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Hosseini SM, Tingzhu Y, Zaohong R, Ullah F, Liang A, Hua G, Yang L. Regulatory impacts of PPARGC1A gene expression on milk production and cellular metabolism in buffalo mammary epithelial cells. Anim Biotechnol 2024; 35:2344210. [PMID: 38785376 DOI: 10.1080/10495398.2024.2344210] [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] [Indexed: 05/25/2024]
Abstract
The PPARGC1A gene plays a fundamental role in regulating cellular energy metabolism, including adaptive thermogenesis, mitochondrial biogenesis, adipogenesis, gluconeogenesis, and glucose/fatty acid metabolism. In a previous study, our group investigated seven SNPs in Mediterranean buffalo associated with milk production traits, and the current study builds on this research by exploring the regulatory influences of the PPARGC1A gene in buffalo mammary epithelial cells (BuMECs). Our findings revealed that knockdown of PPARGC1A gene expression significantly affected the growth of BuMECs, including proliferation, cell cycle, and apoptosis. Additionally, we observed downregulated triglyceride secretion after PPARGC1A knockdown. Furthermore, the critical genes related to milk production, including the STATS, BAD, P53, SREBF1, and XDH genes were upregulated after RNAi, while the FABP3 gene, was downregulated. Moreover, Silencing the PPARGC1A gene led to a significant downregulation of β-casein synthesis in BuMECs. Our study provides evidence of the importance of the PPARGC1A gene in regulating cell growth, lipid, and protein metabolism in the buffalo mammary gland. In light of our previous research, the current study underscores the potential of this gene for improving milk production efficiency and overall dairy productivity in buffalo populations.
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Affiliation(s)
- Seyed Mahdi Hosseini
- National Center for International Research on Animal Genetics, Breeding and Reproduction (NCIRAGBR), College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Ye Tingzhu
- National Center for International Research on Animal Genetics, Breeding and Reproduction (NCIRAGBR), College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Ran Zaohong
- National Center for International Research on Animal Genetics, Breeding and Reproduction (NCIRAGBR), College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Farman Ullah
- National Center for International Research on Animal Genetics, Breeding and Reproduction (NCIRAGBR), College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Aixin Liang
- National Center for International Research on Animal Genetics, Breeding and Reproduction (NCIRAGBR), College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Guohua Hua
- National Center for International Research on Animal Genetics, Breeding and Reproduction (NCIRAGBR), College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Liguo Yang
- National Center for International Research on Animal Genetics, Breeding and Reproduction (NCIRAGBR), College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
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Tan WLA, Hudson NJ, Porto Neto LR, Reverter A, Afonso J, Fortes MRS. An association weight matrix identified biological pathways associated with bull fertility traits in a multi-breed population. Anim Genet 2024; 55:495-510. [PMID: 38692842 DOI: 10.1111/age.13431] [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: 11/16/2023] [Revised: 02/26/2024] [Accepted: 04/01/2024] [Indexed: 05/03/2024]
Abstract
Using seven indicator traits, we investigated the genetic basis of bull fertility and predicted gene interactions from SNP associations. We used percent normal sperm as the key phenotype for the association weight matrix-partial correlation information theory (AWM-PCIT) approach. Beyond a simple list of candidate genes, AWM-PCIT predicts significant gene interactions and associations for the selected traits. These interactions formed a network of 537 genes: 38 genes were transcription cofactors, and 41 genes were transcription factors. The network displayed two distinct clusters, one with 294 genes and another with 243 genes. The network is enriched in fertility-associated pathways: steroid biosynthesis, p53 signalling, and the pentose phosphate pathway. Enrichment analysis also highlighted gene ontology terms associated with 'regulation of neurotransmitter secretion' and 'chromatin formation'. Our network recapitulates some genes previously implicated in another network built with lower-density genotypes. Sequence-level data also highlights additional candidate genes relevant to bull fertility, such as FOXO4, FOXP3, GATA1, CYP27B1, and EBP. A trio of regulatory genes-KDM5C, LRRK2, and PME-was deemed core to the network because of their overarching connections. This trio probably influences bull fertility through their interaction with genes, both known and unknown as to their role in male fertility. Future studies may target the trio and their target genes to enrich our understanding of male fertility further.
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Affiliation(s)
- Wei Liang Andre Tan
- School of Chemistry and Molecular Bioscience, The University of Queensland, St Lucia, Queensland, Australia
| | - Nicholas James Hudson
- School of Agriculture and Food Sustainability, The University of Queensland, Gatton, Queensland, Australia
| | | | | | - Juliana Afonso
- School of Chemistry and Molecular Bioscience, The University of Queensland, St Lucia, Queensland, Australia
- Empresa Brasileira de Pesquisa Agropecuária, Pecuária Sudeste, São Carlos, São Paulo, Brazil
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Colombi D, Rovelli G, Luigi-Sierra MG, Ceccobelli S, Guan D, Perini F, Sbarra F, Quaglia A, Sarti FM, Pasquini M, Amills M, Lasagna E. Population structure and identification of genomic regions associated with productive traits in five Italian beef cattle breeds. Sci Rep 2024; 14:8529. [PMID: 38609445 PMCID: PMC11014930 DOI: 10.1038/s41598-024-59269-z] [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: 12/07/2023] [Accepted: 04/09/2024] [Indexed: 04/14/2024] Open
Abstract
Italy has a long history in beef production, with local breeds such as Marchigiana, Chianina, Romagnola, Maremmana, and Podolica which produce high-quality meat. Selection has improved meat production, precocity, growth ability and muscle development, but the genetic determinism of such traits is mostly unknown. Using 33K SNPs-data from young bulls (N = 4064) belonging to these five Italian breeds, we demonstrated that the Maremmana and Podolica rustic breeds are closely related, while the specialised Marchigiana, Chianina, and Romagnola breeds are more differentiated. A genome-wide association study for growth and muscle development traits (average daily gain during the performance test, weight at 1 year old, muscularity) was conducted in the five Italian breeds. Results indicated a region on chromosome 2, containing the myostatin gene (MSTN), which displayed significant genome-wide associations with muscularity in Marchigiana cattle, a breed in which the muscle hypertrophy phenotype is segregating. Moreover, a significant SNP on chromosome 14 was associated, in the Chianina breed, to muscularity. The identification of diverse genomic regions associated with conformation traits might increase our knowledge about the genomic basis of such traits in Italian beef cattle and, eventually, such information could be used to implement marker-assisted selection of young bulls tested in the performance test.
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Affiliation(s)
- Daniele Colombi
- Department of Agricultural, Food and Environmental Sciences (DSA3), University of Perugia, Borgo XX Giugno 74, 06121, Perugia, Italy
| | - Giacomo Rovelli
- Department of Agricultural, Food and Environmental Sciences (DSA3), University of Perugia, Borgo XX Giugno 74, 06121, Perugia, Italy
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus Universitat Autonòma de Barcelona, Carrer de la Vall Moronta, 08193, Bellaterra de Cerdanyola del Vallés, Spain
| | - Maria Gracia Luigi-Sierra
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus Universitat Autonòma de Barcelona, Carrer de la Vall Moronta, 08193, Bellaterra de Cerdanyola del Vallés, Spain
| | - Simone Ceccobelli
- Department of Agricultural, Food and Environmental Sciences (D3A), Università Politecnica delle Marche, 60131, Ancona, Italy
| | - Dailu Guan
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus Universitat Autonòma de Barcelona, Carrer de la Vall Moronta, 08193, Bellaterra de Cerdanyola del Vallés, Spain
- Department of Animal Science, University of California, Davis, CA, 2251, USA
| | - Francesco Perini
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, 35020, Legnaro, Italy
| | - Fiorella Sbarra
- National Association of Italian Beef-Cattle Breeders (ANABIC), 06132, San Martino in Colle, Perugia, Italy
| | - Andrea Quaglia
- National Association of Italian Beef-Cattle Breeders (ANABIC), 06132, San Martino in Colle, Perugia, Italy
| | - Francesca Maria Sarti
- Department of Agricultural, Food and Environmental Sciences (DSA3), University of Perugia, Borgo XX Giugno 74, 06121, Perugia, Italy
| | - Marina Pasquini
- Department of Agricultural, Food and Environmental Sciences (D3A), Università Politecnica delle Marche, 60131, Ancona, Italy
| | - Marcel Amills
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus Universitat Autonòma de Barcelona, Carrer de la Vall Moronta, 08193, Bellaterra de Cerdanyola del Vallés, Spain.
- Department of Animal and Food Science, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain.
| | - Emiliano Lasagna
- Department of Agricultural, Food and Environmental Sciences (DSA3), University of Perugia, Borgo XX Giugno 74, 06121, Perugia, Italy.
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Arikawa LM, Mota LFM, Schmidt PI, Frezarim GB, Fonseca LFS, Magalhães AFB, Silva DA, Carvalheiro R, Chardulo LAL, Albuquerque LGD. Genome-wide scans identify biological and metabolic pathways regulating carcass and meat quality traits in beef cattle. Meat Sci 2024; 209:109402. [PMID: 38056170 DOI: 10.1016/j.meatsci.2023.109402] [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: 04/25/2023] [Revised: 10/19/2023] [Accepted: 11/28/2023] [Indexed: 12/08/2023]
Abstract
Genome association studies (GWAS) provides knowledge about the genetic architecture of beef-related traits that allow linking the target phenotype to genomic information aiding breeding decision. Thus, the present study aims to uncover the genetic mechanism involved in carcass (REA: rib eye area, BF: backfat thickness, and HCW: hot carcass weight) and meat quality traits (SF: shear-force, MARB: marbling score, and IMF: intramuscular fat content) in Nellore cattle. For this, 6910 young bulls with phenotypic information and 23,859 animals genotyped with 435 k markers were used to perform the weighted single-step GBLUP (WssGBLUP) approach, considering two iterations. The top 10 genomic regions explained 8.13, 11.81, and 9.58% of the additive genetic variance, harboring a total of 119, 143, and 95 positional candidate genes for REA, BF, and HCW, respectively. For meat quality traits, the top 10 windows explained a large proportion of the total genetic variance for SF (14.95%), MARB (17.56%), and IMF (21.41%) surrounding 92, 155, and 111 candidate genes, respectively. Relevant candidate genes (CAST, PLAG1, XKR4, PLAGL2, AQP3/AQP7, MYLK2, WWOX, CARTPT, and PLA2G16) are related to physiological aspects affecting growth, carcass, meat quality, feed intake, and reproductive traits by signaling pathways controlling muscle control, key signal metabolic molecules INS / IGF-1 pathway, lipid metabolism, and adipose tissue development. The GWAS results provided insights into the genetic control of the traits studied and the genes found are potential candidates to be used in the improvement of carcass and meat quality traits.
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Affiliation(s)
- Leonardo Machestropa Arikawa
- São Paulo State University (UNESP), School of Agricultural and Veterinarian Sciences, Department of Animal Science, Via de Acesso Prof. Paulo Donato Castelane, Jaboticabal, SP 14884-900, Brazil.
| | - Lucio Flavio Macedo Mota
- São Paulo State University (UNESP), School of Agricultural and Veterinarian Sciences, Department of Animal Science, Via de Acesso Prof. Paulo Donato Castelane, Jaboticabal, SP 14884-900, Brazil
| | - Patrícia Iana Schmidt
- São Paulo State University (UNESP), School of Agricultural and Veterinarian Sciences, Department of Animal Science, Via de Acesso Prof. Paulo Donato Castelane, Jaboticabal, SP 14884-900, Brazil
| | - Gabriela Bonfá Frezarim
- São Paulo State University (UNESP), School of Agricultural and Veterinarian Sciences, Department of Animal Science, Via de Acesso Prof. Paulo Donato Castelane, Jaboticabal, SP 14884-900, Brazil
| | - Larissa Fernanda Simielli Fonseca
- São Paulo State University (UNESP), School of Agricultural and Veterinarian Sciences, Department of Animal Science, Via de Acesso Prof. Paulo Donato Castelane, Jaboticabal, SP 14884-900, Brazil
| | - Ana Fabrícia Braga Magalhães
- São Paulo State University (UNESP), School of Agricultural and Veterinarian Sciences, Department of Animal Science, Via de Acesso Prof. Paulo Donato Castelane, Jaboticabal, SP 14884-900, Brazil; University of Jequitinhonha and Mucuri Valleys, Department of Animal Science, Rod. MG 367, Diamantina, MG 39100-000, Brazil
| | - Delvan Alves Silva
- São Paulo State University (UNESP), School of Agricultural and Veterinarian Sciences, Department of Animal Science, Via de Acesso Prof. Paulo Donato Castelane, Jaboticabal, SP 14884-900, Brazil; University of Viçosa, Department of Animal Science, Av. PH Rolfs, Viçosa, MG 36570-900, Brazil
| | - Roberto Carvalheiro
- São Paulo State University (UNESP), School of Agricultural and Veterinarian Sciences, Department of Animal Science, Via de Acesso Prof. Paulo Donato Castelane, Jaboticabal, SP 14884-900, Brazil
| | - Luis Artur Loyola Chardulo
- São Paulo State University (UNESP), School of Agricultural and Veterinarian Sciences, Department of Animal Science, Via de Acesso Prof. Paulo Donato Castelane, Jaboticabal, SP 14884-900, Brazil; National Council for Science and Technological Development, Brasilia, DF 71605-001, Brazil
| | - Lucia Galvão de Albuquerque
- São Paulo State University (UNESP), School of Agricultural and Veterinarian Sciences, Department of Animal Science, Via de Acesso Prof. Paulo Donato Castelane, Jaboticabal, SP 14884-900, Brazil; National Council for Science and Technological Development, Brasilia, DF 71605-001, Brazil.
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Zhu J, Wang Y, Su Y, Zheng M, Cui H, Chen Z. RNA sequencing identifies key genes involved in intramuscular fat deposition in chickens at different developmental stages. BMC Genomics 2024; 25:219. [PMID: 38413888 PMCID: PMC10900564 DOI: 10.1186/s12864-023-09819-y] [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: 07/04/2023] [Accepted: 11/20/2023] [Indexed: 02/29/2024] Open
Abstract
BACKGROUND Intramuscular fat (IMF) is an important factor in meat quality, and triglyceride (TG) and Phospholipids (PLIP), as the main components of IMF, are of great significance to the improvement of meat quality. RESULTS In this study, we used 30 RNA sequences generated from the transcriptome of chicken breast muscle tissues at different developmental stages to construct a gene expression matrix to map RNA sequence reads to the chicken genome and identify the transcript of origin. We used weighted gene co-expression network analysis (WGCNA) and identified 27 co-expression modules, 10 of which were related to TG and PLIP. We identified 150 highly-connected hub genes related to TG and PLIP, respectively, which were found to be mainly enriched in the adipocytokine signaling pathway, MAPK signaling pathway, mTOR signaling pathway, FoxO signaling pathway, and TGF-beta signaling pathway. Additionally, using the BioMart database, we identified 134 and 145 candidate genes related to fat development in the TG-related module and PLIP-related module, respectively. Among them, RPS6KB1, BRCA1, CDK1, RPS3, PPARGC1A, ACSL1, NDUFAB1, NDUFA9, ATP5B and PRKAG2 were identified as candidate genes related to fat development and highly-connected hub genes in the module, suggesting that these ten genes may be important candidate genes affecting IMF deposition. CONCLUSIONS RPS6KB1, BRCA1, CDK1, RPS3, PPARGC1A, ACSL1, NDUFAB1, NDUFA9, ATP5B and PRKAG2 may be important candidate genes affecting IMF deposition. The purpose of this study was to identify the co-expressed gene modules related to chicken IMF deposition using WGCNA and determine key genes related to IMF deposition, so as to lay a foundation for further research on the molecular regulation mechanism underlying chicken fat deposition.
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Affiliation(s)
- Jinmei Zhu
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, 266109, China
- State Key Laboratory of Animal Nutrition, Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Yongli Wang
- State Key Laboratory of Animal Nutrition, Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Yongchun Su
- Guangxi Jingling Agriculture and animal Husbandry Group Co., LTD, Nanning, 530049, China
| | - Maiqing Zheng
- State Key Laboratory of Animal Nutrition, Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Huanxian Cui
- State Key Laboratory of Animal Nutrition, Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
| | - Zhiwu Chen
- Guangxi Jingling Agriculture and animal Husbandry Group Co., LTD, Nanning, 530049, China.
