide adenine dinucleotide phosphate (NADPH) content. Results GOT1 knockout significantly decreased lipid deposition in the 3T3-L1 cells (p< 0.01), whereas GOT1 overexpression significantly increased lipid accumulation (p<0.01). At the same time, GOT1 knockout significantly decreased the NADPH content and the expression of MDH1 and ME1 in the 3T3-L1 cells. Overexpression of GOT1 significantly increased the NADPH content and the expression of MDH1 and ME1, suggesting that GOT1 regulated adipocyte differentiation by altering the NADPH content. Conclusion The results preliminarily revealed the effector mechanisms of GOT1 in regulating adipose differentiation. Thus, a theoretical basis is provided for improving the quality of pork and studies on diseases associated with lipid metabolism.
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Affiliation(s)
- Yang Yang
- College of Animal Science, Shanxi Agricultural University, Taigu 030801, China
| | - Zhimin Cheng
- College of Animal Science, Shanxi Agricultural University, Taigu 030801, China.,Shanxi Academy of Advanced Research and Innovation, Taiyuan 030032, China
| | - Wanfeng Zhang
- College of Animal Science, Shanxi Agricultural University, Taigu 030801, China
| | - Wei Hei
- College of Animal Science, Shanxi Agricultural University, Taigu 030801, China
| | - Chang Lu
- College of Animal Science, Shanxi Agricultural University, Taigu 030801, China
| | - Chunbo Cai
- College of Animal Science, Shanxi Agricultural University, Taigu 030801, China
| | - Yan Zhao
- College of Animal Science, Shanxi Agricultural University, Taigu 030801, China
| | - Pengfei Gao
- College of Animal Science, Shanxi Agricultural University, Taigu 030801, China
| | - Xiaohong Guo
- College of Animal Science, Shanxi Agricultural University, Taigu 030801, China
| | - Guoqing Cao
- College of Animal Science, Shanxi Agricultural University, Taigu 030801, China
| | - Bugao Li
- College of Animal Science, Shanxi Agricultural University, Taigu 030801, China
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Wang BB, Hou LM, Zhou WD, Liu H, Tao W, Wu WJ, Niu PP, Zhang ZP, Zhou J, Li Q, Huang RH, Li PH. Genome-wide association study reveals a quantitative trait locus and two candidate genes on Sus scrofa chromosome 5 affecting intramuscular fat content in Suhuai pigs. Animal 2021; 15:100341. [PMID: 34425484 DOI: 10.1016/j.animal.2021.100341] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2020] [Revised: 07/22/2021] [Accepted: 07/23/2021] [Indexed: 12/14/2022] Open
Abstract
Intramuscular fat content (IFC) is an essential quantitative trait of meat, affecting multiple meat quality indicators. A certain amount of IFC could not only improve the sensory score of pork but also increase the flavour, tenderness, juiciness and shelf-life. To dissect the genetic determinants of IFC, two methods, including genome-wide efficient mixed-model analysis (GEMMA) and linkage disequilibrium adjusted kinships (LDAKs), were used to carry out genome-wide association studies for IFC in Suhuai pig population. A total of 14 and 18 significant single nucleotide polymorphisms (SNPs) were identified by GEMMA and LDAK, respectively. The results of these two methods were highly consistent and all 14 significant SNPs in GEMMA were detected by LDAK. Seven of the 18 SNPs reached the genome-wide significance level (P < 9.85E-07) while 11 cases reached the suggestive significance level (P < 1.77E-05). These significant SNPs were mainly distributed on Sus scrofa chromosome (SSC) 5, 3, and 7. Moreover, one locus resides in a 2.27 Mb (71.37-73.64 Mb) region on SSC5 harbouring 13 significant SNPs associated with IFC, and the lead SNP (rs81302978) also locates in this region. Linkage disequilibrium (LD) analysis showed that there were four pairs of complete LD (r2 = 1) among these 13 SNPs, and the remaining 9 SNPs with incomplete LD (r2 ≠ 1) were selected for subsequent analyses of IFC. Association analyses showed that 7 out of 9 SNPs were significantly associated with IFC (P < 0.05) in 330 Suhuai pigs, and the other 2 SNPs tended to reach a significant association level with IFC (P < 0.1). The phenotypic variance explained (PVE) range of these 9 SNPs was 0.92-3.55%. Meanwhile, the lead SNP was also significantly associated (rs81302978) with IFC (P < 0.05) in 378 commercial hybrid pigs (Pietrain × Duroc) × (Landrace × Yorkshire) (PDLY), and the PVE was 1.38%. Besides, two lipid metabolism-relevant candidate genes, the leucine rich repeat kinase 2 (LRRK2) and PDZ domain containing ring finger 4 (PDZRN4) were identified in the 2.27 Mb region on SSC5. In conclusion, our results may provide a set of markers useful for genetic improvement of IFC in pigs and will advance the genome selection process of IFC on pig breeding programmes.
