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He S, Wang Y, Luo Y, Xue M, Wu M, Tan H, Peng Y, Wang K, Fang M. Integrated analysis strategy of genome-wide functional gene mining reveals DKK2 gene underlying meat quality in Shaziling synthesized pigs. BMC Genomics 2024; 25:30. [PMID: 38178019 PMCID: PMC10765619 DOI: 10.1186/s12864-023-09925-x] [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: 07/09/2023] [Accepted: 12/18/2023] [Indexed: 01/06/2024] Open
Abstract
BACKGROUND Shaziling pig is a well-known indigenous breed in China who has superior meat quality traits. However, the genetic mechanism and genomic evidence underlying meat quality characteristics of Shaziling pigs are still unclear. To explore and investigate the germplasm characteristics of Shaziling pigs, we totally analyzed 67 individual's whole genome sequencing data for the first time (20 Shaziling pigs [S], 20 Dabasha pigs [DBS], 11 Yorkshire pigs [Y], 10 Berkshire pigs [BKX], 5 Basha pigs [BS] and 1 Warthog). RESULTS A total of 2,538,577 SNPs with high quality were detected and 9 candidate genes which was specifically selected in S and shared in S to DBS were precisely mined and screened using an integrated analysis strategy of identity-by-descent (IBD) and selective sweep. Of them, dickkopf WNT signaling pathway inhibitor 2 (DKK2), the antagonist of Wnt signaling pathway, was the most promising candidate gene which was not only identified an association of palmitic acid and palmitoleic acid quantitative trait locus in PigQTLdb, but also specifically selected in S compared to other 48 Chinese local pigs of 12 populations and 39 foreign pigs of 4 populations. Subsequently, a mutation at 12,726-bp of DKK2 intron 1 (g.114874954 A > C) was identified associated with intramuscular fat content using method of PCR-RFLP in 21 different pig populations. We observed DKK2 specifically expressed in adipose tissues. Overexpression of DKK2 decreased the content of triglyceride, fatty acid synthase and expression of relevant genes of adipogenic and Wnt signaling pathway, while interference of DKK2 got contrary effect during adipogenesis differentiation of porcine preadipocytes and 3T3-L1 cells. CONCLUSIONS Our findings provide an analysis strategy for mining functional genes of important economic traits and provide fundamental data and molecular evidence for improving pig meat quality traits and molecular breeding.
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Affiliation(s)
- Shuaihan He
- State Key Laboratory of Animal Biotech Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Yubei Wang
- Sanya Institute of China Agricultural University, Sanya, 572025, China
| | - Yabiao Luo
- State Key Laboratory of Animal Biotech Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Mingming Xue
- State Key Laboratory of Animal Biotech Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Maisheng Wu
- Xiangtan Bureau of Animal Husbandry and Veterinary Medicine and Aquatic Product, Xiangtan, 411102, China
| | - Hong Tan
- Xiangtan Bureau of Animal Husbandry and Veterinary Medicine and Aquatic Product, Xiangtan, 411102, China
| | - Yinglin Peng
- Hunan Institute of Animal & Veterinary Science, Changsha, 410131, China
| | - Kejun Wang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450002, China.
| | - Meiying Fang
- State Key Laboratory of Animal Biotech Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
- Sanya Institute of China Agricultural University, Sanya, 572025, China.
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2
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Afonso J, Shim WJ, Boden M, Salinas Fortes MR, da Silva Diniz WJ, de Lima AO, Rocha MIP, Cardoso TF, Bruscadin JJ, Gromboni CF, Nogueira ARA, Mourão GB, Zerlotini A, Coutinho LL, de Almeida Regitano LC. Repressive epigenetic mechanisms, such as the H3K27me3 histone modification, were predicted to affect muscle gene expression and its mineral content in Nelore cattle. Biochem Biophys Rep 2023; 33:101420. [PMID: 36654922 PMCID: PMC9841166 DOI: 10.1016/j.bbrep.2023.101420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 12/12/2022] [Accepted: 01/02/2023] [Indexed: 01/07/2023] Open
Abstract
Epigenetic repression has been linked to the regulation of different cell states. In this study, we focus on the influence of this repression, mainly by H3K27me3, over gene expression in muscle cells, which may affect mineral content, a phenotype that is relevant to muscle function and beef quality. Based on the inverse relationship between H3K27me3 and gene expression (i.e., epigenetic repression) and on contrasting sample groups, we computationally predicted regulatory genes that affect muscle mineral content. To this end, we applied the TRIAGE predictive method followed by a rank product analysis. This methodology can predict regulatory genes that might be affected by repressive epigenetic regulation related to mineral concentration. Annotation of orthologous genes, between human and bovine, enabled our investigation of gene expression in the Longissimus thoracis muscle of Bos indicus cattle. The animals under study had a contrasting mineral content in their muscle cells. We identified candidate regulatory genes influenced by repressive epigenetic mechanisms, linking histone modification to mineral content in beef samples. The discovered candidate genes take part in multiple biological pathways, i.e., impulse transmission, cell signalling, immunological, and developmental pathways. Some of these genes were previously associated with mineral content or regulatory mechanisms. Our findings indicate that epigenetic repression can partially explain the gene expression profiles observed in muscle samples with contrasting mineral content through the candidate regulators here identified.