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Ma Z, Chang Y, Brito LF, Li Y, Yang T, Wang Y, Yang N. Multitrait meta-analyses identify potential candidate genes for growth-related traits in Holstein heifers. J Dairy Sci 2023; 106:9055-9070. [PMID: 37641329 DOI: 10.3168/jds.2023-23462] [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: 03/07/2023] [Accepted: 06/20/2023] [Indexed: 08/31/2023]
Abstract
Understanding the underlying pleiotropic relationships among growth and body size traits is important for refining breeding strategies in dairy cattle for optimal body size and growth rate. Therefore, we performed single-trait GWAS for monthly-recorded body weight (BW), hip height, body length, and chest girth from birth to 12 mo of age in Holstein animals, followed by stepwise multiple regression of independent or lowly-linked markers from GWAS loci using conditional and joint association analyses (COJO). Subsequently, we conducted a multitrait meta-analysis to detect pleiotropic markers. Based on the single-trait GWAS, we identified 170 significant SNPs, in which 59 of them remained significant after the COJO analyses. The most significant SNP, located at BTA7:3,676,741, explained 2.93% of the total phenotypic variance for BW6 (BW at 6 mo of age). We identified 17 SNPs with potential pleiotropic effects based on the multitrait meta-analyses, which resulted in 3 additional SNPs in comparison to those detected based on the single-trait GWAS. The identified quantitative trait loci regions overlap with genes known to influence human growth-related traits. According to positional and functional analyses, we proposed HMGA2, HNF4G, MED13L, BHLHE40, FRZB, DMP1, TRIB3, and GATAD2A as important candidate genes influencing the studied traits. The combination of single-trait GWAS and meta-analyses of GWAS results improved the efficiency of detecting associated SNPs, and provided new insights into the genetic mechanisms of growth and development in Holstein cattle.
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Affiliation(s)
- Z Ma
- Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture of China, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, 100193, Beijing, China; Beijing Sunlon Livestock Development Co. Ltd., 100029, Beijing, China
| | - Y Chang
- Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture of China, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, 100193, Beijing, China
| | - Luiz F Brito
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907
| | - Y Li
- Beijing Sunlon Livestock Development Co. Ltd., 100029, Beijing, China
| | - T Yang
- Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture of China, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, 100193, Beijing, China
| | - Y Wang
- Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture of China, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, 100193, Beijing, China.
| | - N Yang
- Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture of China, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, 100193, Beijing, China.
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Luo M, Wang H, Zhang J, Yixi K, Shu S, Fu C, Zhong J, Peng W. IMF deposition ceRNA network analysis and functional study of HIF1a in yak. Front Vet Sci 2023; 10:1272238. [PMID: 37915947 PMCID: PMC10616239 DOI: 10.3389/fvets.2023.1272238] [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: 08/03/2023] [Accepted: 10/02/2023] [Indexed: 11/03/2023] Open
Abstract
The concentration of intramuscular fat (IMF) is a crucial determinant of yak meat quality. However, the molecular mechanisms that regulate IMF in yak remain largely elusive. In our study, we conducted transcriptome sequencing on the longissimus dorsi muscle tissues of yaks with varying IMF contents. We then filtered differentially expressed genes (DEGs), microRNAs (DEMs), and long non-coding RNAs (DELs) to elucidate potential regulatory pathways of adipogenesis in yaks. Overall, our research sheds light on an array of potential mRNAs and noncoding RNAs implicated in IMF deposition and elaborates on the role of HIF1α in yaks. These findings contribute valuable insights that can serve as a guide for further research into the molecular mechanisms governing IMF deposition.
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Affiliation(s)
- Mengning Luo
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Sichuan Province and Ministry of Education, Southwest Minzu University, Chengdu, China
| | - Hui Wang
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Sichuan Province and Ministry of Education, Southwest Minzu University, Chengdu, China
| | - Jun Zhang
- Qinghai Academy of Animal Science and Veterinary Medicine, Qinghai University, Xining, China
| | - Kangzhu Yixi
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Sichuan Province and Ministry of Education, Southwest Minzu University, Chengdu, China
| | - Shi Shu
- Qinghai Academy of Animal Science and Veterinary Medicine, Qinghai University, Xining, China
| | - Changqi Fu
- Qinghai Academy of Animal Science and Veterinary Medicine, Qinghai University, Xining, China
| | - Jincheng Zhong
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Sichuan Province and Ministry of Education, Southwest Minzu University, Chengdu, China
| | - Wei Peng
- Qinghai Academy of Animal Science and Veterinary Medicine, Qinghai University, Xining, China
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Bordonaro S, Chessari G, Mastrangelo S, Senczuk G, Chessa S, Castiglioni B, Tumino S, Marletta D, Criscione A. Genome-wide population structure, homozygosity, and heterozygosity patterns of Nero Siciliano pig in the framework of Italian and cosmopolitan breeds. Anim Genet 2023; 54:591-605. [PMID: 37381662 DOI: 10.1111/age.13344] [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: 06/13/2023] [Revised: 06/13/2023] [Accepted: 06/15/2023] [Indexed: 06/30/2023]
Abstract
Analysis of genomic data is becoming more and more common for the effective management of livestock breeding programmes, even in the case of local populations. In this work, the genome-wide data of Nero Siciliano pig breed were compared to that of wild boar, Italian local and cosmopolitan breeds to investigate its genetic structure, and runs of homozygosity (ROH) and heterozygosity patterns. The Nero Siciliano has been reported to have the highest rate of genetic diversity among the Italian breeds, and a genetic variability comparable to that of the cosmopolitan breeds. Analyses of genomic structure and relationships underlined its proximity to wild boar, and an internal substructure probably linked to different family lines. The breed showed a low value of inbreeding estimated from ROH, and the highest diversity index among the Italian breeds, even if lower than that of the cosmopolitans. Four ROH islands in three chromosomes (SSC8, SSC11, and SSC14) and one heterozygosity-rich region (SSC1) were identified in Nero Siciliano, highlighting genomic regions related to productive QTL. Across breeds, SSC8 and SSC14 were the chromosomes with most ROH islands, with Mora Romagnola and wild boar showing the highest level of autozygosity. Chromosomes SSC2, SSC6, SSC8 and SSC13 showed the majority of runs of heterozygosity regions, mainly found in the cosmopolitan pig breeds, which reported several genes associated with health-related QTL. The outlined results can help to better identify the genomic profile of this local breed in order to plan matings, maintain adequate internal diversity and exploit the production system.
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Affiliation(s)
- Salvatore Bordonaro
- Dipartimento di Agricoltura, Alimentazione e Ambiente, Università di Catania, Catania, Italy
| | - Giorgio Chessari
- Dipartimento di Agricoltura, Alimentazione e Ambiente, Università di Catania, Catania, Italy
| | - Salvatore Mastrangelo
- Dipartimento Scienze Agrarie, Alimentari e Forestali, Università di Palermo, Palermo, Italy
| | - Gabriele Senczuk
- Dipartimento di Agricoltura, Ambiente e Alimenti, Università del Molise, Campobasso, Italy
| | - Stefania Chessa
- Dipartimento di Scienze Veterinarie, Università di Torino, Torino, Italy
| | - Bianca Castiglioni
- Istituto di Biologia e Biotecnologia Agraria, National Research Council, Lodi, Italy
| | - Serena Tumino
- Dipartimento di Agricoltura, Alimentazione e Ambiente, Università di Catania, Catania, Italy
| | - Donata Marletta
- Dipartimento di Agricoltura, Alimentazione e Ambiente, Università di Catania, Catania, Italy
| | - Andrea Criscione
- Dipartimento di Agricoltura, Alimentazione e Ambiente, Università di Catania, Catania, Italy
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Yudin NS, Larkin DM. Candidate genes for domestication and resistance to cold climate according to whole genome sequencing data of Russian cattle and sheep breeds. Vavilovskii Zhurnal Genet Selektsii 2023; 27:463-470. [PMID: 37867610 PMCID: PMC10587008 DOI: 10.18699/vjgb-23-56] [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: 12/02/2022] [Revised: 02/19/2023] [Accepted: 02/20/2023] [Indexed: 10/24/2023] Open
Abstract
It is known that different species of animals, when living in the same environmental conditions, can form similar phenotypes. The study of the convergent evolution of several species under the influence of the same environmental factor makes it possible to identify common mechanisms of genetic adaptation. Local cattle and sheep breeds have been formed over thousands of years under the influence of domestication, as well as selection aimed at adaptation to the local environment and meeting human needs. Previously, we identified a number of candidate genes in genome regions potentially selected during domestication and adaptation to the climatic conditions of Russia, in local breeds of cattle and sheep using whole genome genotyping data. However, these data are of low resolution and do not reveal most nucleotide substitutions. The aim of the work was to create, using the whole genome sequencing data, a list of genes associated with domestication, selection and adaptation in Russian cattle and sheep breeds, as well as to identify candidate genes and metabolic pathways for selection for cold adaptation. We used our original data on the search for signatures of selection in the genomes of Russian cattle (Yakut, Kholmogory, Buryat, Wagyu) and sheep (Baikal, Tuva) breeds. We used the HapFLK, DCMS, FST and PBS methods to identify DNA regions with signatures of selection. The number of candidate genes in potentially selective regions was 946 in cattle and 151 in sheep. We showed that the studied Russian cattle and sheep breeds have at least 10 genes in common, apparently involved in the processes of adaptation/selection, including adaptation to a cold climate, including the ASTN2, PM20D1, TMEM176A, and GLIS1 genes. Based on the intersection with the list of selected genes in at least two Arctic/Antarctic mammal species, 20 and 8 genes, have been identified in cattle and sheep, respectively, that are potentially involved in cold adaptation. Among them, the most promising for further research are the ASPH, NCKAP5L, SERPINF1, and SND1 genes. Gene ontology analysis indicated the existence of possible common biochemical pathways for adaptation to cold in domestic and wild mammals associated with cytoskeleton disassembly and apoptosis.
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Affiliation(s)
- N S Yudin
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - D M Larkin
- Royal Veterinary College, University of London, London, United Kingdom
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10
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Dehghanian Reyhan V, Ghafouri F, Sadeghi M, Miraei-Ashtiani SR, Kastelic JP, Barkema HW, Shirali M. Integrated Comparative Transcriptome and circRNA-lncRNA-miRNA-mRNA ceRNA Regulatory Network Analyses Identify Molecular Mechanisms Associated with Intramuscular Fat Content in Beef Cattle. Animals (Basel) 2023; 13:2598. [PMID: 37627391 PMCID: PMC10451991 DOI: 10.3390/ani13162598] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 08/05/2023] [Accepted: 08/08/2023] [Indexed: 08/27/2023] Open
Abstract
Intramuscular fat content (IMF), one of the most important carcass traits in beef cattle, is controlled by complex regulatory factors. At present, molecular mechanisms involved in regulating IMF and fat metabolism in beef cattle are not well understood. Our objective was to integrate comparative transcriptomic and competing endogenous RNA (ceRNA) network analyses to identify candidate messenger RNAs (mRNAs) and regulatory RNAs involved in molecular regulation of longissimus dorsi muscle (LDM) tissue for IMF and fat metabolism of 5 beef cattle breeds (Angus, Chinese Simmental, Luxi, Nanyang, and Shandong Black). In total, 34 circRNAs, 57 lncRNAs, 15 miRNAs, and 374 mRNAs were identified by integrating gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses. Furthermore, 7 key subnets with 16 circRNAs, 43 lncRNAs, 7 miRNAs, and 237 mRNAs were detected through clustering analyses, whereas GO enrichment analysis of identified RNAs revealed 48, 13, and 28 significantly enriched GO terms related to IMF in biological process, molecular function, and cellular component categories, respectively. The main metabolic-signaling pathways associated with IMF and fat metabolism that were enriched included metabolic, calcium, cGMP-PKG, thyroid hormone, and oxytocin signaling pathways. Moreover, MCU, CYB5R1, and BAG3 genes were common among the 10 comparative groups defined as important candidate marker genes for fat metabolism in beef cattle. Contributions of transcriptome profiles from various beef breeds and a competing endogenous RNA (ceRNA) regulatory network underlying phenotypic differences in IMF provided novel insights into molecular mechanisms associated with meat quality.
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Affiliation(s)
- Vahid Dehghanian Reyhan
- Department of Animal Science, University College of Agriculture and Natural Resources, University of Tehran, Karaj 77871-31587, Iran; (V.D.R.); (F.G.); (S.R.M.-A.)
| | - Farzad Ghafouri
- Department of Animal Science, University College of Agriculture and Natural Resources, University of Tehran, Karaj 77871-31587, Iran; (V.D.R.); (F.G.); (S.R.M.-A.)
| | - Mostafa Sadeghi
- Department of Animal Science, University College of Agriculture and Natural Resources, University of Tehran, Karaj 77871-31587, Iran; (V.D.R.); (F.G.); (S.R.M.-A.)
| | - Seyed Reza Miraei-Ashtiani
- Department of Animal Science, University College of Agriculture and Natural Resources, University of Tehran, Karaj 77871-31587, Iran; (V.D.R.); (F.G.); (S.R.M.-A.)
| | - John P. Kastelic
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada; (J.P.K.); (H.W.B.)
| | - Herman W. Barkema
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada; (J.P.K.); (H.W.B.)
| | - Masoud Shirali
- Agri-Food and Biosciences Institute, Hillsborough BT26 6DR, UK
- School of Biological Sciences, Queen’s University Belfast, Belfast BT9 5AJ, UK
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11
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Wang P, Li X, Zhu Y, Wei J, Zhang C, Kong Q, Nie X, Zhang Q, Wang Z. Genome-wide association analysis of milk production, somatic cell score, and body conformation traits in Holstein cows. Front Vet Sci 2022; 9:932034. [PMID: 36268046 PMCID: PMC9578681 DOI: 10.3389/fvets.2022.932034] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 09/09/2022] [Indexed: 11/04/2022] Open
Abstract
Milk production and body conformation traits are critical economic traits for dairy cows. To understand the basic genetic structure for those traits, a genome wide association study was performed on milk yield, milk fat yield, milk fat percentage, milk protein yield, milk protein percentage, somatic cell score, body form composite index, daily capacity composite index, feed, and leg conformation traits, based on the Illumina Bovine HD100k BeadChip. A total of 57, 12 and 26 SNPs were found to be related to the milk production, somatic cell score and body conformation traits in the Holstein cattle. Genes with pleiotropic effect were also found in this study. Seven significant SNPs were associated with multi-traits and were located on the PLEC, PLEKHA5, TONSL, PTGER4, and LCORL genes. In addition, some important candidate genes, like GPAT3, CEBPB, AGO2, SLC37A1, and FNDC3B, were found to participate in fat metabolism or mammary gland development. These results can be used as candidate genes for milk production, somatic cell score, and body conformation traits of Holstein cows, and are helpful for further gene function analysis to improve milk production and quality.