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Affiliation(s)
- B B Wang
- Institute of Swine Science, Nanjing Agricultural University, Nanjing 210095, China; Huaian Academy, Nanjing Agricultural University, Huaian 223005, China
| | - L M Hou
- Institute of Swine Science, Nanjing Agricultural University, Nanjing 210095, China; Huaian Academy, Nanjing Agricultural University, Huaian 223005, China
| | - W D Zhou
- Institute of Swine Science, Nanjing Agricultural University, Nanjing 210095, China
| | - H Liu
- Institute of Swine Science, Nanjing Agricultural University, Nanjing 210095, China; Huaian Academy, Nanjing Agricultural University, Huaian 223005, China
| | - W Tao
- Institute of Swine Science, Nanjing Agricultural University, Nanjing 210095, China; Huaian Academy, Nanjing Agricultural University, Huaian 223005, China
| | - W J Wu
- Institute of Swine Science, Nanjing Agricultural University, Nanjing 210095, China
| | - P P Niu
- Huaian Academy, Nanjing Agricultural University, Huaian 223005, China
| | - Z P Zhang
- Huaian Academy, Nanjing Agricultural University, Huaian 223005, China
| | - J Zhou
- Huaiyin Pig Breeding Farm of Huaian City, Huaian 223322, China
| | - Q Li
- Huaiyin Pig Breeding Farm of Huaian City, Huaian 223322, China
| | - R H Huang
- Institute of Swine Science, Nanjing Agricultural University, Nanjing 210095, China; Huaian Academy, Nanjing Agricultural University, Huaian 223005, China
| | - P H Li
- Institute of Swine Science, Nanjing Agricultural University, Nanjing 210095, China; Huaian Academy, Nanjing Agricultural University, Huaian 223005, China.
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Yan G, Liu X, Xiao S, Xin W, Xu W, Li Y, Huang T, Qin J, Xie L, Ma J, Zhang Z, Huang L. An imputed whole-genome sequence-based GWAS approach pinpoints causal mutations for complex traits in a specific swine population. SCIENCE CHINA-LIFE SCIENCES 2021; 65:781-794. [PMID: 34387836 DOI: 10.1007/s11427-020-1960-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Accepted: 05/19/2021] [Indexed: 01/08/2023]
Abstract
Sequencing-based genome-wide association studies (GWAS) have facilitated the identification of causal associations between genetic variants and traits in diverse species. However, it is cost-prohibitive for the majority of research groups to sequence a large number of samples. Here, we carried out genotype imputation to increase the density of single nucleotide polymorphisms in a large-scale Swine F2 population using a reference panel including 117 individuals, followed by a series of GWAS analyses. The imputation accuracies reached 0.89 and 0.86 for allelic concordance and correlation, respectively. A quantitative trait nucleotide (QTN) affecting the chest vertebrate was detected directly, while the investigation of another QTN affecting the residual glucose failed due to the presence of similar haplotypes carrying wild-type and mutant allelesin the reference panel used in this study. A high imputation accuracy was confirmed by Sanger sequencing technology for the most significant loci. Two candidate genes, CPNE5 and MYH3, affecting meat-related traits were proposed. Collectively, we illustrated four scenarios in imputation-based GWAS that may be encountered by researchers, and our results will provide an extensive reference for future genotype imputation-based GWAS analyses in the future.