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Affiliation(s)
| | - Woo Jun Shim
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia,Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Mikael Boden
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | | | | | - Andressa Oliveira de Lima
- Division of Medical Genetics, Department of Genome Sciences, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Marina Ibelli Pereira Rocha
- Post-graduation Program of Evolutionary Genetics and Molecular Biology, Federal University of São Carlos, São Carlos, São Paulo, Brazil
| | | | - Jennifer Jessica Bruscadin
- Post-graduation Program of Evolutionary Genetics and Molecular Biology, Federal University of São Carlos, São Carlos, São Paulo, Brazil
| | | | | | - Gerson Barreto Mourão
- Department of Agroindustry, Food and Nutrition, University of São Paulo/ESALQ, Piracicaba, Brazil
| | - Adhemar Zerlotini
- Bioinformatic Multi-user Laboratory, Embrapa Informática Agropecuária, Campinas, São Paulo, Brazil
| | - Luiz Lehmann Coutinho
- Department of Animal Science, University of São Paulo/ESALQ, Piracicaba, São Paulo, Brazil
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3
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Bruscadin JJ, Cardoso TF, da Silva Diniz WJ, de Souza MM, Afonso J, Vieira D, Malheiros J, Andrade BGN, Petrini J, Ferraz JBS, Zerlotini A, Mourão GB, Coutinho LL, de Almeida Regitano LC. Differential Allele-Specific Expression Revealed Functional Variants and Candidate Genes Related to Meat Quality Traits in B. indicus Muscle. Genes (Basel) 2022; 13:genes13122336. [PMID: 36553605 PMCID: PMC9777870 DOI: 10.3390/genes13122336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 12/03/2022] [Accepted: 12/07/2022] [Indexed: 12/14/2022] Open
Abstract
Traditional transcriptomics approaches have been used to identify candidate genes affecting economically important livestock traits. Regulatory variants affecting these traits, however, remain under covered. Genomic regions showing allele-specific expression (ASE) are under the effect of cis-regulatory variants, being useful for improving the accuracy of genomic selection models. Taking advantage of the better of these two methods, we investigated single nucleotide polymorphisms (SNPs) in regions showing differential ASE (DASE SNPs) between contrasting groups for beef quality traits. For these analyses, we used RNA sequencing data, imputed genotypes and genomic estimated breeding values of muscle-related traits from 190 Nelore (Bos indicus) steers. We selected 40 contrasting unrelated samples for the analysis (N = 20 animals per contrasting group) and used a beta-binomial model to identify ASE SNPs in only one group (i.e., DASE SNPs). We found 1479 DASE SNPs (FDR ≤ 0.05) associated with 55 beef-quality traits. Most DASE genes were involved with tenderness and muscle homeostasis, presenting a co-expression module enriched for the protein ubiquitination process. The results overlapped with epigenetics and phenotype-associated data, suggesting that DASE SNPs are potentially linked to cis-regulatory variants affecting simultaneously the transcription and phenotype through chromatin state modulation.
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Affiliation(s)
- Jennifer Jessica Bruscadin
- Center of Biological Sciences and Health, Federal University of São Carlos, São Carlos 13560-000, SP, Brazil
- Embrapa Pecuária Sudeste, São Carlos 13560-000, SP, Brazil
| | | | | | | | - Juliana Afonso
- Embrapa Pecuária Sudeste, São Carlos 13560-000, SP, Brazil
| | - Dielson Vieira
- Embrapa Pecuária Sudeste, São Carlos 13560-000, SP, Brazil
- Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Jessica Malheiros
- Federal University of Latin American Integration-UNILA, Foz do Iguaçu 85851-000, PR, Brazil
| | | | - Juliana Petrini
- Center for Functional Genomics, Department of Animal Science, 13400-000, University of São Paulo (ESALQ—USP), Piracicaba 13400-000, SP, Brazil
| | - José Bento Sterman Ferraz
- Department of Veterinary Medicine, University of São Paulo (FMVZ—USP), Pirassununga 13630-000, SP, Brazil
| | | | - Gerson Barreto Mourão
- Center for Functional Genomics, Department of Animal Science, 13400-000, University of São Paulo (ESALQ—USP), Piracicaba 13400-000, SP, Brazil
| | - Luiz Lehmann Coutinho
- Center for Functional Genomics, Department of Animal Science, 13400-000, University of São Paulo (ESALQ—USP), Piracicaba 13400-000, SP, Brazil
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4
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de Souza MM, Niciura SCM, Rocha MIP, Pan Z, Zhou H, Bruscadin JJ, da Silva Diniz WJ, Afonso J, de Oliveira PSN, Mourão GB, Zerlotini A, Coutinho LL, Koltes JE, de Almeida Regitano LC. DNA methylation may affect beef tenderness through signal transduction in Bos indicus. Epigenetics Chromatin 2022; 15:15. [PMID: 35562812 PMCID: PMC9107245 DOI: 10.1186/s13072-022-00449-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 04/12/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Beef tenderness is a complex trait of economic importance for the beef industry. Understanding the epigenetic mechanisms underlying this trait may help improve the accuracy of breeding programs. However, little is known about epigenetic effects on Bos taurus muscle and their implications in tenderness, and no studies have been conducted in Bos indicus. RESULTS Comparing methylation profile of Bos indicus skeletal muscle with contrasting beef tenderness at 14 days after slaughter, we identified differentially methylated cytosines and regions associated with this trait. Interestingly, muscle that became tender beef had higher levels of hypermethylation compared to the tough group. Enrichment analysis of predicted target genes suggested that differences in methylation between tender and tough beef may affect signal transduction pathways, among which G protein signaling was a key pathway. In addition, different methylation levels were found associated with expression levels of GNAS, PDE4B, EPCAM and EBF3 genes. The differentially methylated elements correlated with EBF3 and GNAS genes overlapped CpG islands and regulatory elements. GNAS, a complex imprinted gene, has a key role on G protein signaling pathways. Moreover, both G protein signaling pathway and the EBF3 gene regulate muscle homeostasis, relaxation, and muscle cell-specificity. CONCLUSIONS We present differentially methylated loci that may be of interest to decipher the epigenetic mechanisms affecting tenderness. Supported by the previous knowledge about regulatory elements and gene function, the methylation data suggests EBF3 and GNAS as potential candidate genes and G protein signaling as potential candidate pathway associated with beef tenderness via methylation.