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Affiliation(s)
- Peng Wang
- Heilongjiang Animal Husbandry Service, Harbin, China
| | - Xue Li
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China,Bioinformatics Center, Northeast Agricultural University, Harbin, China
| | - Yihao Zhu
- Heilongjiang Animal Husbandry Service, Harbin, China
| | - Jiani Wei
- School of mathematics, University of Edinburgh, Edinburgh, United Kingdom
| | - Chaoxin Zhang
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China,Bioinformatics Center, Northeast Agricultural University, Harbin, China
| | - Qingfang Kong
- Heilongjiang Animal Husbandry Service, Harbin, China
| | - Xu Nie
- Heilongjiang Animal Husbandry Service, Harbin, China
| | - Qi Zhang
- College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Zhipeng Wang
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China,Bioinformatics Center, Northeast Agricultural University, Harbin, China,*Correspondence: Zhipeng Wang
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12
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Chen Z, Teng J, Diao S, Xu Z, Ye S, Qiu D, Zhang Z, Pan Y, Li J, Zhang Q, Zhang Z. Insights into the architecture of human-induced polygenic selection in Duroc pigs. J Anim Sci Biotechnol 2022; 13:99. [PMID: 36127741 PMCID: PMC9490910 DOI: 10.1186/s40104-022-00751-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 07/03/2022] [Indexed: 11/10/2022] Open
Abstract
Background As one of the most utilized commercial composite boar lines, Duroc pigs have been introduced to China and undergone strongly human-induced selection over the past decades. However, the efficiencies and limitations of previous breeding of Chinese Duroc pigs are largely understudied. The objective of this study was to uncover directional polygenic selection in the Duroc pig genome, and investigate points overlooked in the past breeding process. Results Here, we utilized the Generation Proxy Selection Mapping (GPSM) on a dataset of 1067 Duroc pigs with 8,766,074 imputed SNPs. GPSM detected a total of 5649 putative SNPs actively under selection in the Chinese Duroc pig population, and the potential functions of the selection regions were mainly related to production, meat and carcass traits. Meanwhile, we observed that the allele frequency of variants related to teat number (NT) relevant traits was also changed, which might be influenced by genes that had pleiotropic effects. First, we identified the direction of selection on NT traits by \documentclass[12pt]{minimal}
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\begin{document}$$\hat{G}$$\end{document}G^, and further pinpointed large-effect genomic regions associated with NT relevant traits by selection signature and GWAS. Combining results of NT relevant traits-specific selection signatures and GWAS, we found three common genome regions, which were overlapped with QTLs related to production, meat and carcass traits besides “teat number” QTLs. This implied that there were some pleiotropic variants underlying NT and economic traits. We further found that rs346331089 has pleiotropic effects on NT and economic traits, e.g., litter size at weaning (LSW), litter weight at weaning (LWW), days to 100 kg (D100), backfat thickness at 100 kg (B100), and loin muscle area at 100 kg (L100) traits. Conclusions The selected loci that we identified across methods displayed the past breeding process of Chinese Duroc pigs, and our findings could be used to inform future breeding decision. Supplementary Information The online version contains supplementary material available at 10.1186/s40104-022-00751-x.
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Affiliation(s)
- Zitao Chen
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, P.R. China.,Department of Animal Science, College of Animal Science, Zhejiang University, 866# Yuhangtang Road, Hangzhou, 310058, P.R. China
| | - Jinyan Teng
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, P.R. China
| | - Shuqi Diao
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, P.R. China
| | - Zhiting Xu
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, P.R. China
| | - Shaopan Ye
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, P.R. China.,Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, 243 Daxue Road, Shantou, 515063, P.R. China
| | - Dingjie Qiu
- Fujian Yongcheng Agricultural & Animal Husbandry Sci-Tech Group Co., Ltd., Fuqing, 350399, P.R. China
| | - Zhe Zhang
- Department of Animal Science, College of Animal Science, Zhejiang University, 866# Yuhangtang Road, Hangzhou, 310058, P.R. China
| | - Yuchun Pan
- Department of Animal Science, College of Animal Science, Zhejiang University, 866# Yuhangtang Road, Hangzhou, 310058, P.R. China
| | - Jiaqi Li
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, P.R. China
| | - Qin Zhang
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, Shandong Agricultural University, Tai'an, 271018, P.R. China
| | - Zhe Zhang
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, P.R. China.
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13
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Use of a graph neural network to the weighted gene co-expression network analysis of Korean native cattle. Sci Rep 2022; 12:9854. [PMID: 35701465 PMCID: PMC9197844 DOI: 10.1038/s41598-022-13796-9] [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: 11/09/2021] [Accepted: 05/27/2022] [Indexed: 11/25/2022] Open
Abstract
In the general framework of the weighted gene co-expression network analysis (WGCNA), a hierarchical clustering algorithm is commonly used to module definition. However, hierarchical clustering depends strongly on the topological overlap measure. In other words, this algorithm may assign two genes with low topological overlap to different modules even though their expression patterns are similar. Here, a novel gene module clustering algorithm for WGCNA is proposed. We develop a gene module clustering network (gmcNet), which simultaneously addresses single-level expression and topological overlap measure. The proposed gmcNet includes a “co-expression pattern recognizer” (CEPR) and “module classifier”. The CEPR incorporates expression features of single genes into the topological features of co-expressed ones. Given this CEPR-embedded feature, the module classifier computes module assignment probabilities. We validated gmcNet performance using 4,976 genes from 20 native Korean cattle. We observed that the CEPR generates more robust features than single-level expression or topological overlap measure. Given the CEPR-embedded feature, gmcNet achieved the best performance in terms of modularity (0.261) and the differentially expressed signal (27.739) compared with other clustering methods tested. Furthermore, gmcNet detected some interesting biological functionalities for carcass weight, backfat thickness, intramuscular fat, and beef tenderness of Korean native cattle. Therefore, gmcNet is a useful framework for WGCNA module clustering.
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14
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Mészárosová M, Mészáros G, Moravčíková N, Pavlík I, Margetín M, Kasarda R. Within- and between-Breed Selection Signatures in the Original and Improved Valachian Sheep. Animals (Basel) 2022; 12:ani12111346. [PMID: 35681809 PMCID: PMC9179888 DOI: 10.3390/ani12111346] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 05/13/2022] [Accepted: 05/23/2022] [Indexed: 11/16/2022] Open
Abstract
This study explored the genomic diversity and selection signatures in two Slovakian national breeds, the Original Valachian and the Improved Valachian sheep. As they are an important animal genetic resource within the country, but with decreasing population size, our aim is to identify potentially valuable genomic regions. A total of 97 sheep (18 male and 79 female) from the Original Valachian, and 69 sheep (25 male and 44 female) from the Improved Valachian populations were genotyped using the GeneSeek GGP Ovine 50 K chip. The inbreeding levels were assessed with runs of homozygosity (ROH). The selection signatures within breeds were identified based on the top 1% of most homozygous regions within the breed, the so-called ROH islands. The selection signatures between breeds were assessed based on variance in linkage disequilibrium. Overall, we have identified selection signatures with quantitative trait loci (QTL) and genes pointing towards all three production purposes of the Valachian sheep, milk, meat, and wool, including their quality characteristics. Another group with apparent large importance was the various traits related to health and resistance to parasites, which is well in line with the sturdy nature of this breed.
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Affiliation(s)
- Mária Mészárosová
- Faculty of Agrobiology and Food Resources, Institute of Nutrition and Genomics, Slovak University of Agriculture in Nitra, Tr. A. Hlinku 2, 94976 Nitra, Slovakia; (M.M.); (R.K.)
| | - Gábor Mészáros
- Department of Sustainable Agricultural Systems, Division of Livestock Sciences, University of Natural Resources and Life Sciences, Vienna, Gregor-Mendel-Straße 33, 1180 Vienna, Austria;
| | - Nina Moravčíková
- Faculty of Agrobiology and Food Resources, Institute of Nutrition and Genomics, Slovak University of Agriculture in Nitra, Tr. A. Hlinku 2, 94976 Nitra, Slovakia; (M.M.); (R.K.)
- Correspondence:
| | - Ivan Pavlík
- Research Institute of Animal Production—NPPC Slovakia, Hlohovecká 2, 95141 Nitra—Lužianky, Slovakia;
| | - Milan Margetín
- Faculty of Agrobiology and Food Resources, Institute of Animal Science, Slovak University of Agriculture in Nitra, Tr. A. Hlinku 2, 94976 Nitra, Slovakia;
| | - Radovan Kasarda
- Faculty of Agrobiology and Food Resources, Institute of Nutrition and Genomics, Slovak University of Agriculture in Nitra, Tr. A. Hlinku 2, 94976 Nitra, Slovakia; (M.M.); (R.K.)
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15
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Pan C, Yang C, Wang S, Ma Y. Identifying Key Genes and Functionally Enriched Pathways of Diverse Adipose Tissue Types in Cattle. Front Genet 2022; 13:790690. [PMID: 35237299 PMCID: PMC8884536 DOI: 10.3389/fgene.2022.790690] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 01/26/2022] [Indexed: 12/26/2022] Open
Abstract
Background: Fat is a tissue that not just stores energy and plays a protective role; it is also a vital endocrine organ that generates and integrates signals to influence metabolism. Meanwhile, the excessive accumulation of lipids in adipose tissue can lead to metabolic disturbance and diseases. To date, the complicated molecular mechanisms of bovine adipose tissue are still unknown. This study aimed to identify key genes and functionally enriched pathways in various adipose tissue types. Results: The RNAseq data of 264 samples were downloaded from Gene Expression Omnibus (GEO) and analyzed by weighted gene co-expression network analysis (WGCNA). We identified 19 modules that significantly associated with at least one adipose tissue type. The brown module from GSE39618 was most closely associated with intramuscular fat tissue, which contained 550 genes. These genes were significantly enriched in pathways that related to inflammation and disease, such as TNF signaling pathway, IL-17 signaling pathway, and NF-kappa B signaling pathway. The pink module (GSE39618) that contained 58 genes was most closely associated with omental fat tissue. The turquoise (GSE39618), blue (GSE116775), and yellow (GSE65125) module were most closely associated with subcutaneous fat tissue. Genes in these modules were significantly enriched in pathways related to fat metabolism, such as the PPAR signaling pathway, fatty acid metabolism and PI3K-Akt signaling pathway. At last, key genes for intramuscular fat (PTGS2 and IL6), omental fat (ARHGEF5 and WT1), and subcutaneous fat (KIT, QR6Q1, PKD2L1, etc.) were obtained and verified. In addition, it was found that IL10 and VCAM1 might be potential genes to distinguish adipose and muscle. Conclusion: The study applied WGCNA to generate a landscape of adipose tissue and provide a basis for identifying potential pathways and hub genes of different adipose tissue types.
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Affiliation(s)
- Cuili Pan
- School of Agriculture, Ningxia University, Yinchuan, China
- Key Laboratory of Ruminant Molecular and Cellular Breeding, Ningxia Hui Autonomous Region, Ningxia University, Yinchuan, China
| | - Chaoyun Yang
- School of Agriculture, Ningxia University, Yinchuan, China
- Key Laboratory of Ruminant Molecular and Cellular Breeding, Ningxia Hui Autonomous Region, Ningxia University, Yinchuan, China
| | - Shuzhe Wang
- School of Agriculture, Ningxia University, Yinchuan, China
- Key Laboratory of Ruminant Molecular and Cellular Breeding, Ningxia Hui Autonomous Region, Ningxia University, Yinchuan, China
| | - Yun Ma
- School of Agriculture, Ningxia University, Yinchuan, China
- Key Laboratory of Ruminant Molecular and Cellular Breeding, Ningxia Hui Autonomous Region, Ningxia University, Yinchuan, China
- *Correspondence: Yun Ma,
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16
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Raymond PW, Velie BD, Wade CM. Forensic DNA phenotyping: Canis familiaris breed classification and skeletal phenotype prediction using functionally significant skeletal SNPs and indels. Anim Genet 2021; 53:247-263. [PMID: 34963196 DOI: 10.1111/age.13165] [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: 10/21/2020] [Revised: 11/30/2021] [Accepted: 12/12/2021] [Indexed: 11/29/2022]
Abstract
This review highlights a novel application of breed identification and prediction of skeletal traits in forensic investigations using canine DNA evidence. Currently, genotyping methods used for canine breed classification involve the application of highly polymorphic short tandem repeats in addition to larger commercially available SNP arrays. Both applications face technical challenges. An additional approach to breed identification could be through genotyping SNPs and indels that characterise the array of skeletal differences displayed across domestic dog populations. Research has shown that a small number of genetic variants of large effect drive differences in skeletal phenotypes among domestic dog breeds. This feature makes functionally significant canine skeletal variants a cost-effective target for forensic investigators to classify individuals according to their breed. Further analysis of these skeletal variants would enable the prediction of external appearance. To date, functionally significant genes with genetic variants associated with differences in size, bulk, skull shape, ear shape, limb length, digit type, and tail morphology have been uncovered. Recommendations of a cost-effective genotyping method that can be readily designed and applied by forensic investigators have been given. Further advances to improve the field of canine skeletal forensic DNA phenotyping include the refinement of phenotyping methods, further biological validation of the skeletal genetic variants and establishing a publicly available database for storage of allele frequencies of the skeletal genetic variants in the wider domestic dog population.
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Affiliation(s)
- Patrick W Raymond
- School of Life and Environmental Sciences, University of Sydney, Sydney, Australia
| | - Brandon D Velie
- School of Life and Environmental Sciences, University of Sydney, Sydney, Australia
| | - Claire M Wade
- School of Life and Environmental Sciences, University of Sydney, Sydney, Australia
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17
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Alexandre PA, Naval-Sánchez M, Menzies M, Nguyen LT, Porto-Neto LR, Fortes MRS, Reverter A. Chromatin accessibility and regulatory vocabulary across indicine cattle tissues. Genome Biol 2021; 22:273. [PMID: 34548076 PMCID: PMC8454054 DOI: 10.1186/s13059-021-02489-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 09/08/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Spatiotemporal changes in the chromatin accessibility landscape are essential to cell differentiation, development, health, and disease. The quest of identifying regulatory elements in open chromatin regions across different tissues and developmental stages is led by large international collaborative efforts mostly focusing on model organisms, such as ENCODE. Recently, the Functional Annotation of Animal Genomes (FAANG) has been established to unravel the regulatory elements in non-model organisms, including cattle. Now, we can transition from prediction to validation by experimentally identifying the regulatory elements in tropical indicine cattle. The identification of regulatory elements, their annotation and comparison with the taurine counterpart, holds high promise to link regulatory regions to adaptability traits and improve animal productivity and welfare. RESULTS We generate open chromatin profiles for liver, muscle, and hypothalamus of indicine cattle through ATAC-seq. Using robust methods for motif discovery, motif enrichment and transcription factor binding sites, we identify potential master regulators of the epigenomic profile in these three tissues, namely HNF4, MEF2, and SOX factors, respectively. Integration with transcriptomic data allows us to confirm some of their target genes. Finally, by comparing our results with Bos taurus data we identify potential indicine-specific open chromatin regions and overlaps with indicine selective sweeps. CONCLUSIONS Our findings provide insights into the identification and analysis of regulatory elements in non-model organisms, the evolution of regulatory elements within two cattle subspecies as well as having an immediate impact on the animal genetics community in particular for a relevant productive species such as tropical cattle.
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Affiliation(s)
- Pâmela A Alexandre
- CSIRO Agriculture & Food, 306 Carmody Rd., QLD, 4067, Brisbane, Australia.
| | - Marina Naval-Sánchez
- CSIRO Agriculture & Food, 306 Carmody Rd., QLD, 4067, Brisbane, Australia
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Moira Menzies
- CSIRO Agriculture & Food, 306 Carmody Rd., QLD, 4067, Brisbane, Australia
| | - Loan T Nguyen
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, 4072, Australia
| | | | - Marina R S Fortes
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Antonio Reverter
- CSIRO Agriculture & Food, 306 Carmody Rd., QLD, 4067, Brisbane, Australia
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He G, Gu J, Wang H, Cheng S, Xiong Q, Ke M, Hu Y, Feng J, Song L, Liu Z, Xu Y. Nr2e1 deficiency aggravates insulin resistance and chronic inflammation of visceral adipose tissues in a diet-induced obese mice model. Life Sci 2021; 278:119562. [PMID: 33915130 DOI: 10.1016/j.lfs.2021.119562] [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: 03/05/2021] [Revised: 04/11/2021] [Accepted: 04/23/2021] [Indexed: 10/21/2022]
Abstract
AIMS To investigate the nuclear receptor subfamily 2 group E member 1 (Nr2e1) expression in adipose tissues of obese mice and assess the role of Nr2e1 in insulin resistance and chronic inflammation of the adipose tissues. MAIN METHODS An obese model was established in Nr2e1 knockout (KO) mice and their wild type (WT) littermates through a long-term high-fat diet (HFD) feeding regime. The epididymal fat weight, body weight, and daily food intake were recorded. The blood lipid profile, blood inflammatory factors, and the levels of fasting blood glucose (FBG) and fasting insulin were determined. We estimated insulin resistance by the homeostasis model assessment (HOMA). The expression of inflammatory factors and F4/80 was examined by polymerase chain reaction (PCR) and western blotting to assess adipose tissues inflammation. We also determined the molecules of insulin signaling and the nuclear factor kappa B (NF-κB) pathway by western blotting. KEY FINDINGS The Nr2e1 expression was upregulated in WT obese mice when compared with that in control mice. Despite a lower body weight and epididymal fat mass in Nr2e1-/- mice, these rats showed increased inflammatory cytokines secretion, more pronounced hyperlipidemia, and impaired insulin sensitivity after HFD treatment. Further investigation revealed that Nr2e1 deletion affected the expression of insulin signaling and NF-κB pathway-related molecules in visceral adipose tissues. SIGNIFICANCE Nr2e1 may act as a potential target to improve insulin sensitivity and inflammation in obesity and related complications.