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Affiliation(s)
- Guorong Yan
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
- Institute of Photomedicine, Shanghai Skin Disease Hospital, School of Medicine, Tongji University, Shanghai, 200092, China
| | - Xianxian Liu
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Shijun Xiao
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Wenshui Xin
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Wenwu Xu
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Yiping Li
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Tao Huang
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Jiangtao Qin
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Lei Xie
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Junwu Ma
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China.
| | - Zhiyan Zhang
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China.
| | - Lusheng Huang
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
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Ding R, Qiu Y, Zhuang Z, Ruan D, Wu J, Zhou S, Ye J, Cao L, Hong L, Xu Z, Zheng E, Li Z, Wu Z, Yang J. Genome-wide association studies reveals polygenic genetic architecture of litter traits in Duroc pigs. Theriogenology 2021; 173:269-278. [PMID: 34403972 DOI: 10.1016/j.theriogenology.2021.08.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 08/08/2021] [Accepted: 08/09/2021] [Indexed: 01/02/2023]
Abstract
With continuous improvement of sow litter size, breeders are gradually paying more attention to the quality of litter traits that directly impact the production efficiency of pig companies, such as the rate of piglets born alive (RBA) and the rate of healthy births (RHB). The objectives of this study are to dissect the genetic basis of litter traits in pig and to identify valuable genes and genetic markers, especially pleiotropic, for pig breeding. Herein, 1140 Duroc pigs and 2046 reproduction records, 5 litter traits, including the number of healthy births (NHB), number of deformed fetuses (NDF), number of stillborn (NSB), RBA, and RHB, were used in this study. Subsequently, a genome-wide association study (GWAS) was performed for the five litter traits in the first two parities from two Duroc populations. A total of 76 significantly related SNPs and 10 potential candidate genes (CAV1, DAB2, FGF12, FHOD3, DYNC2H1, GRHL1, TCTN3, PYROXD2, MMP8, MMP13, and PGR) were detected, including 13 pleiotropic SNPs that affected more than one litter trait. Finally, the functional enrichment analysis of functional genes that were closest to these significant SNPs indicated that most of the significant pathways were associated with hormone secretion and embryo and organ development. This study advances our understanding of the genetic mechanisms of litter traits, especially the survival rate of piglets born, and provides an opportunity to increase the quality of litter using marker-assisted selection or genomic selection in pigs.
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Affiliation(s)
- Rongrong Ding
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, 510642, PR China; Guangdong Wens Breeding Swine Technology Co., Ltd., Guangdong, 527400, PR China
| | - Yibin Qiu
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, 510642, PR China
| | - Zhanwei Zhuang
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, 510642, PR China
| | - Donglin Ruan
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, 510642, PR China
| | - Jie Wu
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, 510642, PR China
| | - Shenping Zhou
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, 510642, PR China
| | - Jian Ye
- Guangdong Wens Breeding Swine Technology Co., Ltd., Guangdong, 527400, PR China
| | - Lu Cao
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, 510642, PR China
| | - Linjun Hong
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, 510642, PR China
| | - Zheng Xu
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, 510642, PR China
| | - Enqin Zheng
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, 510642, PR China; Lingnan Guangdong Laboratory of Modern Agriculture, Guangzhou, 510642, PR China
| | - Zicong Li
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, 510642, PR China; Lingnan Guangdong Laboratory of Modern Agriculture, Guangzhou, 510642, PR China
| | - Zhenfang Wu
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, 510642, PR China; Guangdong Wens Breeding Swine Technology Co., Ltd., Guangdong, 527400, PR China; Lingnan Guangdong Laboratory of Modern Agriculture, Guangzhou, 510642, PR China.
| | - Jie Yang
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, 510642, PR China; Lingnan Guangdong Laboratory of Modern Agriculture, Guangzhou, 510642, PR China.