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Affiliation(s)
- Marcela Maria de Souza
- Empresa Brasileira de Pesquisa Agropecuária, Embrapa Pecuária Sudeste, São Carlos, Brazil.,Department of Animal Science, Iowa State University, Ames, USA
| | | | - Marina Ibelli Pereira Rocha
- Empresa Brasileira de Pesquisa Agropecuária, Embrapa Pecuária Sudeste, São Carlos, Brazil.,Department of Genetics and Evolution, Federal University of São Carlos, São Carlos, Brazil
| | - Zhangyuan Pan
- Department of Animal Science, University of California, Davis, CA, USA
| | - Huaijun Zhou
- Department of Animal Science, University of California, Davis, CA, USA
| | - Jennifer Jessica Bruscadin
- Empresa Brasileira de Pesquisa Agropecuária, Embrapa Pecuária Sudeste, São Carlos, Brazil.,Department of Genetics and Evolution, Federal University of São Carlos, São Carlos, Brazil
| | - Wellison Jarles da Silva Diniz
- Empresa Brasileira de Pesquisa Agropecuária, Embrapa Pecuária Sudeste, São Carlos, Brazil.,Department of Animal Science, Auburn University, Auburn, Alabama, USA
| | - Juliana Afonso
- Empresa Brasileira de Pesquisa Agropecuária, Embrapa Pecuária Sudeste, São Carlos, Brazil
| | | | - Gerson B Mourão
- Department of Animal Science, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, Brazil
| | - Adhemar Zerlotini
- Embrapa Informática Agropecuária, Empresa Brasileira de Pesquisa Agropecuária, Campinas, Brazil
| | - Luiz Lehmann Coutinho
- Department of Animal Science, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, Brazil
| | - James E Koltes
- Department of Animal Science, Iowa State University, Ames, USA
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5
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Duarte INH, Bessa AFDO, Rola LD, Genuíno MVH, Rocha IM, Marcondes CR, Regitano LCDA, Munari DP, Berry DP, Buzanskas ME. Cross-population selection signatures in Canchim composite beef cattle. PLoS One 2022; 17:e0264279. [PMID: 35363779 PMCID: PMC8975110 DOI: 10.1371/journal.pone.0264279] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 02/07/2022] [Indexed: 12/15/2022] Open
Abstract
Analyses of livestock genomes have been used to detect selection signatures, which are genomic regions associated with traits under selection leading to a change in allele frequency. The objective of the present study was to characterize selection signatures in Canchim composite beef cattle using cross-population analyses with the founder Nelore and Charolais breeds. High-density single nucleotide polymorphism genotypes were available on 395 Canchim representing the target population, along with genotypes from 809 Nelore and 897 Charolais animals representing the reference populations. Most of the selection signatures were co-located with genes whose functions agree with the expectations of the breeding programs; these genes have previously been reported to associate with meat quality, as well as reproductive traits. Identified genes were related to immunity, adaptation, morphology, as well as behavior, could give new perspectives for understanding the genetic architecture of Canchim. Some selection signatures identified genes that were recently introduced in Canchim, such as the loci related to the polled trait.
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Affiliation(s)
| | | | - Luciana Diniz Rola
- Departamento de Zootecnia, Universidade Federal da Paraíba, Areia, Paraíba, Brazil
| | | | - Iasmin Marques Rocha
- Departamento de Zootecnia, Universidade Federal da Paraíba, Areia, Paraíba, Brazil
| | | | | | - Danísio Prado Munari
- Departamento de Engenharia e Ciências Exatas, Universidade Estadual Paulista, Jaboticabal, São Paulo, Brazil
| | - Donagh Pearse Berry
- Teagasc, Animal & Grassland Research and Innovation Centre, Moorepark, Fermoy Co. Cork., Ireland
| | - Marcos Eli Buzanskas
- Departamento de Zootecnia, Universidade Federal da Paraíba, Areia, Paraíba, Brazil
- * E-mail:
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6
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Fonseca PADS, Caldwell T, Mandell I, Wood K, Cánovas A. Genome-wide association study for meat tenderness in beef cattle identifies patterns of the genetic contribution in different post-mortem stages. Meat Sci 2022; 186:108733. [PMID: 35007800 DOI: 10.1016/j.meatsci.2022.108733] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Revised: 01/01/2022] [Accepted: 01/03/2022] [Indexed: 12/13/2022]
Abstract
The beef tenderization process during the post-mortem period is one of the most important sensorial attributes and it is well-established. The aim of this study was to identify the genetic contribution pattern to meat tenderness at 7-(LMD7), 14-(LMD14), and 21-(LMD21) days post-mortem. The heritabilities for LMD7 (0.194), LMD14 (0.142) and LMD21 (0.048) are well established in the population evaluated here. However, its genetic contribution in terms of genomic candidate regions is still poorly understood. Tenderness was measured in the Longissiums thoracis using Warner-Bratzler shear force in the three post-mortem periods. A total of 4323 crossbred beef cattle were phenotyped and genotyped using the Illumina BovineSNP50K. The percentage of the total genetic variance was estimated using the weighted single-step genomic best linear unbiased prediction method. The main candidate windows for LMD7 were associated with proteolysis of myofibrillar structures and the weakening endomysium and perimysium. Candidate windows for LMD14 and LMD21 were mapped in bovine QTLs for body composition, height and growth. Results presented herein highlight, the largest contribution of proteolysis related processes before 14-days post-mortem and body composition characteristics in later stages for meat tenderness.