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Affiliation(s)
- Guangzhen He
- Department of Endocrinology, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China; Department of Pediatrics, Affiliated Taihe Hospital of Hubei University of Medicine, Shiyan, Hubei, China
| | - Jiaowei Gu
- Department of Pediatrics, Affiliated Taihe Hospital of Hubei University of Medicine, Shiyan, Hubei, China
| | - Huawei Wang
- Department of Endocrinology, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China
| | - Siyuan Cheng
- Department of Endocrinology, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China
| | - Qing Xiong
- Department of Endocrinology, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China
| | - Mengting Ke
- Department of Endocrinology, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China
| | - Yong Hu
- Department of Endocrinology, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China
| | - Jieyuan Feng
- Department of Endocrinology, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China
| | - Linyang Song
- Department of Endocrinology, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China
| | - Zheng Liu
- Department of Endocrinology and Metabolism, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China.
| | - Yancheng Xu
- Department of Endocrinology, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China.
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19
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Han F, Li J, Zhao R, Liu L, Li L, Li Q, He J, Liu N. Identification and co-expression analysis of long noncoding RNAs and mRNAs involved in the deposition of intramuscular fat in Aohan fine-wool sheep. BMC Genomics 2021; 22:98. [PMID: 33526009 PMCID: PMC7852088 DOI: 10.1186/s12864-021-07385-9] [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: 03/25/2020] [Accepted: 01/13/2021] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Intramuscular fat (IMF) content has become one of the most important indicators for measuring meat quality, and levels of IMF are affected by various genes. Long non-coding RNAs (lncRNAs) are widely expressed non-coding RNAs that play an important regulatory role in a variety of biological processes; however, research on the lncRNAs involved in sheep IMF deposition is still in its infancy. Aohan fine-wool sheep (AFWS), one of China's most important meat-hair, dual-purpose sheep breed, provides a great model for studying the role of lncRNAs in the regulation of IMF deposition. We identified lncRNAs by RNA sequencing in Longissimus thoracis et lumborum (LTL) samples of sheep at two ages: 2 months (Mth-2) and 12 months (Mth-12). RESULTS We identified a total of 26,247 genes and 6935 novel lncRNAs in LTL samples of sheep. Among these, 199 mRNAs and 61 lncRNAs were differentially expressed. We then compared the structural characteristics of lncRNAs and mRNAs. We obtained target genes of differentially expressed lncRNAs (DELs) and performed enrichment analyses using Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG). We found that target mRNAs were enriched in metabolic processes and developmental pathways. One pathway was significantly enriched, namely tight junction. Based on the analysis of critical target genes, we obtained seven candidate lncRNAs that potentially regulated lipid deposition and constructed a lncRNA-mRNA co-expression network that included MSTRG.4051.3-FZD4, MSTRG.16157.3-ULK1, MSTRG.21053.3-PAQR3, MSTRG.19941.2-TPI1, MSTRG.12864.1-FHL1, MSTRG.2469.2-EXOC6 and MSTRG.21381.1-NCOA1. We speculated that these candidate lncRNAs might play a role by regulating the expression of target genes. We randomly selected five mRNAs and five lncRNAs to verify the accuracy of the sequencing data by qRT-PCR. CONCLUSIONS Our study identified the differentially expressed mRNAs and lncRNAs during intramuscular lipid deposition in Aohan fine-wool sheep. The work may widen the knowledge about the annotation of the sheep genome and provide a working basis for investigating intramuscular fat deposition in sheep.
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Affiliation(s)
- Fuhui Han
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, 266109, China
| | - Jing Li
- Qufu Animal Husbandry and Veterinary Technical Service Center, Qufu, 273100, China
| | - Ranran Zhao
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, 266109, China
| | - Lirong Liu
- China Animal Health and Epidemiology Center, Qingdao, 266032, China
| | - Lanlan Li
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, 266109, China
| | - Qian Li
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, 266109, China
| | - Jianning He
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, 266109, China.
| | - Nan Liu
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, 266109, China.
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20
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Duan X, An B, Du L, Chang T, Liang M, Yang BG, Xu L, Zhang L, Li J, E G, Gao H. Genome-Wide Association Analysis of Growth Curve Parameters in Chinese Simmental Beef Cattle. Animals (Basel) 2021; 11:ani11010192. [PMID: 33467455 PMCID: PMC7830728 DOI: 10.3390/ani11010192] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 01/11/2021] [Accepted: 01/11/2021] [Indexed: 12/17/2022] Open
Abstract
The objective of the present study was to perform a genome-wide association study (GWAS) for growth curve parameters using nonlinear models that fit original weight-age records. In this study, data from 808 Chinese Simmental beef cattle that were weighed at 0, 6, 12, and 18 months of age were used to fit the growth curve. The Gompertz model showed the highest coefficient of determination (R2 = 0.954). The parameters' mature body weight (A), time-scale parameter (b), and maturity rate (K) were treated as phenotypes for single-trait GWAS and multi-trait GWAS. In total, 9, 49, and 7 significant SNPs associated with A, b, and K were identified by single-trait GWAS; 22 significant single nucleotide polymorphisms (SNPs) were identified by multi-trait GWAS. Among them, we observed several candidate genes, including PLIN3, KCNS3, TMCO1, PRKAG3, ANGPTL2, IGF-1, SHISA9, and STK3, which were previously reported to associate with growth and development. Further research for these candidate genes may be useful for exploring the full genetic architecture underlying growth and development traits in livestock.
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Affiliation(s)
- Xinghai Duan
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (X.D.); (B.A.); (L.D.); (T.C.); (M.L.); (L.X.); (L.Z.); (J.L.)
- College of Animal Science and Technology, Southwest University, Chongqing 400715, China;
| | - Bingxing An
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (X.D.); (B.A.); (L.D.); (T.C.); (M.L.); (L.X.); (L.Z.); (J.L.)
| | - Lili Du
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (X.D.); (B.A.); (L.D.); (T.C.); (M.L.); (L.X.); (L.Z.); (J.L.)
| | - Tianpeng Chang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (X.D.); (B.A.); (L.D.); (T.C.); (M.L.); (L.X.); (L.Z.); (J.L.)
| | - Mang Liang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (X.D.); (B.A.); (L.D.); (T.C.); (M.L.); (L.X.); (L.Z.); (J.L.)
| | - Bai-Gao Yang
- College of Animal Science and Technology, Southwest University, Chongqing 400715, China;
| | - Lingyang Xu
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (X.D.); (B.A.); (L.D.); (T.C.); (M.L.); (L.X.); (L.Z.); (J.L.)
| | - Lupei Zhang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (X.D.); (B.A.); (L.D.); (T.C.); (M.L.); (L.X.); (L.Z.); (J.L.)
| | - Junya Li
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (X.D.); (B.A.); (L.D.); (T.C.); (M.L.); (L.X.); (L.Z.); (J.L.)
| | - Guangxin E
- College of Animal Science and Technology, Southwest University, Chongqing 400715, China;
- Correspondence: (G.E); (H.G.)
| | - Huijiang Gao
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (X.D.); (B.A.); (L.D.); (T.C.); (M.L.); (L.X.); (L.Z.); (J.L.)
- Correspondence: (G.E); (H.G.)
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21
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Huang J, Feng X, Zhu R, Guo D, Wei Y, Cao X, Ma Y, Shi D. Comparative transcriptome analysis reveals that PCK1 is a potential gene affecting IMF deposition in buffalo. BMC Genomics 2020; 21:710. [PMID: 33045988 PMCID: PMC7552535 DOI: 10.1186/s12864-020-07120-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 10/02/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND In China, although buffaloes are abundant, beef is mainly obtained from cattle, and this preference is mainly attributed to the low intramuscular fat (IMF) content of buffalo. Genetic factors are an important driver that affects IMF deposition. RESULTS To reveal the intrinsic factors responsible for the low IMF content of buffalo, mRNA expression patterns in muscle and adipose tissue between buffalo and cattle were characterized by RNA sequencing analysis. The IMF content in Nanyang cattle was higher than that in Xinyang buffalo. A total of 1566 mRNAs expressed in adipose tissue showed differential expression between the longissimus dorsi muscles of buffalo and cattle. Functional annotation suggested a difference in the glycolysis/gluconeogenesis pathway between the two species. The results of RT-qPCR analysis and gain-of-function experiments confirmed the positive association between the IMF content and phosphoenolpyruvate carboxykinase 1 (PCK1) expression in buffalo. In both mouse C2C12 cells and cultured bovine myocytes, the activity of the PCK1 promoter in buffalo is lower than that in cattle. However, in mouse 3T3-L1 adipocytes and cultured bovine adipocytes, the activity of PCK1 in buffalo promoter is higher than that in cattle. CONCLUSIONS These results indicate the important role of PCK1 in buffalo IMF deposition and illustrate the differences between buffalo and cattle promoter activity that drive PCK1 expression. This research helps to establish a foundation for further studies investigating IMF deposition in buffalo.
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Affiliation(s)
- Jieping Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530005, Guangxi, China. .,College of Life Sciences, Xinyang Normal University, Xinyang, 464000, Henan, China.
| | - Xue Feng
- College of Life Sciences, Xinyang Normal University, Xinyang, 464000, Henan, China
| | - Ruirui Zhu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530005, Guangxi, China
| | - Duo Guo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530005, Guangxi, China
| | - Yutong Wei
- College of Life Sciences, Xinyang Normal University, Xinyang, 464000, Henan, China
| | - Xiaodan Cao
- College of Life Sciences, Xinyang Normal University, Xinyang, 464000, Henan, China
| | - Yun Ma
- College of Life Sciences, Xinyang Normal University, Xinyang, 464000, Henan, China.,School of Agriculture, Ningxia University, Yinchuan, 750021, Ningxia, China
| | - Deshun Shi
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530005, Guangxi, China
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22
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Naserkheil M, Bahrami A, Lee D, Mehrban H. Integrating Single-Step GWAS and Bipartite Networks Reconstruction Provides Novel Insights into Yearling Weight and Carcass Traits in Hanwoo Beef Cattle. Animals (Basel) 2020; 10:ani10101836. [PMID: 33050182 PMCID: PMC7601430 DOI: 10.3390/ani10101836] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 10/02/2020] [Accepted: 10/06/2020] [Indexed: 12/13/2022] Open
Abstract
Simple Summary Hanwoo is an indigenous cattle breed in Korea and popular for meat production owing to its rapid growth and high-quality meat. Its yearling weight and carcass traits (backfat thickness, carcass weight, eye muscle area, and marbling score) are economically important for the selection of young and proven bulls. In recent decades, the advent of high throughput genotyping technologies has made it possible to perform genome-wide association studies (GWAS) for the detection of genomic regions associated with traits of economic interest in different species. In this study, we conducted a weighted single-step genome-wide association study which combines all genotypes, phenotypes and pedigree data in one step (ssGBLUP). It allows for the use of all SNPs simultaneously along with all phenotypes from genotyped and ungenotyped animals. Our results revealed 33 relevant genomic regions related to the traits of interest. Gene set enrichment analysis indicated that the identified candidate genes were related to biological processes and functional terms that were involved in growth and lipid metabolism. In conclusion, these results suggest that the incorporation of GWAS results and network analysis can help us to better understand the genetic bases underlying growth and carcass traits. Abstract In recent years, studies on the biological mechanisms underlying complex traits have been facilitated by innovations in high-throughput genotyping technology. We conducted a weighted single-step genome-wide association study (WssGWAS) to evaluate backfat thickness, carcass weight, eye muscle area, marbling score, and yearling weight in a cohort of 1540 Hanwoo beef cattle using BovineSNP50 BeadChip. The WssGWAS uncovered thirty-three genomic regions that explained more than 1% of the additive genetic variance, mostly located on chromosomes 6 and 14. Among the identified window regions, seven quantitative trait loci (QTL) had pleiotropic effects and twenty-six QTL were trait-specific. Significant pathways implicated in the measured traits through Gene Ontology (GO) term enrichment analysis included the following: lipid biosynthetic process, regulation of lipid metabolic process, transport or localization of lipid, regulation of growth, developmental growth, and multicellular organism growth. Integration of GWAS results of the studied traits with pathway and network analyses facilitated the exploration of the respective candidate genes involved in several biological functions, particularly lipid and growth metabolism. This study provides novel insight into the genetic bases underlying complex traits and could be useful in developing breeding schemes aimed at improving growth and carcass traits in Hanwoo beef cattle.
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Affiliation(s)
- Masoumeh Naserkheil
- Department of Animal Science, University College of Agriculture and Natural Resources, University of Tehran, Karaj 77871-31587, Iran; (M.N.); (A.B.)
| | - Abolfazl Bahrami
- Department of Animal Science, University College of Agriculture and Natural Resources, University of Tehran, Karaj 77871-31587, Iran; (M.N.); (A.B.)
| | - Deukhwan Lee
- Department of Animal Life and Environment Sciences, Hankyong National University, Jungang-ro 327, Anseong-si, Gyeonggi-do 17579, Korea
- Correspondence: ; Tel.: +82-31-670-5091
| | - Hossein Mehrban
- Department of Animal Science, Shahrekord University, Shahrekord 88186-34141, Iran;
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23
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Raza SHA, Khan S, Amjadi M, Abdelnour SA, Ohran H, Alanazi KM, Abd El-Hack ME, Taha AE, Khan R, Gong C, Schreurs NM, Zhao C, Wei D, Zan L. Genome-wide association studies reveal novel loci associated with carcass and body measures in beef cattle. Arch Biochem Biophys 2020; 694:108543. [PMID: 32798459 DOI: 10.1016/j.abb.2020.108543] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 07/26/2020] [Accepted: 08/08/2020] [Indexed: 12/18/2022]
Abstract
Genomic selection has an essential role in the livestock economy by increasing selection productivity. Genomics provides a mechanism to increase the rate of genetic gain using marker-assisted selection. Various quantitative trait loci (QTL) associated with body, carcass and meat quality traits in beef cattle have been found. It is widely accepted that QTL traits in livestock species are regulated by several genes and factors from the environment. Genome-wide association studies (GWAS) are a powerful approach in identifying QTL and to establish genomic regions harboring the genes and polymorphisms associated with specific characteristics in beef cattle. Due to their impact on economic returns, growth, carcass and meat quality traits of cattle are frequently used as essential criteria in selection in breeding programs., GWAS has been used in beef cattle breeding and genetic program and some progress has been made. Furthermore, numerous genes and markers related to productivity traits in beef cattle have been found. This review summarizes the advances in the use of GWAS in beef cattle production and outlines the associations with growth, carcass, and meat quality.
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Affiliation(s)
- Sayed Haidar Abbas Raza
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China.
| | - Samiullah Khan
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
| | - Motahareh Amjadi
- Department of Genetics, Eötvös Loránd University, Budapest, Hungary
| | - Sameh A Abdelnour
- Department of Animal Production, Faculty of Agriculture, Zagazig University, Zagazig, 44511, Egypt
| | - Hussien Ohran
- Department of Physiology, University of Sarajevo, Veterinary Faculty, Zmajaod Bosne 90, 71000, Sarajevo, Bosnia and Herzegovina
| | - Khalid M Alanazi
- Zoology Department, College of Science, King Saud University, P.O. Box 2455, Riyadh, 11451, Saudi Arabia
| | - Mohamed E Abd El-Hack
- Department of Poultry, Faculty of Agriculture, Zagazig University, Zagazig, 44511, Egypt
| | - Ayman E Taha
- Department of Animal Husbandry and Animal Wealth Development, Faculty of Veterinary Medicine, Alexandria University, Edfina, 22578, Egypt
| | - Rajwali Khan
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Cheng Gong
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Nicola M Schreurs
- Animal Science, School of Agriculture and Environment, Massey University, Palmerston North, New Zealand
| | - Chunping Zhao
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Dawei Wei
- School of Agriculture, Ningxia University, Yinchuan, China
| | - Linsen Zan
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China; National Beef Cattle Improvement Center, Northwest A&F University, Yangling, 712100, China.