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Gu H, Zhou Y, Yang J, Li J, Peng Y, Zhang X, Miao Y, Jiang W, Bu G, Hou L, Li T, Zhang L, Xia X, Ma Z, Xiong Y, Zuo B. Targeted overexpression of PPARγ in skeletal muscle by random insertion and CRISPR/Cas9 transgenic pig cloning enhances oxidative fiber formation and intramuscular fat deposition. FASEB J 2021; 35:e21308. [PMID: 33481304 DOI: 10.1096/fj.202001812rr] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Revised: 12/08/2020] [Accepted: 12/11/2020] [Indexed: 11/11/2022]
Abstract
Peroxisome proliferator-activated receptor gamma (PPARγ) is a master regulator of adipogenesis and lipogenesis. To understand its roles in fiber formation and fat deposition in skeletal muscle, we successfully generated muscle-specific overexpression of PPARγ in two pig models by random insertion and CRISPR/Cas9 transgenic cloning procedures. The content of intramuscular fat was significantly increased in PPARγ pigs while had no changes on lean meat ratio. PPARγ could promote adipocyte differentiation by activating adipocyte differentiating regulators such as FABP4 and CCAAT/enhancer-binding protein (C/EBP), along with enhanced expression of LPL, FABP4, and PLIN1 to proceed fat deposition. Proteomics analyses demonstrated that oxidative metabolism of fatty acids and respiratory chain were activated in PPARγ pigs, thus, gathered more Ca2+ in PPARγ pigs. Raising of Ca2+ could result in increased phosphorylation of CAMKII and p38 MAPK in PPARγ pigs, which can stimulate MEF2 and PGC1α to affect fiber type and oxidative capacity. These results support that skeletal muscle-specific overexpression of PPARγ can promote oxidative fiber formation and intramuscular fat deposition in pigs.
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Affiliation(s)
- Hao Gu
- Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs & Key Laboratory of Agriculture Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, P.R. China
| | - Ying Zhou
- Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs & Key Laboratory of Agriculture Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, P.R. China
| | - Jinzeng Yang
- Department of Human Nutrition, Food and Animal Sciences, University of Hawaii at Manoa, Honolulu, HI, USA
| | - Jianan Li
- Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs & Key Laboratory of Agriculture Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, P.R. China
| | - Yaxin Peng
- Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs & Key Laboratory of Agriculture Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, P.R. China
| | - Xia Zhang
- Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs & Key Laboratory of Agriculture Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, P.R. China
| | - Yiliang Miao
- Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs & Key Laboratory of Agriculture Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, P.R. China
| | - Wei Jiang
- Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs & Key Laboratory of Agriculture Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, P.R. China
| | - Guowei Bu
- Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs & Key Laboratory of Agriculture Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, P.R. China
| | - Liming Hou
- Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs & Key Laboratory of Agriculture Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, P.R. China
| | - Ting Li
- Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs & Key Laboratory of Agriculture Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, P.R. China
| | - Lin Zhang
- Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs & Key Laboratory of Agriculture Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, P.R. China
| | - Xiaoliang Xia
- Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs & Key Laboratory of Agriculture Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, P.R. China
| | - Zhiyuan Ma
- Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs & Key Laboratory of Agriculture Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, P.R. China
| | - Yuanzhu Xiong
- Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs & Key Laboratory of Agriculture Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, P.R. China
| | - Bo Zuo
- Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs & Key Laboratory of Agriculture Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, P.R. China
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Zheng Q, Zhu C, Jing J, Ling Y, Qin S, Wang J, Zha L, Liu Y, Fang F. Morphological changes and functional circRNAs screening of rabbit skeletal muscle development. BMC Genomics 2021; 22:469. [PMID: 34167469 PMCID: PMC8223307 DOI: 10.1186/s12864-021-07706-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Accepted: 05/10/2021] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND The temporal expression pattern of circular RNAs (circRNAs) across developmental stages is essential for skeletal muscle growth and functional analysis. However, there are few analyses on the potential functions of circRNAs in rabbit skeletal muscle development. RESULTS Initially, the paraffin sections showed extremely significant differences in the diameter, number, area and density of skeletal muscle fibers of the fetus, child, adult rabbit hind legs (P < 0.01). Then, RNA-seq libraries of these three stages were constructed. A total of 481 differentially expressed circRNAs (DE-circRNAs) and 5,658 differentially expressed genes (DEGs) were identified. Subsequently, DE-circRNAs, whose host genes were DEGs or non-DEGs, were analyzed by GO respectively. In the fetus vs. child group, up-regulated DE-circRNAs (whose host genes were DEGs) were related to muscle fiber structure, and down-regulated ones were related to mitosis. The up-regulated DE-circRNAs (whose host genes were non-DEGs) were involved in enzyme activity, methylation and glycosylation, and the down-regulated ones were involved in mitosis and catabolism. In the fetus vs. adult group, the up-regulated DE-circRNAs (whose host genes were DEGs) were related to skeletal muscle basic structure, and the down-regulated ones were also associated with cell proliferation. But the up-regulated DE-circRNAs (whose host genes were non-DEGs) were connected with regulation of histone ubiquitination, chromatin and organelles. The down-regulated DE-circRNAs were connected with the catabolism processes. In addition, novel_circ_0022663 and novel_circ_0005489, which might have coding potential, and novel_circ_0004210 and novel_circ_0001669, which might have miRNA sponge capability, were screened out. CONCLUSIONS In this study, hind leg muscles of fetus, child and adult rabbits were collected for paraffin section and RNA-seq to observe the structural changes of skeletal muscle and obtain circRNA expression profiles at different stages. These data provided a catalog of circRNAs related to muscle development in New Zealand rabbits, allowing us to better understand the functional transitions in mammalian muscle development.