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Affiliation(s)
- Pablo Augusto de Souza Fonseca
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Tim Caldwell
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Ira Mandell
- Centre for Nutrition Modelling, Department of Animal Biosciences, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Katharine Wood
- Centre for Nutrition Modelling, Department of Animal Biosciences, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Angela Cánovas
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, Ontario N1G 2W1, Canada.
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7
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Illa SK, Mukherjee S, Nath S, Mukherjee A. Genome-Wide Scanning for Signatures of Selection Revealed the Putative Genomic Regions and Candidate Genes Controlling Milk Composition and Coat Color Traits in Sahiwal Cattle. Front Genet 2021; 12:699422. [PMID: 34306039 PMCID: PMC8299338 DOI: 10.3389/fgene.2021.699422] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 06/14/2021] [Indexed: 11/13/2022] Open
Abstract
Background In the evolutionary time scale, selection shapes the genetic variation and alters the architecture of genome in the organisms. Selection leaves detectable signatures at the genomic coordinates that provide clues about the protein-coding regions. Sahiwal is a valuable indicine cattle adapted to tropical environments with desirable milk attributes. Insights into the genomic regions under putative selection may reveal the molecular mechanisms affecting the quantitative and other important traits. To understand this, the present investigation was undertaken to explore signatures of selection in the genome of Sahiwal cattle using a medium-density genotyping INDUS chip. Result De-correlated composite of multiple selection signals (DCMS), which combines five different univariate statistics, was computed in the dataset to detect the signatures of selection in the Sahiwal genome. Gene annotations, Quantitative Trait Loci (QTL) enrichment, and functional analyses were carried out for the identification of significant genomic regions. A total of 117 genes were identified, which affect a number of important economic traits. The QTL enrichment analysis highlighted 14 significant [False Discovery Rate (FDR)-corrected p-value ≤ 0.05] regions on chromosomes BTA 1, 3, 6, 11, 20, and 21. The top three enriched QTLs were found on BTA 6, 20, and 23, which are associated with exterior, health, milk production, and reproduction traits. The present study on selection signatures revealed some key genes related with coat color (PDGFRA, KIT, and KDR), facial pigmentation (LEF), milk fat percent (MAP3K1, HADH, CYP2U1, and SGMS2), sperm membrane integrity (OSTC), lactation persistency (MRPS30, NNT, CCL28, HMGCS1, NIM1K, ZNF131, and CCDC152), milk yield (GHR and ZNF469), reproduction (NKX2-1 and DENND1A), and bovine tuberculosis susceptibility (RNF144B and PAPSS1). Further analysis of candidate gene prioritization identified four hub genes, viz., KIT, KDR, MAP3K1, and LEF, which play a role in coat color, facial pigmentation, and milk fat percentage in cattle. Gene enrichment analysis revealed significant Gene ontology (GO) terms related to breed-specific coat color and milk fat percent. Conclusion The key candidate genes and putative genomic regions associated with economic traits were identified in Sahiwal using single nucleotide polymorphism data and the DCMS method. It revealed selection for milk production, coat color, and adaptability to tropical climate. The knowledge about signatures of selection and candidate genes affecting phenotypes have provided a background information that can be further utilized to understand the underlying mechanism involved in these traits in Sahiwal cattle.
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Affiliation(s)
- Satish Kumar Illa
- Division of Animal Genetics and Breeding, Indian Council of Agricultural Research-National Dairy Research Institute, Karnal, India
| | - Sabyasachi Mukherjee
- Division of Animal Genetics and Breeding, Indian Council of Agricultural Research-National Dairy Research Institute, Karnal, India
| | - Sapna Nath
- Artificial Breeding Research Center, Indian Council of Agricultural Research-National Dairy Research Institute, Karnal, India
| | - Anupama Mukherjee
- Division of Animal Genetics and Breeding, Indian Council of Agricultural Research-National Dairy Research Institute, Karnal, India
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8
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Enhancing the Nutritional Value of Red Meat through Genetic and Feeding Strategies. Foods 2021; 10:foods10040872. [PMID: 33923499 PMCID: PMC8073878 DOI: 10.3390/foods10040872] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 04/12/2021] [Accepted: 04/13/2021] [Indexed: 12/20/2022] Open
Abstract
Consumption of red meat contributes to the intake of many essential nutrients in the human diet including protein, essential fatty acids, and several vitamins and trace minerals, with high iron content, particularly in meats with high myoglobin content. Demand for red meat continues to increase worldwide, particularly in developing countries where food nutrient density is a concern. Dietary and genetic manipulation of livestock can influence the nutritional value of meat products, providing opportunities to enhance the nutritional value of meat. Studies have demonstrated that changes in livestock nutrition and breeding strategies can alter the nutritional value of red meat. Traditional breeding strategies, such as genetic selection, have influenced multiple carcass and meat quality attributes relevant to the nutritional value of meat including muscle and fat deposition. However, limited studies have combined both genetic and nutritional approaches. Future studies aiming to manipulate the composition of fresh meat should aim to balance potential impacts on product quality and consumer perception. Furthermore, the rapidly emerging fields of phenomics, nutrigenomics, and integrative approaches, such as livestock precision farming and systems biology, may help better understand the opportunities to improve the nutritional value of meat under both experimental and commercial conditions.