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24
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Qiu L, Fan X, Zhang Y, Teng X, Miao Y. Molecular characterization, tissue expression and polymorphisms of buffalo PPARGC1A gene. Arch Anim Breed 2020; 63:249-259. [PMID: 32775610 PMCID: PMC7405651 DOI: 10.5194/aab-63-249-2020] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 06/24/2020] [Indexed: 01/18/2023] Open
Abstract
PPARGC1A exerts important functions in activating many nuclear receptors and
transcription factors that are related to energy balance. Previous studies have
shown that PPARGC1A gene is associated with lactation traits of dairy cattle.
However, the functional role of the buffalo PPARGC1A gene is still unknown. In this
work, the complete coding sequence (CDS) of buffalo PPARGC1A was isolated and
characterized for swamp and river buffalo. The CDS length of PPARGC1A for both types
of buffalo was the same, which was composed of 2394 nucleotides and encoded
a peptide composed of 797 amino acid residues. This protein belonged to a
hydrophilic protein and contained one RRM_PPARGC1A domain (AA 674–764) without a signal peptide or a transmembrane domain. The
differential expressions of this gene in 10 buffalo tissues in lactation and
non-lactation displayed that the PPARGC1A was highly expressed in the muscle, heart,
liver, brain and kidney of both non-lactating and lactating periods, but its
expression was significantly different in the muscle, heart, liver, small
intestine, mammary gland, rumen, spleen and lung between the two periods.
Eight single nucleotide polymorphisms (SNPs) were found in buffalo, in which
the c.778C>T, c.1257G>A and c.1311G>A
were shared by two types of buffalo with similar allele frequencies, while
the c.419C>T, c.759A>G, c.920C>A,
c.926G>A and c.1509A>T were only observed in river
buffalo. The SNP419, SNP920 and SNP926 were non-synonymous, which led to the
amino acid changes of p.Ser140Phe, p.Pro307His and p.Arg309Lys. Seven
nucleotide differential sites were identified in the PPARGC1A gene between buffalo and
other Bovidae species. Phylogenetic analysis indicated that buffaloes were
independently clustered into one branch, but they were closely related to
the species of the Bos genus. The results indicate that buffalo PPARGC1A is an
inducible transcriptional coactivator involved in regulating carbohydrate
and fat metabolism. It can exert a functional role in a variety of buffalo
tissues and may participate in milk fat synthesis and development in the
mammary gland.
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Affiliation(s)
- Lihua Qiu
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, Yunnan, China
| | - Xinyang Fan
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, Yunnan, China
| | - Yongyun Zhang
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, Yunnan, China.,Teaching Demonstration Center of the Basic Experiments of Agricultural Majors, Yunnan Agricultural University, Kunming 650201, Yunnan, China
| | - Xiaohong Teng
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, Yunnan, China
| | - Yongwang Miao
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, Yunnan, China
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25
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Wang X, Cheng J, Qin W, Chen H, Chen G, Shang X, Zhang M, Balsai N, Chen H. Polymorphisms in 5' proximal regulating region of THRSP gene are associated with fat production in pigs. 3 Biotech 2020; 10:267. [PMID: 32509500 DOI: 10.1007/s13205-020-02266-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 05/18/2020] [Indexed: 01/17/2023] Open
Abstract
Chinese and imported pig breeds differ in fat production potential, which is associated with the polymorphisms in the 5' proximal regulating region (5'PRR) of thyroid hormone responsive gene (THRSP). In three Chinese breeds (Dingyuan, CDY; Wannanhua, CWH; and Jixi, CJX) and one introduced breed (Yorkshire, YKS), three variant sites were located at T/C-400, A/G-376, and G/A-98 in the 5'PRR. Chinese pig breeds had higher C-400 allele frequencies than YKS. The frequencies of A-376 in CDY and G-376 in CWH were about 0.8. G-98 allele frequencies in CWH and YKS were 0.8617 and 0.8149, respectively. TGG was the dominant haplotype in YKS, CGG in CWH and CJX, and CAA in CDY. According to haplotype frequency, four breeds were clustered into three types, which was consistent with the geographical distribution of the breeds. In CDY, the average backfat thickness (BFT) was the highest with the CC-400 genotype, followed by CT-400 and TT-400 genotypes. In YKS, the pigs with CC-400 or CT-400 genotypes had higher BFT and average daily weight gain, whereas those with CC-400 or TT-400 genotypes had larger lion-eye area. No significant difference was observed in carcass traits among different genotypes at the A/G-376 and G/A-98 loci. The mRNA abundance of THRSP expression for the CCAGAG genotype was significantly higher than that for CTAGAG or TTAGAG genotype. These results indicated that the polymorphisms and genotype distribution of THRSP were closely related to the potential for fat production in pig breeds, which were the result of adaptation to artificial selection and natural selection.
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Affiliation(s)
- Xiaohong Wang
- School of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036 China
- Experimental Animal Center of Anhui Medical University, Hefei, 230032 China
| | - Jin Cheng
- School of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036 China
| | - Wenjuan Qin
- School of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036 China
- Anhui Agricultural University International Immunization Center, Hefei, 230036 China
| | - Hua Chen
- School of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036 China
| | - Gongwei Chen
- School of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036 China
| | - Xuanjian Shang
- School of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036 China
| | - Mengting Zhang
- School of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036 China
| | - Nyamsuren Balsai
- School of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036 China
| | - Hongquan Chen
- School of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036 China
- Key Laboratory of Local Livestock and Poultry Genetic Resources Conservation and Biobreeding of Anhui Province, Hefei, 230036 China
- Anhui Agricultural University International Immunization Center, Hefei, 230036 China
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26
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Use of gene expression profile to identify potentially relevant transcripts to myofibrillar fragmentation index trait. Funct Integr Genomics 2020; 20:609-619. [PMID: 32285226 DOI: 10.1007/s10142-020-00738-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 03/14/2020] [Accepted: 03/17/2020] [Indexed: 12/22/2022]
Abstract
The myofibrillar fragmentation index (MFI) is an indicative trait for meat tenderness. Longissimus thoracis muscle samples from the 20 most extreme bulls (out of 80 bulls set) for MFI (high (n = 10) and low (n = 10) groups) trait were used to perform transcriptomic analysis, using RNA Sequencing (RNA-Seq). An average of 24.616 genes was expressed in the Nellore muscle transcriptome analysis. A total of 96 genes were differentially expressed (p value ≤ 0.001) between the two groups of divergent bulls for MFI. The HEBP2 and BDH1 genes were overexpressed in animals with high MFI. The MYBPH and MYL6, myosin encoders, were identified. The differentially expressed genes were related to increase mitochondria efficiency, especially in cells under oxidative stress conditions, and these also were related to zinc and calcium binding, membrane transport, and muscle constituent proteins, such as actin and myosin. Most of those genes were involved in metabolic pathways of oxidation-reduction, transport of lactate in the plasma membrane, and muscle contraction. This is the first study applying MFI phenotypes in transcriptomic studies to identify and understand differentially expressed genes for beef tenderness. These results suggest that differences detected in gene expression between high and low MFI animals are related to reactive mechanisms and structural components of oxidative fibers under the condition of cellular stress. Some genes may be selected as positional candidate genes to beef tenderness, MYL6, MYBPH, TRIM63, TRIM55, TRIOBP, and CHRNG genes. The use of MFI phenotypes could enhance results of meat tenderness studies.
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27
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Grigoletto L, Ferraz JBS, Oliveira HR, Eler JP, Bussiman FO, Abreu Silva BC, Baldi F, Brito LF. Genetic Architecture of Carcass and Meat Quality Traits in Montana Tropical ® Composite Beef Cattle. Front Genet 2020; 11:123. [PMID: 32180796 PMCID: PMC7057717 DOI: 10.3389/fgene.2020.00123] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 02/03/2020] [Indexed: 12/16/2022] Open
Abstract
The Montana Tropical® Composite is a recently developed beef cattle population that is rapidly expanding in Brazil and other tropical countries. This is mainly due to its improved meat quality and adaptation to tropical climate conditions compared to Zebu and Taurine cattle breeds, respectively. This study aimed to investigate the genetic architecture of ultrasound-based carcass and meat quality traits in Montana Tropical® Composite beef cattle. Therefore, we estimated variance components and genetic parameters and performed genome-wide association studies using the weighted single-step Genomic Best Linear Unbiased Prediction (GBLUP) approach. A pedigree dataset containing 28,480 animals was used, in which 1,436 were genotyped using a moderate-density Single Nucleotide Polymorphism panel (30K; 30,105 SNPs). A total of 9,358, 5,768, 7,996, and 1,972 phenotypic records for the traits Longissimus muscle area (LMA), backfat thickness (BFT), rump fat thickness (RFT), and for marbling score (MARB), respectively, were used for the analyses. Moderate to high heritability estimates were obtained and ranged from 0.16 ± 0.03 (RFT) to 0.33 ± 0.05 (MARB). A high genetic correlation was observed between BFT and RFT (0.97 ± 0.02), suggesting that a similar set of genes affects both traits. The most relevant genomic regions associated with LMA, BFT, RFT, and MARB were found on BTA10 (5.4–5.8 Mb), BTA27 (25.2–25.5 Mb), BTA18 (60.6–61.0 Mb), and BTA21 (14.8–15.4 Mb). Two overlapping genomic regions were identified for RFT and MARB (BTA13:47.9–48.1 Mb) and for BFT and RFT (BTA13:61.5–62.3 Mb). Candidate genes identified in this study, including PLAG1, LYN, WWOX, and PLAGL2, were previously reported to be associated with growth, stature, skeletal muscle growth, fat thickness, and fatty acid composition. Our results indicate that ultrasound-based carcass and meat quality traits in the Montana Tropical® Composite beef cattle are heritable, and therefore, can be improved through selective breeding. In addition, various novel and already known genomic regions related to these traits were identified, which contribute to a better understanding of the underlying genetic background of LMA, BFT, RFT, and MARB in the Montana Tropical Composite population.
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Affiliation(s)
- Laís Grigoletto
- Department of Animal Sciences, College of Animal Sciences and Food Engineering, University of São Paulo, Pirassununga, Brazil.,Department of Animal Sciences, Purdue University, West Lafayette, IN, United States
| | - José B S Ferraz
- Department of Animal Sciences, College of Animal Sciences and Food Engineering, University of São Paulo, Pirassununga, Brazil
| | - Hinayah R Oliveira
- Department of Animal Sciences, Purdue University, West Lafayette, IN, United States
| | - Joanir P Eler
- Department of Animal Sciences, College of Animal Sciences and Food Engineering, University of São Paulo, Pirassununga, Brazil
| | - Fernando O Bussiman
- Department of Animal Sciences, College of Animal Sciences and Food Engineering, University of São Paulo, Pirassununga, Brazil
| | - Barbara C Abreu Silva
- Department of Animal Sciences, College of Animal Sciences and Food Engineering, University of São Paulo, Pirassununga, Brazil
| | - Fernando Baldi
- Department of Animal Sciences, College of Agricultural and Veterinary Sciences, São Paulo State University, Jaboticabal, Brazil
| | - Luiz F Brito
- Department of Animal Sciences, Purdue University, West Lafayette, IN, United States
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de las Heras-Saldana S, Clark SA, Duijvesteijn N, Gondro C, van der Werf JHJ, Chen Y. Combining information from genome-wide association and multi-tissue gene expression studies to elucidate factors underlying genetic variation for residual feed intake in Australian Angus cattle. BMC Genomics 2019; 20:939. [PMID: 31810463 PMCID: PMC6898931 DOI: 10.1186/s12864-019-6270-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 11/07/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Genome-wide association studies (GWAS) are extensively used to identify single nucleotide polymorphisms (SNP) underlying the genetic variation of complex traits. However, much uncertainly often still exists about the causal variants and genes at quantitative trait loci (QTL). The aim of this study was to identify QTL associated with residual feed intake (RFI) and genes in these regions whose expression is also associated with this trait. Angus cattle (2190 steers) with RFI records were genotyped and imputed to high density arrays (770 K) and used for a GWAS approach to identify QTL associated with RFI. RNA sequences from 126 Angus divergently selected for RFI were analyzed to identify the genes whose expression was significantly associated this trait with special attention to those genes residing in the QTL regions. RESULTS The heritability for RFI estimated for this Angus population was 0.3. In a GWAS, we identified 78 SNPs associated with RFI on six QTL (on BTA1, BTA6, BTA14, BTA17, BTA20 and BTA26). The most significant SNP was found on chromosome BTA20 (rs42662073) and explained 4% of the genetic variance. The minor allele frequencies of significant SNPs ranged from 0.05 to 0.49. All regions, except on BTA17, showed a significant dominance effect. In 1 Mb windows surrounding the six significant QTL, we found 149 genes from which OAS2, STC2, SHOX, XKR4, and SGMS1 were the closest to the most significant QTL on BTA17, BTA20, BTA1, BTA14, and BTA26, respectively. In a 2 Mb windows around the six significant QTL, we identified 15 genes whose expression was significantly associated with RFI: BTA20) NEURL1B and CPEB4; BTA17) RITA1, CCDC42B, OAS2, RPL6, and ERP29; BTA26) A1CF, SGMS1, PAPSS2, and PTEN; BTA1) MFSD1 and RARRES1; BTA14) ATP6V1H and MRPL15. CONCLUSIONS Our results showed six QTL regions associated with RFI in a beef Angus population where five of these QTL contained genes that have expression associated with this trait. Therefore, here we show that integrating information from gene expression and GWAS studies can help to better understand the genetic mechanisms that determine variation in complex traits.
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Affiliation(s)
| | - Samuel A. Clark
- School of Environmental and Rural Science, University of New England, Armidale, NSW Australia
| | - Naomi Duijvesteijn
- School of Environmental and Rural Science, University of New England, Armidale, NSW Australia
| | - Cedric Gondro
- School of Environmental and Rural Science, University of New England, Armidale, NSW Australia
- Department of Animal Science, Michigan State University, East Lansing, MI USA
| | | | - Yizhou Chen
- Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Menangle, NSW Australia
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Xiong Q, Wu Y, Yang M, Wu G, Wang Y, Wang H, Feng J, Song L, Tong B, He G, Xu Y. Nr2e1 ablation impairs liver glucolipid metabolism and induces inflammation, high-fat diets amplify the damage. Biomed Pharmacother 2019; 120:109503. [DOI: 10.1016/j.biopha.2019.109503] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2019] [Revised: 09/17/2019] [Accepted: 09/26/2019] [Indexed: 02/08/2023] Open
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Campos GS, Sollero BP, Reimann FA, Junqueira VS, Cardoso LL, Yokoo MJI, Boligon AA, Braccini J, Cardoso FF. Tag‐SNP selection using Bayesian genomewide association study for growth traits in Hereford and Braford cattle. J Anim Breed Genet 2019; 137:449-467. [DOI: 10.1111/jbg.12458] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 11/03/2019] [Accepted: 11/05/2019] [Indexed: 01/20/2023]
Affiliation(s)
| | | | | | | | - Leandro Lunardini Cardoso
- Departamento de Zootecnia Universidade Federal de Pelotas Pelotas Brazil
- Embrapa Pecuária Sul Bagé Brazil
| | | | | | - José Braccini
- Departamento de Zootecnia Universidade Federal do Rio Grande do Sul Porto Alegre Brazil
| | - Fernando Flores Cardoso
- Departamento de Zootecnia Universidade Federal de Pelotas Pelotas Brazil
- Embrapa Pecuária Sul Bagé Brazil
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Association of Twelve Candidate Gene Polymorphisms with the Intramuscular Fat Content and Average Backfat Thickness of Chinese Suhuai Pigs. Animals (Basel) 2019; 9:ani9110858. [PMID: 31652864 PMCID: PMC6912197 DOI: 10.3390/ani9110858] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 10/18/2019] [Accepted: 10/21/2019] [Indexed: 12/16/2022] Open
Abstract
Simple Summary Appropriate intramuscular fat content (IFC) is the goal of consumers and the direction that breeders must pursue. However, it is difficult to improve the IFC but not average backfat thickness (ABT) by traditional breeding methods, and pigs must be slaughtered to accurately measure IFC. Marker-assisted selection (MAS) provides an economic and efficient method to improve the IFC in pigs. Our research indicated that the FABP3 (rs1110770079) single nucleotide polymorphism (SNP) could be a candidate gene associated with IFC (but not ABT), and IFC could be improved by selecting the individuals with a favorable genotype (GG) of FABP3 (rs1110770079) SNP for pig breeding. Abstract The present study aimed to identify the molecular markers for genes that influence intramuscular fat content (IFC), but not average backfat thickness (ABT). A total of 330 Suhuai pigs were slaughtered, and measurements of IFC and ABT were obtained. Phenotypic and genetic correlations between IFC and ABT were calculated. Thirteen single nucleotide polymorphisms (SNPs) among 12 candidate genes for IFC were analyzed, including FABP3, LIPE, IGF1, IGF2, LEP, LEPR, MC4R, PHKG1, RETN, RYR1, SCD, and UBE3C. Associations of the evaluated SNPs with IFCIFC and ABT were performed. Our results showed that the means of IFC and ABT were 1.99 ± 0.03 % and 26.68 ± 0.28 mm, respectively. The coefficients of variation (CVs) of IFC and ABT were 31.21% and 19.36%, respectively. The phenotypic and genetic correlations between IFC and ABT were moderate. Only the FABP3 (rs1110770079) was associated with IFC (p < 0.05) but not with ABT. Besides, there was a tendency for associations of RYR1 (rs344435545) and SCD (rs80912566) with IFC (p < 0.1). Our results indicated that the FABP3 (rs1110770079) SNP could be used as a marker to improve IFC without changing ABT in the Suhuai pig breeding system.