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Affiliation(s)
- Qi Zheng
- College of Animal Science and Technology, Anhui Agricultural University, Anhui, Hefei, P.R. China.,Anhui Province Key Laboratory of Local Livestock and Poultry Genetic Resource Conservation and Bio-Breeding, Anhui Agricultural University, Hefei, P.R. China
| | - Cuiyun Zhu
- College of Animal Science and Technology, Anhui Agricultural University, Anhui, Hefei, P.R. China.,Anhui Province Key Laboratory of Local Livestock and Poultry Genetic Resource Conservation and Bio-Breeding, Anhui Agricultural University, Hefei, P.R. China
| | - Jing Jing
- College of Animal Science and Technology, Anhui Agricultural University, Anhui, Hefei, P.R. China.,Anhui Province Key Laboratory of Local Livestock and Poultry Genetic Resource Conservation and Bio-Breeding, Anhui Agricultural University, Hefei, P.R. China
| | - Yinghui Ling
- College of Animal Science and Technology, Anhui Agricultural University, Anhui, Hefei, P.R. China. .,Anhui Province Key Laboratory of Local Livestock and Poultry Genetic Resource Conservation and Bio-Breeding, Anhui Agricultural University, Hefei, P.R. China.
| | - Shuaiqi Qin
- College of Animal Science and Technology, Anhui Agricultural University, Anhui, Hefei, P.R. China.,Anhui Province Key Laboratory of Local Livestock and Poultry Genetic Resource Conservation and Bio-Breeding, Anhui Agricultural University, Hefei, P.R. China
| | - Jiao Wang
- College of Animal Science and Technology, Anhui Agricultural University, Anhui, Hefei, P.R. China.,Anhui Province Key Laboratory of Local Livestock and Poultry Genetic Resource Conservation and Bio-Breeding, Anhui Agricultural University, Hefei, P.R. China
| | - Lisha Zha
- College of Animal Science and Technology, Anhui Agricultural University, Anhui, Hefei, P.R. China. .,Anhui Province Key Laboratory of Local Livestock and Poultry Genetic Resource Conservation and Bio-Breeding, Anhui Agricultural University, Hefei, P.R. China.