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9
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Bruscadin JJ, de Souza MM, de Oliveira KS, Rocha MIP, Afonso J, Cardoso TF, Zerlotini A, Coutinho LL, Niciura SCM, de Almeida Regitano LC. Muscle allele-specific expression QTLs may affect meat quality traits in Bos indicus. Sci Rep 2021; 11:7321. [PMID: 33795794 PMCID: PMC8016890 DOI: 10.1038/s41598-021-86782-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 03/17/2021] [Indexed: 02/01/2023] Open
Abstract
Single nucleotide polymorphisms (SNPs) located in transcript sequences showing allele-specific expression (ASE SNPs) were previously identified in the Longissimus thoracis muscle of a Nelore (Bos indicus) population consisting of 190 steers. Given that the allele-specific expression pattern may result from cis-regulatory SNPs, called allele-specific expression quantitative trait loci (aseQTLs), in this study, we searched for aseQTLs in a window of 1 Mb upstream and downstream from each ASE SNP. After this initial analysis, aiming to investigate variants with a potential regulatory role, we further screened our aseQTL data for sequence similarity with transcription factor binding sites and microRNA (miRNA) binding sites. These aseQTLs were overlapped with methylation data from reduced representation bisulfite sequencing (RRBS) obtained from 12 animals of the same population. We identified 1134 aseQTLs associated with 126 different ASE SNPs. For 215 aseQTLs, one allele potentially affected the affinity of a muscle-expressed transcription factor to its binding site. 162 aseQTLs were predicted to affect 149 miRNA binding sites, from which 114 miRNAs were expressed in muscle. Also, 16 aseQTLs were methylated in our population. Integration of aseQTL with GWAS data revealed enrichment for traits such as meat tenderness, ribeye area, and intramuscular fat . To our knowledge, this is the first report of aseQTLs identification in bovine muscle. Our findings indicate that various cis-regulatory and epigenetic mechanisms can affect multiple variants to modulate the allelic expression. Some of the potential regulatory variants described here were associated with the expression pattern of genes related to interesting phenotypes for livestock. Thus, these variants might be useful for the comprehension of the genetic control of these phenotypes.
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Affiliation(s)
- Jennifer Jessica Bruscadin
- grid.411247.50000 0001 2163 588XPost-Graduation Program of Evolutionary Genetics and Molecular Biology, Center of Biological Sciences and Health, Federal University of São Carlos, São Carlos, SP Brazil
| | - Marcela Maria de Souza
- grid.34421.300000 0004 1936 7312Post-Doctoral Fellow, Department of Animal Science, Iowa State University, Ames, IA USA
| | - Karina Santos de Oliveira
- grid.411247.50000 0001 2163 588XPost-Graduation Program of Evolutionary Genetics and Molecular Biology, Center of Biological Sciences and Health, Federal University of São Carlos, São Carlos, SP Brazil
| | - Marina Ibelli Pereira Rocha
- grid.411247.50000 0001 2163 588XPost-Graduation Program of Evolutionary Genetics and Molecular Biology, Center of Biological Sciences and Health, Federal University of São Carlos, São Carlos, SP Brazil
| | - Juliana Afonso
- grid.11899.380000 0004 1937 0722Department of Animal Science, University of São Paulo/ESALQ, Piracicaba, SP Brazil
| | - Tainã Figueiredo Cardoso
- grid.460200.00000 0004 0541 873XEmbrapa Pecuária Sudeste, P. O. Box 339, São Carlos, SP 13564-230 Brazil
| | - Adhemar Zerlotini
- grid.460200.00000 0004 0541 873XEmbrapa Informática Agropecuária, Campinas, SP Brazil
| | - Luiz Lehmann Coutinho
- grid.11899.380000 0004 1937 0722Department of Animal Science, University of São Paulo/ESALQ, Piracicaba, SP Brazil
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10
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Jeong JY, Kim M, Ji SY, Baek YC, Lee S, Oh YK, Reddy KE, Seo HW, Cho S, Lee HJ. Metabolomics Analysis of the Beef Samples with Different Meat Qualities and Tastes. Food Sci Anim Resour 2020; 40:924-937. [PMID: 33305277 PMCID: PMC7713764 DOI: 10.5851/kosfa.2020.e59] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 07/24/2020] [Accepted: 07/28/2020] [Indexed: 11/25/2022] Open
Abstract
The purpose of this study was to investigate the meat metabolite profiles related
to differences in beef quality attributes (i.e., high-marbled and low-marbled
groups) using nuclear magnetic resonance (NMR) spectroscopy. The beef of
different marbling scores showed significant differences in water content and
fat content. High-marbled meat had mainly higher taste compounds than
low-marbled meat. Metabolite analysis showed differences between two marbling
groups based on partial least square discriminant analysis (PLS-DA). Metabolites
identified by PLS-DA, such as N,N-dimethylglycine, creatine, lactate, carnosine,
carnitine, sn-glycero-3-phosphocholine, betaine, glycine, glucose, alanine,
tryptophan, methionine, taurine, tyrosine, could be directly linked to marbling
groups. Metabolites from variable importance in projection plots were identified
and estimated high sensitivity as candidate markers for beef quality attributes.
These potential markers were involved in beef taste-related pathways including
carbohydrate and amino acid metabolism. Among these metabolites, carnosine,
creatine, glucose, and lactate had significantly higher in high-marbled meat
compared to low-marbled meat (p<0.05). Therefore, these results will
provide an important understanding of the roles of taste-related metabolites in
beef quality attributes. Our findings suggest that metabolomics analysis of
taste compounds and meat quality may be a powerful method for the discovery of
novel biomarkers underlying the quality of beef products.