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Zhou C, Shen D, Li C, Cai W, Liu S, Yin H, Shi S, Cao M, Zhang S. Comparative Transcriptomic and Proteomic Analyses Identify Key Genes Associated With Milk Fat Traits in Chinese Holstein Cows. Front Genet 2019; 10:672. [PMID: 31456815 PMCID: PMC6700372 DOI: 10.3389/fgene.2019.00672] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 06/27/2019] [Indexed: 12/12/2022] Open
Abstract
Milk fat is the most important energy substance in milk and contributes to its quality and health benefits. However, the genetic mechanisms underlying milk fat synthesis are not fully understood. The development of RNA sequencing and tandem mass tag technologies has facilitated the identification of eukaryotic genes associated with complex traits. In this study, we used these methods to obtain liver transcriptomic and proteomic profiles of Chinese Holstein cows (n = 6). Comparative analyses of cows with extremely high vs. low milk fat percentage phenotypes yielded 321 differentially expressed genes (DEGs) and 76 differentially expressed proteins (DEPs). Functional annotation of these DEGs and DEPs revealed 26 genes that were predicted to influence lipid metabolism through insulin, phosphatidylinositol 3-kinase/Akt, mitogen-activated protein kinase, 5′ AMP-activated protein kinase, mammalian target of rapamycin, and peroxisome proliferator-activated receptor signaling pathways; these genes are considered as the most promising candidate regulators of milk fat synthesis. The findings of this study enhance the understanding of the genetic basis and molecular mechanisms of milk fat synthesis, which could lead to the development of cow breeds that produce milk with higher nutritional value.
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Affiliation(s)
- Chenghao Zhou
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Dan Shen
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Cong Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Wentao Cai
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Shuli Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Hongwei Yin
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Shaolei Shi
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Mingyue Cao
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Shengli Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
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Peripolli E, Stafuzza NB, Amorim ST, Lemos MVA, Grigoletto L, Kluska S, Ferraz JBS, Eler JP, Mattos EC, Baldi F. Genome‐wide scan for runs of homozygosity in the composite Montana Tropical
®
beef cattle. J Anim Breed Genet 2019; 137:155-165. [DOI: 10.1111/jbg.12428] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 07/09/2019] [Accepted: 07/11/2019] [Indexed: 12/17/2022]
Affiliation(s)
- Elisa Peripolli
- Faculdade de Ciências Agrárias e Veterinárias, Departamento de Zootecnia UNESP Univ Estadual Paulista Júlio de Mesquita Filho Jaboticabal Brazil
| | | | - Sabrina Thaise Amorim
- Faculdade de Ciências Agrárias e Veterinárias, Departamento de Zootecnia UNESP Univ Estadual Paulista Júlio de Mesquita Filho Jaboticabal Brazil
| | - Marcos Vinícius Antunes Lemos
- Faculdade de Ciências Agrárias e Veterinárias, Departamento de Zootecnia UNESP Univ Estadual Paulista Júlio de Mesquita Filho Jaboticabal Brazil
| | - Laís Grigoletto
- Faculdade de Zootecnia e Engenharia de Alimentos, Departamento de Medicina Veterinária Universidade de São Paulo Pirassununga Brazil
| | - Sabrina Kluska
- Faculdade de Ciências Agrárias e Veterinárias, Departamento de Zootecnia UNESP Univ Estadual Paulista Júlio de Mesquita Filho Jaboticabal Brazil
| | - José Bento Sterman Ferraz
- Faculdade de Zootecnia e Engenharia de Alimentos, Departamento de Medicina Veterinária Universidade de São Paulo Pirassununga Brazil
| | - Joanir Pereira Eler
- Faculdade de Zootecnia e Engenharia de Alimentos, Departamento de Medicina Veterinária Universidade de São Paulo Pirassununga Brazil
| | - Elisângela Chicaroni Mattos
- Faculdade de Zootecnia e Engenharia de Alimentos, Departamento de Medicina Veterinária Universidade de São Paulo Pirassununga Brazil
| | - Fernando Baldi
- Faculdade de Ciências Agrárias e Veterinárias, Departamento de Zootecnia UNESP Univ Estadual Paulista Júlio de Mesquita Filho Jaboticabal Brazil
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Bayes Factor-Based Regulatory Gene Network Analysis of Genome-Wide Association Study of Economic Traits in a Purebred Swine Population. Genes (Basel) 2019; 10:genes10040293. [PMID: 30974885 PMCID: PMC6523153 DOI: 10.3390/genes10040293] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2019] [Revised: 03/08/2019] [Accepted: 04/01/2019] [Indexed: 01/06/2023] Open
Abstract
Early stage prediction of economic trait performance is important and directly linked to profitability of farm pig production. Genome-wide association study (GWAS) has been applied to find causative genomic regions of traits. This study established a regulatory gene network using GWAS for critical economic pig characteristics, centered on easily measurable body fat thickness in live animals. We genotyped 2,681 pigs using Illumina Porcine SNP60, followed by GWAS to calculate Bayes factors for 47,697 single nucleotide polymorphisms (SNPs) of seven traits. Using this information, SNPs were annotated with specific genes near genome locations to establish the association weight matrix. The entire network consisted of 226 nodes and 6,921 significant edges. For in silico validation of their interactions, we conducted regulatory sequence analysis of predicted target genes of transcription factors (TFs). Three key regulatory TFs were identified to guarantee maximum coverage: AT-rich interaction domain 3B (ARID3B), glial cell missing homolog 1 (GCM1), and GLI family zinc finger 2 (GLI2). We identified numerous genes targeted by ARID3B, associated with cellular processes. GCM1 and GLI2 were involved in developmental processes, and their shared target genes regulated multicellular organismal process. This system biology-based function analysis might contribute to enhancing understanding of economic pig traits.
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Gui L, Jia J. Effect of single nucleotide polymorphisms in the UCP3 and FOXO1
genes on carcass quality traits in Qinchuan cattle. JOURNAL OF ANIMAL AND FEED SCIENCES 2018. [DOI: 10.22358/jafs/97366/2018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Gui LS, Raza SHA, Garcia M, Sun YG, Ullah I, Han YC. Genetic variants in the SIRT6 transcriptional regulatory region affect gene activity and carcass quality traits in indigenous Chinese beef cattle (Bos taurus). BMC Genomics 2018; 19:785. [PMID: 30382814 PMCID: PMC6211504 DOI: 10.1186/s12864-018-5149-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 10/08/2018] [Indexed: 01/21/2023] Open
Abstract
Background The aim of this study was to analyze potential influences of polymorphisms within the regulatory region of the bovine SIRT6 gene on carcass quality traits. Expression analyses suggested that SIRT6 gene is predominately expressed in kidney, compared with other tissues. In 535 indigenous Chinese beef cattle, two novel single nucleotide polymorphisms (SNPs) were identified within the promoter region of the SIRT6 gene. Results Association analysis indicated that G allele of the c.-1100 A > G had a positive effect on fat deposition, and the Hap4/4 diplotype had more favourable results than other dipoltypes with respect to the evaluation of carcass quality traits. Furthermore, promoter activity associated with the Hap3 haplotype was measured at higher levels than the Hap1 haplotype, which would be in agreement with the previously described association analysis. Conclusion The SIRT6 promoter variants significantly affect transcriptional levels and subsequently significantly influence bovine intramscular fat content.
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Affiliation(s)
- Lin-Sheng Gui
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, Qinghai Province, 810016, People's Republic of China.,College of Agriculture and Animal Husbandry, Qinghai University, Xining, Qinghai Province, 810016, People's Republic of China
| | - Sayed Haidar Abbas Raza
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Matthew Garcia
- Utah State University, School of Animal Dairy and Veterinary Sciences, Logan, UT, 84322, USA
| | - Yong-Gang Sun
- Academy of Animal Science and Veterinary Medicine, Qinghai University, Xining, Qinghai Province, 810016, People's Republic of China
| | - Irfan Ullah
- College of Bio-medical engineering Chongqing University Chongqing, Shapingba 400044, People's Republic of China
| | - Yin-Cang Han
- Academy of Animal Science and Veterinary Medicine, Qinghai University, Xining, Qinghai Province, 810016, People's Republic of China.
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Iung LHDS, Mulder HA, Neves HHDR, Carvalheiro R. Genomic regions underlying uniformity of yearling weight in Nellore cattle evaluated under different response variables. BMC Genomics 2018; 19:619. [PMID: 30115034 PMCID: PMC6097312 DOI: 10.1186/s12864-018-5003-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 08/08/2018] [Indexed: 02/22/2023] Open
Abstract
BACKGROUND In livestock, residual variance has been studied because of the interest to improve uniformity of production. Several studies have provided evidence that residual variance is partially under genetic control; however, few investigations have elucidated genes that control it. The aim of this study was to identify genomic regions associated with within-family residual variance of yearling weight (YW; N = 423) in Nellore bulls with high density SNP data, using different response variables. For this, solutions from double hierarchical generalized linear models (DHGLM) were used to provide the response variables, as follows: a DGHLM assuming non-null genetic correlation between mean and residual variance (rmv ≠ 0) to obtain deregressed EBV for mean (dEBVm) and residual variance (dEBVv); and a DHGLM assuming rmv = 0 to obtain two alternative response variables for residual variance, dEBVv_r0 and log-transformed variance of estimated residuals (ln_[Formula: see text]). RESULTS The dEBVm and dEBVv were highly correlated, resulting in common regions associated with mean and residual variance of YW. However, higher effects on variance than the mean showed that these regions had effects on the variance beyond scale effects. More independent association results between mean and residual variance were obtained when null rmv was assumed. While 13 and 4 single nucleotide polymorphisms (SNPs) showed a strong association (Bayes Factor > 20) with dEBVv and ln_[Formula: see text], respectively, only suggestive signals were found for dEBVv_r0. All overlapping 1-Mb windows among top 20 between dEBVm and dEBVv were previously associated with growth traits. The potential candidate genes for uniformity are involved in metabolism, stress, inflammatory and immune responses, mineralization, neuronal activity and bone formation. CONCLUSIONS It is necessary to use a strategy like assuming null rmv to obtain genomic regions associated with uniformity that are not associated with the mean. Genes involved not only in metabolism, but also stress, inflammatory and immune responses, mineralization, neuronal activity and bone formation were the most promising biological candidates for uniformity of YW. Although no clear evidence of using a specific response variable was found, we recommend consider different response variables to study uniformity to increase evidence on candidate regions and biological mechanisms behind it.
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Affiliation(s)
- Laiza Helena de Souza Iung
- School of Agricultural and Veterinarian Sciences, São Paulo State University (Unesp), Via de Acesso Prof. Paulo Donato Castelane, S/N, Vila Industrial, FCAV/UNESP, Jaboticabal, São Paulo, 14884-900 Brazil
| | - Herman Arend Mulder
- Wageningen University & Research Animal Breeding and Genomics, P.O. Box 338, 6700 AH Wageningen, The Netherlands
| | | | - Roberto Carvalheiro
- School of Agricultural and Veterinarian Sciences, São Paulo State University (Unesp), Via de Acesso Prof. Paulo Donato Castelane, S/N, Vila Industrial, FCAV/UNESP, Jaboticabal, São Paulo, 14884-900 Brazil
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Rodriguez-Valera Y, Renand G, Naves M, Fonseca-Jiménez Y, Moreno-Probance TI, Ramos-Onsins S, Rocha D, Ramayo-Caldas Y. Genetic diversity and selection signatures of the beef 'Charolais de Cuba' breed. Sci Rep 2018; 8:11005. [PMID: 30030481 PMCID: PMC6054659 DOI: 10.1038/s41598-018-29453-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 07/12/2018] [Indexed: 01/19/2023] Open
Abstract
In this study, we used BovineSNP50 Genotyping BeadChip data to estimate the structure, putative ancestral origin as well as to identify regions with selective sweeps that may have had an important role in the adaptation to tropical conditions of the 'Charolais de Cuba' (CHCU) breed. According to a principal component analysis, CHCU samples cluster together with taurine breeds with an estimated 93% of taurus ancestral alleles. Despite the short period since importation, we detected differentiation (Fst = 0.049) between the French Charolaise (CHA) and CHCU. However, CHA breed was the closest breed to CHCU followed by other hybrids breed with a clear CHA origin. Linkage disequilibrium (r2) decay tends to be lower in CHCU compared to CHA probably due to a less intense artificial selection programs of CHCU. Signals of recent adaptation to tropical conditions between CHCU and CHA were identified. Genes mapping within those regions reflect different functions related to immunity, metabolic changes and heat tolerance (CHCU) and muscle development and meat quality (CHA) that may have had an important role in the phenotypic differentiation of these breeds. Further studies will expand our knowledge on the molecular basis of adaptation of cattle to tropical conditions and molecular process associated with meat quality traits.
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Affiliation(s)
| | - Gilles Renand
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Michel Naves
- UR143, Unité de Recherches Zootechniques, Institut National de la Recherche Agronomique, Guadeloupe, France
| | | | | | - Sebastian Ramos-Onsins
- Animal Genomics Department, Centre for Research in Agricultural Genomics (CRAG), Campus UAB, Bellaterra, 08193, Spain
| | - Dominique Rocha
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France.
| | - Yuliaxis Ramayo-Caldas
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France. .,Animal Breeding and Genetics Program, Institute for Research and Technology in Food and Agriculture (IRTA), Torre Marimon, Caldes de Montbui, 08140, Spain. .,Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona (UAB), 08193, Bellaterra, Spain.