| | - Ya Liu
- College of Animal Science and Technology, Anhui Agricultural University, Anhui, Hefei, P.R. China.,Anhui Province Key Laboratory of Local Livestock and Poultry Genetic Resource Conservation and Bio-Breeding, Anhui Agricultural University, Hefei, P.R. China
| | - Fugui Fang
- College of Animal Science and Technology, Anhui Agricultural University, Anhui, Hefei, P.R. China.,Anhui Province Key Laboratory of Local Livestock and Poultry Genetic Resource Conservation and Bio-Breeding, Anhui Agricultural University, Hefei, P.R. China
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Huang C, Zhong L, Zou X, Huang Y, Cai L, Ma J. Evidence Against the Causal Relationship Between a Putative Cis-Regulatory Variant of MYH3 and Intramuscular Fat Content in Pigs. Front Vet Sci 2021; 8:672852. [PMID: 34150892 PMCID: PMC8206472 DOI: 10.3389/fvets.2021.672852] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 04/29/2021] [Indexed: 01/12/2023] Open
Abstract
Improving meat quality has become the main goal of modern pig breeding. Intramuscular fat content (IMF) is an important trait influencing meat quality of livestock, but the molecular mechanism behind this trait is still unclear. Recently, Cho et al. reported the discovery of the first causal mutation affecting IMF and red flesh color (a*) in pigs, namely XM_013981330.2:g.−1805_−1810del, a 6-bp deletion variant in the porcine MYH3 promoter region. The objective of this study was to reassess the causality of this mutation for its potential commercial application. By Sanger sequencing, we firstly identified several new variants (including a 4-bp deletion) at or near the 6-bp deletion site, which formed four haplotypes in multiple breeds. Unexpectedly, the 6-bp deletion allele, previously determined as the MYH3 Q allele because of its significantly positive effect on IMF and a*, was found not only in Chinese indigenous breeds, but also in four western commercial breeds with relatively lower IMF levels, including Duroc, Large White, Landrace and Pietrain. More surprisingly, we found that the MYH3 Q allele and the haplotypes harboring it had no significant effects on IMF, marbling and color score in three large-scale divergent pig populations: the heterogeneous F6 and F7 pigs and commercial crossbred Duroc × (Landrace × Yorkshire) pigs. Transient transfection analysis in porcine satellite cells showed that the 6-bp deletion variants had a negligible effect on transcription of reporter gene, but could attenuate the MRF (myogenesis regulatory factors)-induced increase in luciferase activity of the MYH3 promoter vector. The MYH3 protein level in muscle did not differ significantly among the haplotype groups. Therefore, our results cannot support the causal relationship between the 6-bp deletion in MYH3 and IMF trait, suggesting that the causal mutation for the IMF QTL on SSC12 needs to be further identified.
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Affiliation(s)
- Cong Huang
- State Key Laboratory for Swine Genetics, Breeding, and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Liepeng Zhong
- State Key Laboratory for Swine Genetics, Breeding, and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Xiaoxiao Zou
- State Key Laboratory for Swine Genetics, Breeding, and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Yizhong Huang
- State Key Laboratory for Swine Genetics, Breeding, and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Liping Cai
- State Key Laboratory for Swine Genetics, Breeding, and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Junwu Ma
- State Key Laboratory for Swine Genetics, Breeding, and Production Technology, Jiangxi Agricultural University, Nanchang, China
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Zhuang Z, Ding R, Qiu Y, Wu J, Zhou S, Quan J, Zheng E, Li Z, Wu Z, Yang J. A large-scale genome-wide association analysis reveals QTL and candidate genes for intramuscular fat content in Duroc pigs. Anim Genet 2021; 52:518-522. [PMID: 34060118 DOI: 10.1111/age.13069] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/10/2021] [Indexed: 01/30/2023]
Abstract
This study aimed at identifying genomic regions and genes associated with intramuscular fat content (IMF) in Duroc pigs using a weighted single-step GWAS. Data from 3912 pigs, of which 3770 animals were genotyped with GeneSeek Porcine 50K Bead chip, were used for the association analysis. We identified 19 genomic regions that each explained >1% of the additive genetic variance associated with IMF. Notably, a consistent QTL on SSC7 (117.42-117.92 Mb) was confirmed, explaining 3.70% of the additive genetic variance, and two genes, BDKRB2 and ATG2B, were highlighted as promising candidates for IMF. Two QTL (SSC7, 94.19-94.64 Mb; SSC14, 123.25-123.75 Mb), which harbored MED6 and MAP3K9 genes and TCF7L2 gene respectively, were newly identified as associated with IMF. In conclusion, we identified a consistent QTL and additional genomic regions and genes that contributed to the genetic variance of IMF using a large-scale sample size of genotyped pigs and genealogical information.