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Affiliation(s)
- Jin Young Jeong
- Animal Nutrition & Physiology Team, National Institute of Animal Science, Wanju 55365, Korea
| | - Minseok Kim
- Animal Nutrition & Physiology Team, National Institute of Animal Science, Wanju 55365, Korea.,Department of Animal Science, College of Agriculture and Life Sciences, Chonnam National University, Gwangju 61186, Korea
| | - Sang-Yun Ji
- Animal Nutrition & Physiology Team, National Institute of Animal Science, Wanju 55365, Korea
| | - Youl-Chang Baek
- Animal Nutrition & Physiology Team, National Institute of Animal Science, Wanju 55365, Korea
| | - Seul Lee
- Animal Nutrition & Physiology Team, National Institute of Animal Science, Wanju 55365, Korea
| | - Young Kyun Oh
- Animal Nutrition & Physiology Team, National Institute of Animal Science, Wanju 55365, Korea
| | - Kondreddy Eswar Reddy
- Animal Nutrition & Physiology Team, National Institute of Animal Science, Wanju 55365, Korea
| | - Hyun-Woo Seo
- Animal Products Utilization Division, National Institute of Animal Science, Wanju 55365, Korea
| | - Soohyun Cho
- Animal Products Utilization Division, National Institute of Animal Science, Wanju 55365, Korea
| | - Hyun-Jeong Lee
- Animal Nutrition & Physiology Team, National Institute of Animal Science, Wanju 55365, Korea.,Dairy Science Division, National Institute of Animal Science, Cheonan 31000, Korea
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11
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Marín-Garzón NA, Magalhães AFB, Mota LFM, Fonseca LFS, Chardulo LAL, Albuquerque LG. Genome-wide association study identified genomic regions and putative candidate genes affecting meat color traits in Nellore cattle. Meat Sci 2020; 171:108288. [PMID: 32949820 DOI: 10.1016/j.meatsci.2020.108288] [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: 07/02/2019] [Revised: 08/10/2020] [Accepted: 08/21/2020] [Indexed: 01/08/2023]
Abstract
Single and multiple-trait GWAS were conducted to detect genomic regions and candidate genes associated with meat color traits (L*, lightness; a*, redness; b*, yellowness) in Nellore cattle. Phenotypic records of 5000 animals, and 3794 genotypes for 614,274 SNPs were used. The BLUPF90 family programs were used through single step GWAS approach. The top 10 genomic regions from single-trait GWAS explained 13.64%, 15.12% and 13% of genetic variance of L*, a* and b*, which harbored 129, 70, and 84 candidate genes, respectively. Regarding multiple-trait GWAS, the top 10 SNP windows explained 17.46%, 18.98% and 13.74% of genetic variance of L*, a* and b*, and harbored 124, 86, and 82 candidate genes, respectively. Pleiotropic effects were evidenced by the overlapping regions detected on BTA 15 and 26 associated with L* and a* (genetic correlation of -0.53), and on BTA 18 associated with a* and b* (genetic correlation of 0.60). Similar genomic regions located on BTA 2, 5, 6, and 18 were detected through single and multi-trait GWAS. Overlapped regions harbored a total of 30 functional candidate genes involved in mitochondrial activity, structural integrity of muscles, lipid oxidation, anaerobic metabolism, and muscular pH.
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Affiliation(s)
- N A Marín-Garzón
- São Paulo State University (Unesp), College of Agricultural and Veterinarian Sciences, Via de Acesso Professor Paulo Donato Castelane Castellane S/N - Vila Industrial, 14884-900 Jaboticabal, SP, Brazil.
| | - A F B Magalhães
- APTA Beef Cattle Center, Animal Science Institute, Sertãozinho, São Paulo, Brazil
| | - L F M Mota
- São Paulo State University (Unesp), College of Agricultural and Veterinarian Sciences, Via de Acesso Professor Paulo Donato Castelane Castellane S/N - Vila Industrial, 14884-900 Jaboticabal, SP, Brazil
| | - L F S Fonseca
- São Paulo State University (Unesp), College of Agricultural and Veterinarian Sciences, Via de Acesso Professor Paulo Donato Castelane Castellane S/N - Vila Industrial, 14884-900 Jaboticabal, SP, Brazil
| | - L A L Chardulo
- São Paulo State University (Unesp), College of Veterinary and Animal Science, Botucatu, SP, Brazil; National Council for Science and Technological Development (CNPq), Brasília, Brazil
| | - L G Albuquerque
- São Paulo State University (Unesp), College of Agricultural and Veterinarian Sciences, Via de Acesso Professor Paulo Donato Castelane Castellane S/N - Vila Industrial, 14884-900 Jaboticabal, SP, Brazil; National Council for Science and Technological Development (CNPq), Brasília, Brazil
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12
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da Silva Diniz WJ, Banerjee P, Mazzoni G, Coutinho LL, Cesar ASM, Afonso J, Gromboni CF, Nogueira ARA, Kadarmideen HN, de Almeida Regitano LC. Interplay among miR-29 family, mineral metabolism, and gene regulation in Bos indicus muscle. Mol Genet Genomics 2020; 295:1113-1127. [PMID: 32444960 DOI: 10.1007/s00438-020-01683-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 05/04/2020] [Indexed: 11/26/2022]
Abstract
An interplay between gene expression, mineral concentration, and beef quality traits in Bos indicus muscle has been reported previously under a network approach. However, growing evidence suggested that miRNAs not only modulate gene expression but are also involved with mineral homeostasis. To our knowledge, understanding of the miRNA-gene expression-mineral concentration relationship in mammals is still minimal. Therefore, we carried out a miRNA co-expression and multi-level miRNA-mRNA integration analyses to predict the putative drivers (miRNAs and genes) associated with muscle mineral concentration in Nelore steers. In this study, we identified calcium and iron to be the pivotal minerals associated with miRNAs and gene targets. Furthermore, we identified the miR-29 family (miR-29a, -29b, -29c, -29d-3p, and -29e) as the putative key regulators modulating mineral homeostasis. The miR-29 family targets genes involved with AMPK, insulin, mTOR, and thyroid hormone signaling pathways. Finally, we reported an interplay between miRNAs and minerals acting cooperatively to modulate co-expressed genes and signaling pathways both involved with mineral and energy homeostasis in Nelore muscle. Although we provided some evidence to understand this complex relationship, future work should determine the functional implications of minerals for miRNA levels and their feedback regulation system.\\An interplay between gene expression, mineral concentration, and beef quality traits in Bos indicus muscle has been reported previously under a network approach. However, growing evidence suggested that miRNAs not only modulate gene expression but are also involved with mineral homeostasis. To our knowledge, understanding of the miRNA-gene expression-mineral concentration relationship in mammals is still minimal. Therefore, we carried out a miRNA co-expression and multi-level miRNA-mRNA integration analyses to predict the putative drivers (miRNAs and genes) associated with muscle mineral concentration in Nelore steers. In this study, we identified calcium and iron to be the pivotal minerals associated with miRNAs and gene targets. Furthermore, we identified the miR-29 family (miR-29a, -29b, -29c, -29d-3p, and -29e) as the putative key regulators modulating mineral homeostasis. The miR-29 family targets genes involved with AMPK, insulin, mTOR, and thyroid hormone signaling pathways. Finally, we reported an interplay between miRNAs and minerals acting cooperatively to modulate co-expressed genes and signaling pathways both involved with mineral and energy homeostasis in Nelore muscle. Although we provided some evidence to understand this complex relationship, future work should determine the functional implications of minerals for miRNA levels and their feedback regulation system.