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Cardoso DF, de Albuquerque LG, Reimer C, Qanbari S, Erbe M, do Nascimento AV, Venturini GC, Scalez DCB, Baldi F, de Camargo GMF, Mercadante MEZ, do Santos Gonçalves Cyrillo JN, Simianer H, Tonhati H. Genome-wide scan reveals population stratification and footprints of recent selection in Nelore cattle. Genet Sel Evol 2018; 50:22. [PMID: 29720080 PMCID: PMC5930444 DOI: 10.1186/s12711-018-0381-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 02/20/2018] [Indexed: 12/11/2022] Open
Abstract
Background This study aimed at (1) assessing the genomic stratification of experimental lines of Nelore cattle that have experienced different selection regimes for growth traits, and (2) identifying genomic regions that have undergone recent selection. We used a sample of 763 animals genotyped with the Illumina BovineHD BeadChip, among which 674 animals originated from two lines that are maintained under directional selection for increased yearling body weight and 89 animals from a control line that is maintained under stabilizing selection. Results Multidimensional analysis of the genomic dissimilarity matrix and admixture analysis revealed a substantial level of population stratification between the directional selection lines and the stabilizing selection control line. Two of the three tests used to detect selection signatures (FST, XP-EHH and iHS) revealed six candidate regions with indications of selection, which strongly indicates truly positive signals. The set of identified candidate genes included several genes with roles that are functionally related to growth metabolism, such as COL14A1, CPT1C, CRH, TBC1D1, and XKR4. Conclusions The current study identified genetic stratification that resulted from almost four decades of divergent selection in an experimental Nelore population, and highlighted autosomal genomic regions that present patterns of recent selection. Our findings provide a basis for a better understanding of the metabolic mechanism that underlies the growth traits, which are modified by selection for yearling body weight. Electronic supplementary material The online version of this article (10.1186/s12711-018-0381-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Diercles F Cardoso
- Department of Animal Science, Faculty of Agrarian and Veterinary Sciences, Sao Paulo State University, Jaboticabal, SP, Brazil.
| | - Lucia Galvão de Albuquerque
- Department of Animal Science, Faculty of Agrarian and Veterinary Sciences, Sao Paulo State University, Jaboticabal, SP, Brazil.,National Counsel of Technological and Scientific Development (CNPq), Brasília, DF, Brazil
| | - Christian Reimer
- Animal Breeding and Genetics Group, Department of Animal Sciences, University of Goettingen, Goettingen, Germany
| | - Saber Qanbari
- Animal Breeding and Genetics Group, Department of Animal Sciences, University of Goettingen, Goettingen, Germany
| | - Malena Erbe
- Animal Breeding and Genetics Group, Department of Animal Sciences, University of Goettingen, Goettingen, Germany.,Institute for Animal Breeding, Bavarian State Research Center for Agriculture, Grub, Germany
| | - André V do Nascimento
- Department of Animal Science, Faculty of Agrarian and Veterinary Sciences, Sao Paulo State University, Jaboticabal, SP, Brazil
| | - Guilherme C Venturini
- Department of Animal Science, Faculty of Agrarian and Veterinary Sciences, Sao Paulo State University, Jaboticabal, SP, Brazil
| | - Daiane C Becker Scalez
- Department of Animal Science, Faculty of Agrarian and Veterinary Sciences, Sao Paulo State University, Jaboticabal, SP, Brazil
| | - Fernando Baldi
- Department of Animal Science, Faculty of Agrarian and Veterinary Sciences, Sao Paulo State University, Jaboticabal, SP, Brazil.,National Counsel of Technological and Scientific Development (CNPq), Brasília, DF, Brazil
| | - Gregório M Ferreira de Camargo
- Department of Animal Science, Faculty of Agrarian and Veterinary Sciences, Sao Paulo State University, Jaboticabal, SP, Brazil
| | - Maria E Zerlotti Mercadante
- National Counsel of Technological and Scientific Development (CNPq), Brasília, DF, Brazil.,APTA Beef Cattle Center, Institute of Animal Science, Sertãozinho, SP, Brazil
| | | | - Henner Simianer
- Animal Breeding and Genetics Group, Department of Animal Sciences, University of Goettingen, Goettingen, Germany
| | - Humberto Tonhati
- Department of Animal Science, Faculty of Agrarian and Veterinary Sciences, Sao Paulo State University, Jaboticabal, SP, Brazil.,National Counsel of Technological and Scientific Development (CNPq), Brasília, DF, Brazil
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Li B, Weng Q, Dong C, Zhang Z, Li R, Liu J, Jiang A, Li Q, Jia C, Wu W, Liu H. A Key Gene, PLIN1, Can Affect Porcine Intramuscular Fat Content Based on Transcriptome Analysis. Genes (Basel) 2018; 9:genes9040194. [PMID: 29617344 PMCID: PMC5924536 DOI: 10.3390/genes9040194] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Revised: 03/22/2018] [Accepted: 03/27/2018] [Indexed: 12/20/2022] Open
Abstract
Intramuscular fat (IMF) content is an important indicator for meat quality evaluation. However, the key genes and molecular regulatory mechanisms affecting IMF deposition remain unclear. In the present study, we identified 75 differentially expressed genes (DEGs) between the higher (H) and lower (L) IMF content of pigs using transcriptome analysis, of which 27 were upregulated and 48 were downregulated. Notably, Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis indicated that the DEG perilipin-1 (PLIN1) was significantly enriched in the fat metabolism-related peroxisome proliferator-activated receptor (PPAR) signaling pathway. Furthermore, we determined the expression patterns and functional role of porcine PLIN1. Our results indicate that PLIN1 was highly expressed in porcine adipose tissue, and its expression level was significantly higher in the H IMF content group when compared with the L IMF content group, and expression was increased during adipocyte differentiation. Additionally, our results confirm that PLIN1 knockdown decreases the triglyceride (TG) level and lipid droplet (LD) size in porcine adipocytes. Overall, our data identify novel candidate genes affecting IMF content and provide new insight into PLIN1 in porcine IMF deposition and adipocyte differentiation.
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Affiliation(s)
- Bojiang Li
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, 210095 Nanjing, China.
| | - Qiannan Weng
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, 210095 Nanjing, China.
| | - Chao Dong
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, 210095 Nanjing, China.
| | - Zengkai Zhang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, 210095 Nanjing, China.
| | - Rongyang Li
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, 210095 Nanjing, China.
| | - Jingge Liu
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, 210095 Nanjing, China.
| | - Aiwen Jiang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, 210095 Nanjing, China.
| | - Qifa Li
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, 210095 Nanjing, China.
| | - Chao Jia
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, 210095 Nanjing, China.
| | - Wangjun Wu
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, 210095 Nanjing, China.
| | - Honglin Liu
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, 210095 Nanjing, China.
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Chen BD, Chen XC, Pan S, Yang YN, He CH, Liu F, Ma X, Gai MT, Ma YT. TT genotype of rs2941484 in the human HNF4G gene is associated with hyperuricemia in Chinese Han men. Oncotarget 2018; 8:26918-26926. [PMID: 28460474 PMCID: PMC5432307 DOI: 10.18632/oncotarget.15851] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 02/20/2017] [Indexed: 12/26/2022] Open
Abstract
The aim of the study is to investigate the association between the human hepatocyte nuclear factor 4 gamma (HNF4G) gene and hyperuricemia in Chinese Han population. A total of 414 hyperuricemia patients and 406 gender and age-matched normouricemic controls were enrolled. Four single nucleotide polymorphisms were genotyped as genetic markers for the human HNF4G gene (rs2977939, rs1805098, rs2941484, rs4735692). Data were analyzed for two separate groups: men and women. For rs2941484, the genotype distribution frequency in hyperuricemic subjects and was significantly different from that in normouricemic controls in men (P = 0.038). Meanwhile, in recessive model of rs2941484, the distribution frequency of TT genotype and CC+CT genotypes also differed significantly between the hyperuricemia men and normouricemic men (P = 0.011). For the other 3 SNPs in both men and women, there was no difference in the genotype and allele and distribution frequency between the hyperuricemia patients and normouricemic controls. In men, after adjustments for BMI, SBP, DBP, fasting glucose, total cholesterol, triglycerides, low density lipoprotein cholesterol and creatinine, the men with the TT genotype of rs2941484 were found to have significantly higher probability of suffering from hyperuricemia than the ones with CT and CC genotypes (OR = 2.170, P < 0.001). Therefore, TT genotype of rs2941484 in the human HNF4G gene might be a gender-specific genetic marker for hyperuricemia in Chinese Han men.
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Affiliation(s)
- Bang-Dang Chen
- Xinjiang Key Laboratory of Cardiovascular Disease, Clinical Medical Research Institute of First Affiliated Hospital of Xinjiang Medical University, Urumqi, China.,Department of Cardiology, First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Xiao-Cui Chen
- Xinjiang Key Laboratory of Cardiovascular Disease, Clinical Medical Research Institute of First Affiliated Hospital of Xinjiang Medical University, Urumqi, China.,Department of Cardiology, First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Shuo Pan
- First Department of Cardiology, People's Hospital of Shaanxi Province, Xi'an, China
| | - Yi-Ning Yang
- Xinjiang Key Laboratory of Cardiovascular Disease, Clinical Medical Research Institute of First Affiliated Hospital of Xinjiang Medical University, Urumqi, China.,Department of Cardiology, First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Chun-Hui He
- Department of Cardiology, First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Fen Liu
- Xinjiang Key Laboratory of Cardiovascular Disease, Clinical Medical Research Institute of First Affiliated Hospital of Xinjiang Medical University, Urumqi, China.,Department of Cardiology, First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Xiang Ma
- Xinjiang Key Laboratory of Cardiovascular Disease, Clinical Medical Research Institute of First Affiliated Hospital of Xinjiang Medical University, Urumqi, China.,Department of Cardiology, First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Min-Tao Gai
- Xinjiang Key Laboratory of Cardiovascular Disease, Clinical Medical Research Institute of First Affiliated Hospital of Xinjiang Medical University, Urumqi, China.,Department of Cardiology, First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Yi-Tong Ma
- Xinjiang Key Laboratory of Cardiovascular Disease, Clinical Medical Research Institute of First Affiliated Hospital of Xinjiang Medical University, Urumqi, China.,Department of Cardiology, First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
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Soares ACC, Guimarães SEF, Kelly MJ, Fortes MRS, E Silva FF, Verardo LL, Mota R, Moore S. Multiple-trait genomewide mapping and gene network analysis for scrotal circumference growth curves in Brahman cattle. J Anim Sci 2018; 95:3331-3345. [PMID: 28805926 DOI: 10.2527/jas.2017.1409] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Fertility traits are economically important in cattle breeding programs. Scrotal circumference (SC) measures are repeatable, easily obtained, highly heritable, and positively correlated with female fertility traits and sperm quality traits in males. A useful approach to summarize SC measures over time is using nonlinear models, which summarize specific measures of SC in a few parameters with biological interpretation. This approach facilitates the selection of bulls with larger SC and maturity index (K), that is, early maturing animals. Because SC is a sex-limited trait, identifying the underlying genomics of growth curve parameters will allow selection across both males and females. We reported the first multitrait genomewide association study (GWAS) of estimated growth curve parameters for SC data in Brahman cattle. Five widely used nonlinear models were tested to fit a total of 3,612 SC records, measured at 6, 12, 18, and 24 mo of age. The von Bertalanffy model, individually fitted for each animal, best fit this SC data. Parameter estimates SC at maturity (A) and K as well as SC at all ages were jointly analyzed in a GWAS to identify 1-Mb regions most strongly associated with each trait. Heritabilities were 0.25 for K and 0.32 for A and ranged from 0.51 to 0.72 for SC at 6 (SC6), 12 (SC12), 18 (SC18), and 24 mo of age (SC24). An overlapping window on chromosome 14 explaining around 0.8% of genetic variance for K, SC12, SC18, and SC24 was observed. The major positional candidate genes within 1 Mb upstream and downstream of this overlapping window were , , , and . Windows of 1 Mb explaining more than 0.4% of each trait on chromosomes 1, 3, 6, 7, 14, 17, 18, 24, 25, and 26 were identified. Pathways and net-work analyses were indicated through transcription factors playing a role on fertility traits: , , , , , , and . Further validation studies on larger populations or other breeds are required to validate these findings and to improve our understanding of the biology and complex genetic architecture of traits associated with scrotal growth and male fertility in cattle.
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Campos BM, do Carmo AS, da Silva TBR, Verardo LL, de Simoni Gouveia JJ, Mendes Malhado CH, Barbosa da Silva MVG, Souza Carneiro PL. Identification of artificial selection signatures in Caracu breed lines selected for milk production and meat production. Livest Sci 2017. [DOI: 10.1016/j.livsci.2017.10.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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Albrecht E, Schering L, Liu Y, Komolka K, Kühn C, Wimmers K, Gotoh T, Maak S. TRIENNIAL GROWTH AND DEVELOPMENT SYMPOSIUM: Factors influencing bovine intramuscular adipose tissue development and cellularity. J Anim Sci 2017; 95:2244-2254. [PMID: 28726981 DOI: 10.2527/jas.2016.1036] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Appearance, distribution, and amount of intramuscular fat (IMF), often referred to as marbling, are highly variable and depend on environmental and genetic factors. On the molecular level, the concerted action of several drivers, including hormones, receptors, transcription factors, etc., determines where clusters of adipocytes arise. Therefore, the aim of future studies remains to identify such factors as biological markers of IMF to increase the ability to identify animals that deposit IMF early in age to increase efficiency of high-quality meat production. In an attempt to unravel the cellular development of marbling, we investigated the abundance of markers for adipogenic differentiation during fattening of cattle and the transcriptome of muscle and dissected IMF. Markers of different stages of adipogenic differentiation are well known from cell culture experiments. They are usually transiently expressed, such as delta-like homolog 1 (DLK1) that is abundant in preadipocytes and absent during differentiation to mature adipocytes. It is even a greater challenge to detect those markers in live animals. Within skeletal muscles, hyperplasia and hypertrophy of adipocytes can be observed throughout life. Therefore, development of marbling requires, on the cellular level, recruitment, proliferation, and differentiation of adipogenic cells to store excess energy in the form of lipids in new cells. In a recent study, we investigated the localization and abundance of early markers of adipogenic differentiation, such as DLK1, in bovine muscle tissue. An inverse relationship between IMF content and number of DLK1-positive cells in bovine muscle was demonstrated. Considering the cellular environment of differentiating adipocytes in muscle and the secretory action of adipocytes and myocytes, it becomes obvious that cross talk between cells via adipokines and myokines may be important for IMF development. Secreted proteins can act on other cells, inhibiting or stimulating their function via autocrine and paracrine actions. Such factors with potential influence on IMF, among them, agouti signaling protein and thrombospondin 4, were identified in transcriptome analyses and further investigated. Furthermore, results from transcriptome analysis indicate involvement of genes that are not directly related to adipogenesis and lipid metabolism, providing new candidates for future research.