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Affiliation(s)
- Z Zhuang
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, 510642, China.,Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, Guangzhou, 510642, China
| | - R Ding
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, 510642, China.,Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, Guangzhou, 510642, China
| | - Y Qiu
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, 510642, China.,Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, Guangzhou, 510642, China
| | - J Wu
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, 510642, China.,Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, Guangzhou, 510642, China
| | - S Zhou
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, 510642, China.,Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, Guangzhou, 510642, China
| | - J Quan
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, 510642, China.,Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, Guangzhou, 510642, China
| | - E Zheng
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, 510642, China.,Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, Guangzhou, 510642, China.,Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, Guangzhou, 510642, China
| | - Z Li
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, 510642, China.,Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, Guangzhou, 510642, China.,State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangzhou, 510642, China.,Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, Guangzhou, 510642, China
| | - Z Wu
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, 510642, China.,Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, Guangzhou, 510642, China.,Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, Guangzhou, 510642, China
| | - J Yang
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, 510642, China.,Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, Guangzhou, 510642, China.,State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangzhou, 510642, China.,Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, Guangzhou, 510642, China
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Albuquerque A, Óvilo C, Núñez Y, Benítez R, López-Garcia A, García F, Félix MDR, Laranjo M, Charneca R, Martins JM. Transcriptomic Profiling of Skeletal Muscle Reveals Candidate Genes Influencing Muscle Growth and Associated Lipid Composition in Portuguese Local Pig Breeds. Animals (Basel) 2021; 11:ani11051423. [PMID: 34065673 PMCID: PMC8156922 DOI: 10.3390/ani11051423] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 05/12/2021] [Accepted: 05/12/2021] [Indexed: 12/24/2022] Open
Abstract
Simple Summary Screening and interpretation of differentially expressed genes and associated biological pathways was conducted among experimental groups with divergent phenotypes providing valuable information about the metabolic events occurring and identification of candidate genes with major regulation roles. This comparative transcriptomic analysis includes the first RNA-seq analysis of the Longissimus lumborum muscle tissue from two Portuguese autochthonous pig breeds with different genetic backgrounds, Alentejano and Bísaro. Moreover, a complementary candidate gene approach was employed to analyse, by real time qPCR, the expression profile of relevant genes involved in lipid metabolism, and therefore with potential impacts on meat composition. This study contributes to explaining the biological basis of phenotypical differences occurring between breeds, particularly the ones related to meat quality traits that affect consumer interest. 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 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.
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Affiliation(s)
- André Albuquerque
- MED-Mediterranean Institute for Agriculture, Environment and Development, Instituto de Investigação e Formação Avançada & Universidade de Évora, Pólo da Mitra, Ap. 94, 7006-554 Évora, Portugal;
- Correspondence: (A.A.); (J.M.M.)
| | - Cristina Óvilo
- Departamento de Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), 28040 Madrid, Spain; (C.Ó.); (Y.N.); (R.B.); (A.L.-G.); (F.G.)
| | - Yolanda Núñez
- Departamento de Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), 28040 Madrid, Spain; (C.Ó.); (Y.N.); (R.B.); (A.L.-G.); (F.G.)
| | - Rita Benítez
- Departamento de Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), 28040 Madrid, Spain; (C.Ó.); (Y.N.); (R.B.); (A.L.-G.); (F.G.)
| | - Adrián López-Garcia
- Departamento de Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), 28040 Madrid, Spain; (C.Ó.); (Y.N.); (R.B.); (A.L.-G.); (F.G.)
| | - Fabián García
- Departamento de Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), 28040 Madrid, Spain; (C.Ó.); (Y.N.); (R.B.); (A.L.-G.); (F.G.)
| | - Maria do Rosário Félix
- MED & Departamento de Fitotecnia, Escola de Ciências e Tecnologia, Universidade de Évora, Pólo da Mitra, Ap. 94, 7006-554 Évora, Portugal;
| | - Marta Laranjo
- MED-Mediterranean Institute for Agriculture, Environment and Development, Instituto de Investigação e Formação Avançada & Universidade de Évora, Pólo da Mitra, Ap. 94, 7006-554 Évora, Portugal;
| | - Rui Charneca
- MED & Departamento de Medicina Veterinária, Escola de Ciências e Tecnologia, Universidade de Évora, Pólo da Mitra, Ap. 94, 7006-554 Évora, Portugal;
| | - José Manuel Martins
- MED & Departamento de Zootecnia, Escola de Ciências e Tecnologia, Universidade de Évora, Pólo da Mitra, Ap. 94, 7006-554 Évora, Portugal
- Correspondence: (A.A.); (J.M.M.)