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Affiliation(s)
- Wellison Jarles da Silva Diniz
- Graduate Program in Evolutionary Genetics and Molecular Biology, Center for Biological and Health Sciences (CCBS), Federal University of São Carlos, São Carlos, São Paulo, Brazil
- Department of Applied Mathematics and Computer Science, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Priyanka Banerjee
- Department of Applied Mathematics and Computer Science, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Gianluca Mazzoni
- Department of Health Technology, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Luiz Lehmann Coutinho
- Department of Animal Science, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, São Paulo, Brazil
| | - Aline Silva Mello Cesar
- Department of Animal Science, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, São Paulo, Brazil
| | - Juliana Afonso
- Graduate Program in Evolutionary Genetics and Molecular Biology, Center for Biological and Health Sciences (CCBS), Federal University of São Carlos, São Carlos, São Paulo, Brazil
| | - Caio Fernando Gromboni
- IFBA, Bahia Federal Institute of Education Science and Technology, Campus Ilhéus, Ilhéus, Bahia, Brazil
| | - Ana Rita Araújo Nogueira
- Empresa Brasileira de Pesquisa Agropecuária, Embrapa Pecuária Sudeste, São Carlos, São Paulo, Brazil
| | - Haja N Kadarmideen
- Department of Applied Mathematics and Computer Science, Technical University of Denmark, Kgs. Lyngby, Denmark
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13
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Afonso J, Fortes MRS, Reverter A, Diniz WJDS, Cesar ASM, Lima AOD, Petrini J, de Souza MM, Coutinho LL, Mourão GB, Zerlotini A, Gromboni CF, Nogueira ARA, Regitano LCDA. Genetic regulators of mineral amount in Nelore cattle muscle predicted by a new co-expression and regulatory impact factor approach. Sci Rep 2020; 10:8436. [PMID: 32439843 PMCID: PMC7242321 DOI: 10.1038/s41598-020-65454-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 05/04/2020] [Indexed: 12/11/2022] Open
Abstract
Mineral contents in bovine muscle can affect meat quality, growth, health, and reproductive traits. To better understand the genetic basis of this phenotype in Nelore (Bos indicus) cattle, we analysed genome-wide mRNA and miRNA expression data from 114 muscle samples. The analysis implemented a new application for two complementary algorithms: the partial correlation and information theory (PCIT) and the regulatory impact factor (RIF), in which we included the estimated genomic breeding values (GEBVs) for the phenotypes additionally to the expression levels, originally proposed for these methods. We used PCIT to determine putative regulatory relationships based on significant associations between gene expression and GEBVs for each mineral amount. Then, RIF was adopted to determine the regulatory impact of genes and miRNAs expression over the GEBVs for the mineral amounts. We also investigated over-represented pathways, as well as pieces of evidences from previous studies carried in the same population and in the literature, to determine regulatory genes for the mineral amounts. For example, NOX1 expression level was positively correlated to Zinc and has been described as Zinc-regulated in humans. Based on our approach, we were able to identify genes, miRNAs and pathways not yet described as underlying mineral amount. The results support the hypothesis that extracellular matrix interactions are the core regulator of mineral amount in muscle cells. Putative regulators described here add information to this hypothesis, expanding the knowledge on molecular relationships between gene expression and minerals.