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45
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Reverter A, Porto-Neto LR, Fortes MRS, Kasarapu P, de Cara MAR, Burrow HM, Lehnert SA. Genomic inbreeding depression for climatic adaptation of tropical beef cattle1. J Anim Sci 2017. [DOI: 10.2527/jas.2017.1643] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
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46
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Buzanskas ME, Grossi DDA, Ventura RV, Schenkel FS, Chud TCS, Stafuzza NB, Rola LD, Meirelles SLC, Mokry FB, Mudadu MDA, Higa RH, da Silva MVGB, de Alencar MM, Regitano LCDA, Munari DP. Candidate genes for male and female reproductive traits in Canchim beef cattle. J Anim Sci Biotechnol 2017; 8:67. [PMID: 28852499 PMCID: PMC5569548 DOI: 10.1186/s40104-017-0199-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 07/13/2017] [Indexed: 01/20/2023] Open
Abstract
Background Beef cattle breeding programs in Brazil have placed greater emphasis on the genomic study of reproductive traits of males and females due to their economic importance. In this study, genome-wide associations were assessed for scrotal circumference at 210 d of age, scrotal circumference at 420 d of age, age at first calving, and age at second calving, in Canchim beef cattle. Data quality control was conducted resulting in 672,778 SNPs and 392 animals. Results Associated SNPs were observed for scrotal circumference at 420 d of age (435 SNPs), followed by scrotal circumference at 210 d of age (12 SNPs), age at first calving (six SNPs), and age at second calving (four SNPs). We investigated whether significant SNPs were within genic or surrounding regions. Biological processes of genes were associated with immune system, multicellular organismal process, response to stimulus, apoptotic process, cellular component organization or biogenesis, biological adhesion, and reproduction. Conclusions Few associations were observed for scrotal circumference at 210 d of age, age at first calving, and age at second calving, reinforcing their polygenic inheritance and the complexity of understanding the genetic architecture of reproductive traits. Finding many associations for scrotal circumference at 420 d of age in various regions of the Canchim genome also reveals the difficulty of targeting specific candidate genes that could act on fertility; nonetheless, the high linkage disequilibrium between loci herein estimated could aid to overcome this issue. Therefore, all relevant information about genomic regions influencing reproductive traits may contribute to target candidate genes for further investigation of causal mutations and aid in future genomic studies in Canchim cattle to improve the breeding program. Electronic supplementary material The online version of this article (doi:10.1186/s40104-017-0199-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Marcos Eli Buzanskas
- Departamento de Zootecnia, Universidade Federal da Paraíba (UFPB), Areia, Paraíba 58397-000 Brazil
| | | | | | - Flavio Schramm Schenkel
- Department of Animal and Poultry Science, University of Guelph, Centre for Genetic Improvement of Livestock (CGIL), Guelph, ON N1G 2W1 Canada
| | - Tatiane Cristina Seleguim Chud
- Departamento de Ciências Exatas, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista (Unesp), Jaboticabal, São Paulo 14884-900 Brazil
| | - Nedenia Bonvino Stafuzza
- Departamento de Ciências Exatas, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista (Unesp), Jaboticabal, São Paulo 14884-900 Brazil
| | - Luciana Diniz Rola
- Departamento de Zootecnia, Núcleo de Pesquisa e Conservação de Cervídeos, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista (Unesp), Jaboticabal, São Paulo 14884-900 Brazil
| | | | - Fabiana Barichello Mokry
- Department of Genetics and Evolution, Federal University of São Carlos (UFSCar), São Carlos, São Paulo 13565-905 Brazil
| | | | | | | | | | | | - Danísio Prado Munari
- Departamento de Ciências Exatas, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista (Unesp), Jaboticabal, São Paulo 14884-900 Brazil
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Zhu M, Liu Z, Gao M, Zhang Y, Li Y, Ling S, Zhang P, Zhao C, Jiang L, Liu Y, Li Q, Li D, Hu S, Li Y. The effect of Bu Zhong Yi Qi decoction on simulated weightlessness‑induced muscle atrophy and its mechanisms. Mol Med Rep 2017; 16:5165-5174. [PMID: 28849026 PMCID: PMC5647051 DOI: 10.3892/mmr.2017.7287] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Accepted: 05/11/2017] [Indexed: 12/17/2022] Open
Abstract
Microgravity has been previously demonstrated to induce skeletal muscle atrophy, loss of muscle force and disorders in myogenesis and metabolism. Current pharmacological strategies exhibit poor efficacy. Bu Zhong Yi Qi decoction (BZ) is a well-known traditional Chinese medicine decoction used for myasthenia gravis. In the present study, its effect on unloading induced muscle atrophy was investigated. The mousetail suspension model was used to simulate weightlessness induced muscle atrophy. The results indicated that BZ could significantly protect muscles from simulated weightlessness-induced atrophy. To elucidate the underlying mechanisms, drugCIPHER-CS methods were introduced to predict its potential targets, significantly enriched pathways and biological processes. The results demonstrated that the calcium signaling pathway, citrate cycle, biosynthetic and lipid metabolic process are affected by BZ. Among the targets, nuclear receptor corepressor 1 (NCoR1) is one of the most important proteins involved in myogenesis and metabolism. The results indicated that BZ significantly downregulated NCoR 1 expression, and further induced muscle differentiation and metabolism by regulating NCoR1-associated gene expression in vivo and in vitro. In summary, the present study indicated that may be effective in combating weightlessness-induced muscle atrophy. Combined with bioinformatics, the underlying mechanism for this decoction was investigated, which provided an improved understanding of this decoction.
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Affiliation(s)
- Mu Zhu
- Department of Chinese Materia Medica, School of Preclinical Medicine, Beijing University of Chinese Medicine, Beijing 100019, P.R. China
| | - Zhongyang Liu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Institute of Radiation Medicine, Beijing 102206, P.R. China
| | - Mingze Gao
- Department of Chinese Materia Medica, School of Preclinical Medicine, Beijing University of Chinese Medicine, Beijing 100019, P.R. China
| | - Yan Zhang
- Department of Chinese Materia Medica, School of Preclinical Medicine, Beijing University of Chinese Medicine, Beijing 100019, P.R. China
| | - Yuheng Li
- State Key Laboratory of Space Medicine Fundamentals and Applications, China Astronaut Research and Training Center, Beijing 100094, P.R. China
| | - Shukuan Ling
- State Key Laboratory of Space Medicine Fundamentals and Applications, China Astronaut Research and Training Center, Beijing 100094, P.R. China
| | - Pengfei Zhang
- State Key Laboratory of Space Medicine Fundamentals and Applications, China Astronaut Research and Training Center, Beijing 100094, P.R. China
| | - Chenyang Zhao
- State Key Laboratory of Space Medicine Fundamentals and Applications, China Astronaut Research and Training Center, Beijing 100094, P.R. China
| | - Lijun Jiang
- State Key Laboratory of Space Medicine Fundamentals and Applications, China Astronaut Research and Training Center, Beijing 100094, P.R. China
| | - Yu Liu
- State Key Laboratory of Space Medicine Fundamentals and Applications, China Astronaut Research and Training Center, Beijing 100094, P.R. China
| | - Qi Li
- State Key Laboratory of Space Medicine Fundamentals and Applications, China Astronaut Research and Training Center, Beijing 100094, P.R. China
| | - Dong Li
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Institute of Radiation Medicine, Beijing 102206, P.R. China
| | - Sumin Hu
- Department of Chinese Materia Medica, School of Preclinical Medicine, Beijing University of Chinese Medicine, Beijing 100019, P.R. China
| | - Yingxian Li
- State Key Laboratory of Space Medicine Fundamentals and Applications, China Astronaut Research and Training Center, Beijing 100094, P.R. China
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Khayatzadeh N, Mészáros G, Utsunomiya YT, Garcia JF, Schnyder U, Gredler B, Curik I, Sölkner J. Locus-specific ancestry to detect recent response to selection in admixed Swiss Fleckvieh cattle. Anim Genet 2016; 47:637-646. [PMID: 27435758 DOI: 10.1111/age.12470] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/30/2016] [Indexed: 01/08/2023]
Abstract
Identification of selection signatures is one of the current endeavors of evolutionary genetics. Admixed populations may be used to infer post-admixture selection. We calculated local ancestry for Swiss Fleckvieh, a composite of Simmental (SI) and Red Holstein Friesian (RHF), to infer such signals. Illumina Bovine SNP50 BeadChip data for 300 admixed, 88 SI and 97 RHF bulls were used. The average RHF ancestry across the whole genome was 0.70. To identify regions with high deviation from average, we considered two significance thresholds, based on a permutation test and extreme deviation from normal distribution. Regions on chromosomes 13 (46.3-47.3 Mb) and 18 (18.7-25.9 Mb) passed both thresholds in the direction of increased SI. Extended haplotype homozygosity within (iHS) and between (Rsb) populations was calculated to explore additional patterns of pre- and post-admixture selection signals. The Rsb score of admixed and SI was significant in a wide region of chromosome 18 (6.6-24.6 Mb) overlapped with one area of strong local ancestry deviation. FTO, with pleiotropic effect on milk and fertility, NOD2 on dairy and NKD1 and SALL1 on fertility traits are located there. Genetic differentiation of RHF and SI (Fst ), an alternative indicator of pre-admixture selection in pure populations, was calculated. No considerable overlap of peaks of local ancestry deviations and Fst was observed. We found two regions with significant signatures of post-admixture selection in this very young composite, applying comparatively stringent significance thresholds. The signals cover relatively large genomic areas and did not allow pinpointing of the gene(s) responsible for the apparent shift in ancestry proportions.
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Affiliation(s)
- N Khayatzadeh
- Division of Livestock Science, Department of Sustainable Agricultural Systems, University of Natural Resources and Life Sciences, Vienna, Gregor-Mendel-Straße 33, A-1180, Vienna, Austria
| | - G Mészáros
- Division of Livestock Science, Department of Sustainable Agricultural Systems, University of Natural Resources and Life Sciences, Vienna, Gregor-Mendel-Straße 33, A-1180, Vienna, Austria.
| | - Y T Utsunomiya
- Departamento de Medicina Veterinária Preventiva e Reprodução Animal, Faculdade de Ciências Agrárias e Veterinárias, UNESP - Univ Estadual Paulista, Jaboticabal, São Paulo, Brazil
| | - J F Garcia
- Departamento de Medicina Veterinária Preventiva e Reprodução Animal, Faculdade de Ciências Agrárias e Veterinárias, UNESP - Univ Estadual Paulista, Jaboticabal, São Paulo, Brazil.,Departamento de Apoio, Saúde e Produção Animal, Faculdade de Medicina Veterinária de Araçatuba, UNESP - Univ Estadual Paulista, Araçatuba, São Paulo, Brazil
| | - U Schnyder
- Qualitas AG, Chamerstrasse 56, CH-6300, Zug, Switzerland
| | - B Gredler
- Qualitas AG, Chamerstrasse 56, CH-6300, Zug, Switzerland
| | - I Curik
- Department of Animal Science, Faculty of Agriculture, University of Zagreb, Svetošimunska cesta 25, 10000, Zagreb, Croatia
| | - J Sölkner
- Division of Livestock Science, Department of Sustainable Agricultural Systems, University of Natural Resources and Life Sciences, Vienna, Gregor-Mendel-Straße 33, A-1180, Vienna, Austria
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Magalhães AFB, de Camargo GMF, Fernandes GA, Gordo DGM, Tonussi RL, Costa RB, Espigolan R, Silva RMDO, Bresolin T, de Andrade WBF, Takada L, Feitosa FLB, Baldi F, Carvalheiro R, Chardulo LAL, de Albuquerque LG. Genome-Wide Association Study of Meat Quality Traits in Nellore Cattle. PLoS One 2016; 11:e0157845. [PMID: 27359122 PMCID: PMC4928802 DOI: 10.1371/journal.pone.0157845] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 06/06/2016] [Indexed: 01/19/2023] Open
Abstract
The objective of this study was to identify genomic regions that are associated with meat quality traits in the Nellore breed. Nellore steers were finished in feedlots and slaughtered at a commercial slaughterhouse. This analysis included 1,822 phenotypic records of tenderness and 1,873 marbling records. After quality control, 1,630 animals genotyped for tenderness, 1,633 animals genotyped for marbling, and 369,722 SNPs remained. The results are reported as the proportion of variance explained by windows of 150 adjacent SNPs. Only windows with largest effects were considered. The genomic regions were located on chromosomes 5, 15, 16 and 25 for marbling and on chromosomes 5, 7, 10, 14 and 21 for tenderness. These windows explained 3,89% and 3,80% of the additive genetic variance for marbling and tenderness, respectively. The genes associated with the traits are related to growth, muscle development and lipid metabolism. The study of these genes in Nellore cattle is the first step in the identification of causal mutations that will contribute to the genetic evaluation of the breed.
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Affiliation(s)
- Ana F. B. Magalhães
- Departamento de Zootecnia, Faculdade de Ciências Agrarias e Veterinárias, Jaboticabal, São Paulo, Brazil
| | - Gregório M. F. de Camargo
- Departamento de Zootecnia, Faculdade de Ciências Agrarias e Veterinárias, Jaboticabal, São Paulo, Brazil
| | - Gerardo A. Fernandes
- Departamento de Zootecnia, Faculdade de Ciências Agrarias e Veterinárias, Jaboticabal, São Paulo, Brazil
| | - Daniel G. M. Gordo
- Departamento de Zootecnia, Faculdade de Ciências Agrarias e Veterinárias, Jaboticabal, São Paulo, Brazil
| | - Rafael L. Tonussi
- Departamento de Zootecnia, Faculdade de Ciências Agrarias e Veterinárias, Jaboticabal, São Paulo, Brazil
| | - Raphael B. Costa
- Departamento de Zootecnia, Faculdade de Ciências Agrarias e Veterinárias, Jaboticabal, São Paulo, Brazil
| | - Rafael Espigolan
- Departamento de Zootecnia, Faculdade de Ciências Agrarias e Veterinárias, Jaboticabal, São Paulo, Brazil
| | - Rafael M. de O. Silva
- Departamento de Zootecnia, Faculdade de Ciências Agrarias e Veterinárias, Jaboticabal, São Paulo, Brazil
| | - Tiago Bresolin
- Departamento de Zootecnia, Faculdade de Ciências Agrarias e Veterinárias, Jaboticabal, São Paulo, Brazil
| | - Willian B. F. de Andrade
- Departamento de Zootecnia, Faculdade de Ciências Agrarias e Veterinárias, Jaboticabal, São Paulo, Brazil
| | - Luciana Takada
- Departamento de Zootecnia, Faculdade de Ciências Agrarias e Veterinárias, Jaboticabal, São Paulo, Brazil
| | - Fabieli L. B. Feitosa
- Departamento de Zootecnia, Faculdade de Ciências Agrarias e Veterinárias, Jaboticabal, São Paulo, Brazil
| | - Fernando Baldi
- Departamento de Zootecnia, Faculdade de Ciências Agrarias e Veterinárias, Jaboticabal, São Paulo, Brazil
- Conselho Nacional de Desenvolvimento Científico e Tecnológico – CNPq, Brasília, Distrito Federal, Brazil
| | - Roberto Carvalheiro
- Departamento de Zootecnia, Faculdade de Ciências Agrarias e Veterinárias, Jaboticabal, São Paulo, Brazil
- Conselho Nacional de Desenvolvimento Científico e Tecnológico – CNPq, Brasília, Distrito Federal, Brazil
| | - Luis A. L. Chardulo
- Conselho Nacional de Desenvolvimento Científico e Tecnológico – CNPq, Brasília, Distrito Federal, Brazil
- Departamento de Melhoramento e Nutrição Animal, Faculdade de Medicina Veterinária e Zootecnia, Botucatu, São Paulo, Brazil
| | - Lucia G. de Albuquerque
- Departamento de Zootecnia, Faculdade de Ciências Agrarias e Veterinárias, Jaboticabal, São Paulo, Brazil
- Conselho Nacional de Desenvolvimento Científico e Tecnológico – CNPq, Brasília, Distrito Federal, Brazil
- * E-mail:
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Ramayo-Caldas Y, Renand G, Ballester M, Saintilan R, Rocha D. Multi-breed and multi-trait co-association analysis of meat tenderness and other meat quality traits in three French beef cattle breeds. Genet Sel Evol 2016; 48:37. [PMID: 27107817 PMCID: PMC4842279 DOI: 10.1186/s12711-016-0216-y] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Accepted: 04/13/2016] [Indexed: 01/19/2023] Open
Abstract
Background Studies to identify markers associated with beef tenderness have focused on Warner–Bratzler shear force (WBSF) but the interplay between the genes associated with WBSF has not been explored. We used the association weight matrix (AWM), a systems biology approach, to identify a set of interacting genes that are co-associated with tenderness and other meat quality traits, and shared across the Charolaise, Limousine and Blonde d’Aquitaine beef cattle breeds. Results Genome-wide association studies were performed using ~500K single nucleotide polymorphisms (SNPs) and 17 phenotypes measured on more than 1000 animals for each breed. First, this multi-trait approach was applied separately for each breed across 17 phenotypes and second, between- and across-breed comparisons at the AWM and functional levels were performed. Genetic heterogeneity was observed, and most of the variants that were associated with WBSF segregated within rather than across breeds. We identified 206 common candidate genes associated with WBSF across the three breeds. SNPs in these common genes explained between 28 and 30 % of the phenotypic variance for WBSF. A reduced number of common SNPs mapping to the 206 common genes were identified, suggesting that different mutations may target the same genes in a breed-specific manner. Therefore, it is likely that, depending on allele frequencies and linkage disequilibrium patterns, a SNP that is identified for one breed may not be informative for another unrelated breed. Well-known candidate genes affecting beef tenderness were identified. In addition, some of the 206 common genes are located within previously reported quantitative trait loci for WBSF in several cattle breeds. Moreover, the multi-breed co-association analysis detected new candidate genes, regulators and metabolic pathways that are likely involved in the determination of meat tenderness and other meat quality traits in beef cattle. Conclusions Our results suggest that systems biology approaches that explore associations of correlated traits increase statistical power to identify candidate genes beyond the one-dimensional approach. Further studies on the 206 common genes, their pathways, regulators and interactions will expand our knowledge on the molecular basis of meat tenderness and could lead to the discovery of functional mutations useful for genomic selection in a multi-breed beef cattle context. Electronic supplementary material The online version of this article (doi:10.1186/s12711-016-0216-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Gilles Renand
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Maria Ballester
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France.,Genètica i Millora Animal, IRTA, 08140, Torre Marimon, Caldes de Montbui, Spain
| | | | - Dominique Rocha
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
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