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Zhou J, Zhang Y, Wu J, Qiao M, Xu Z, Peng X, Mei S. Proteomic and lipidomic analyses reveal saturated fatty acids, phosphatidylinositol, phosphatidylserine, and associated proteins contributing to intramuscular fat deposition. J Proteomics 2021; 241:104235. [PMID: 33894376 DOI: 10.1016/j.jprot.2021.104235] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 04/05/2021] [Accepted: 04/09/2021] [Indexed: 12/15/2022]
Abstract
Intramuscular fat (IMF) content is an important factor in porcine meat quality. Previous studies have screened multiple candidate genes related to IMF deposition, but the lipids that affect IMF deposition and their lipid-protein network remain unknown. In this study, we performed proteomic and lipidomic analyses of the longissimus dorsi (LD) muscle from high-IMF (IMFH) and low-IMF (IMF-L) groups of Xidu black pigs. Eighty-eight proteins and 143 lipids were differentially abundant between the groups. The differentially abundant proteins were found to be involved in cholesterol metabolism, the PPAR signaling pathway, and ferroptosis. The triacylglycerols (TAGs) upregulated in the IMF-H group were mainly shown to be synthesized by saturated fatty acids (SFAs), while the downregulated TAGs were mainly synthesized by polyunsaturated fatty acids (PUFAs). All differentially abundant phosphatidylinositols (PIs) and phosphatidylserines (PSs) were found to be upregulated in the IMF-H group. A correlation analysis of the proteomic and lipidomic revealed candidate proteins (APOA4, VDAC3, PRNP, CTSB, GSPT1) related to TAG, PI, and PS lipids. These results revealed differences in proteins and lipids between the IMF-H and IMF-L groups, which represent new candidate proteins and lipids that should be investigated to determine the molecular mechanisms controlling IMF deposition in pigs. SIGNIFICANCE: Intramuscular fat (IMF) is a key factor affecting meat quality, and meat with a higher IMF content can have a better flavor. In this study, proteomic results show that the ferroptosis pathway, including the PRNP, VDAC3 and CP proteins, affects IMF deposition. Lipid composition is the key factor affecting IMF deposition, but there are few reports on this. In this study, through lipidomic analysis, we suggest that saturated fatty acid (SFA), phosphatidylinositol (PI), and phosphatidylserine (PS) may contribute to IMF deposition. A correlation analysis reveals the potential regulatory network between lipids and proteins. This study clarifies the difference in protein and lipid compositions in longissimus dorsi (LD) muscle with high and low IMF contents. This information suggests that it would be beneficial to increase the intramuscular fat content of pork not only from a genetic perspective but also from a nutritional perspective.
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Affiliation(s)
- Jiawei Zhou
- Institute of Animal Science and Veterinary Medicine, Hubei Academy of Agricultural Sciences, Wuhan 430064, China; Hubei Key Lab for Animal Embryo Engineering and Molecular Breeding, Wuhan 430064, China
| | - Yu Zhang
- Institute of Animal Science and Veterinary Medicine, Hubei Academy of Agricultural Sciences, Wuhan 430064, China; Hubei Key Lab for Animal Embryo Engineering and Molecular Breeding, Wuhan 430064, China
| | - Junjing Wu
- Institute of Animal Science and Veterinary Medicine, Hubei Academy of Agricultural Sciences, Wuhan 430064, China; Hubei Key Lab for Animal Embryo Engineering and Molecular Breeding, Wuhan 430064, China
| | - Mu Qiao
- Institute of Animal Science and Veterinary Medicine, Hubei Academy of Agricultural Sciences, Wuhan 430064, China; Hubei Key Lab for Animal Embryo Engineering and Molecular Breeding, Wuhan 430064, China
| | - Zhong Xu
- Institute of Animal Science and Veterinary Medicine, Hubei Academy of Agricultural Sciences, Wuhan 430064, China; Hubei Key Lab for Animal Embryo Engineering and Molecular Breeding, Wuhan 430064, China
| | - Xianwen Peng
- Institute of Animal Science and Veterinary Medicine, Hubei Academy of Agricultural Sciences, Wuhan 430064, China; Hubei Key Lab for Animal Embryo Engineering and Molecular Breeding, Wuhan 430064, China
| | - Shuqi Mei
- Institute of Animal Science and Veterinary Medicine, Hubei Academy of Agricultural Sciences, Wuhan 430064, China; Hubei Key Lab for Animal Embryo Engineering and Molecular Breeding, Wuhan 430064, China.
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