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Affiliation(s)
- Juliana Afonso
- Department of Evolutionary Genetics and Molecular Biology, Federal University of São Carlos, São Carlos, Brazil
| | - Marina Rufino Salinas Fortes
- School of Chemistry and Molecular Biosciences, Faculty of Sciences, The University of Queensland, Brisbane, Australia
| | - Antonio Reverter
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Brisbane, Australia
| | | | - Aline Silva Mello Cesar
- Department of Agroindustry, Food and Nutrition, University of São Paulo/ESALQ, Piracicaba, Brazil
| | - Andressa Oliveira de Lima
- Department of Evolutionary Genetics and Molecular Biology, Federal University of São Carlos, São Carlos, Brazil
| | - Juliana Petrini
- Department of Statistics, Institute of Exact Sciences, Federal University of Alfenas, Alfenas, Brazil
| | | | | | - Gerson Barreto Mourão
- Department of Agroindustry, Food and Nutrition, University of São Paulo/ESALQ, Piracicaba, Brazil
| | - Adhemar Zerlotini
- Bioinformatic Multi-user Laboratory, Embrapa Informática Agropecuária, Campinas, São Paulo, Brazil
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14
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Hlongwane NL, Hadebe K, Soma P, Dzomba EF, Muchadeyi FC. Genome Wide Assessment of Genetic Variation and Population Distinctiveness of the Pig Family in South Africa. Front Genet 2020; 11:344. [PMID: 32457791 PMCID: PMC7221027 DOI: 10.3389/fgene.2020.00344] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 03/23/2020] [Indexed: 12/12/2022] Open
Abstract
Genetic diversity is of great importance and a prerequisite for genetic improvement and conservation programs in pigs and other livestock populations. The present study provides a genome wide analysis of the genetic variability and population structure of pig populations from different production systems in South Africa relative to global populations. A total of 234 pigs sampled in South Africa and consisting of village (n = 91), commercial (n = 60), indigenous (n = 40), Asian (n = 5) and wild (n = 38) populations were genotyped using Porcine SNP60K BeadChip. In addition, 389 genotypes representing village and commercial pigs from America, Europe, and Asia were accessed from a previous study and used to compare population clustering and relationships of South African pigs with global populations. Moderate heterozygosity levels, ranging from 0.204 for Warthogs to 0.371 for village pigs sampled from Capricorn municipality in Eastern Cape province of South Africa were observed. Principal Component Analysis of the South African pigs resulted in four distinct clusters of (i) Duroc; (ii) Vietnamese; (iii) Bush pig and Warthog and (iv) a cluster with the rest of the commercial (SA Large White and Landrace), village, Wild Boar and indigenous breeds of Koelbroek and Windsnyer. The clustering demonstrated alignment with genetic similarities, geographic location and production systems. The PCA with the global populations also resulted in four clusters that where populated with (i) all the village populations, wild boars, SA indigenous and the large white and landraces; (ii) Durocs (iii) Chinese and Vietnamese pigs and (iv) Warthog and Bush pig. K = 10 (The number of population units) was the most probable ADMIXTURE based clustering, which grouped animals according to their populations with the exception of the village pigs that showed presence of admixture. AMOVA reported 19.92%-98.62% of the genetic variation to be within populations. Sub structuring was observed between South African commercial populations as well as between Indigenous and commercial breeds. Population pairwise F ST analysis showed genetic differentiation (P ≤ 0.05) between the village, commercial and wild populations. A per marker per population pairwise F ST analysis revealed SNPs associated with QTLs for traits such as meat quality, cytoskeletal and muscle development, glucose metabolism processes and growth factors between both domestic populations as well as between wild and domestic breeds. Overall, the study provided a baseline understanding of porcine diversity and an important foundation for porcine genomics of South African populations.
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Affiliation(s)
- Nompilo Lucia Hlongwane
- Biotechnology Platform, Agricultural Research Council, Onderstepoort, South Africa
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Pietermartizburg, South Africa
| | - Khanyisile Hadebe
- Biotechnology Platform, Agricultural Research Council, Onderstepoort, South Africa
| | - Pranisha Soma
- Animal Production Institute, Agricultural Research Council, Irene, South Africa
| | - Edgar Farai Dzomba
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Pietermartizburg, South Africa
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15
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Kamanula M, Munthali CR, Dziwapo A, Kamanula JF. Mineral and phytochemical composition of baobab ( Adansonia digitata L.) root tubers from selected natural populations of Malawi. Malawi Med J 2019; 30:250-255. [PMID: 31798803 PMCID: PMC6863415 DOI: 10.4314/mmj.v30i4.7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Background Most studies on baobab have focused mainly on the nutritional value of baobab fruit pulp. Information on nutritional value and medicinal properties of the baobab root tuber has not been fully investigated and is scarce. This study was conducted to assess mineral and phytochemical composition of baobab root tubers from selected natural populations of Malawi. Methods Baobab seeds from Chikhwawa, Mwanza, Salima, Karonga and Likoma were sown at Mzuzu University. At the age of five months after sowing, mineral content of the resulting root tubers was determined using atomic absorption spectrophotometer whereas phytochemical composition was determined qualitatively. Results Magnesium (44.16mg/100g) and calcium (69.39mg/100g) levels were highest in baobab root tubers from Chikhwawa and Karonga, respectively. Mwanza and Karonga root tubers contained highest amount of lead (0.2100mg/100g) while iron content was highest (8.89mg/100g) in root tubers from Karonga. Salima and Mwanza root tubers showed strong concentration of terpenoids. Moderate concentrations of saponins were detected in Mwanza, Salima, Karonga and Chikhwawa root tubers. Alkaloids and flavonoids were absent in all families from the five sampled provenances. Conclusion Minerals and phytochemicals present in baobab root tubers suggest their nutritional and medicinal potential. However, further research is required to establish the causes of high levels of lead in baobab root tubers.
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Affiliation(s)
- Mussa Kamanula
- Department of Forestry, Mzuzu University, Private Bag 201, Luwinga, Mzuzu
| | | | - Agnes Dziwapo
- Department of Forestry, Mzuzu University, Private Bag 201, Luwinga, Mzuzu
| | - John F Kamanula
- Department of Chemistry, Mzuzu University, Private Bag 201, Luwinga, Mzuzu
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16
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Michailidou S, Tsangaris GT, Tzora A, Skoufos I, Banos G, Argiriou A, Arsenos G. Analysis of genome-wide DNA arrays reveals the genomic population structure and diversity in autochthonous Greek goat breeds. PLoS One 2019; 14:e0226179. [PMID: 31830089 PMCID: PMC6907847 DOI: 10.1371/journal.pone.0226179] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 11/21/2019] [Indexed: 12/02/2022] Open
Abstract
Goats play an important role in the livestock sector in Greece. The national herd consists mainly of two indigenous breeds, the Eghoria and Skopelos. Here, we report the population structure and genomic profiles of these two native goat breeds using Illumina’s Goat SNP50 BeadChip. Moreover, we present a panel of candidate markers acquired using different genetic models for breed discrimination. Quality control on the initial dataset resulted in 48,841 SNPs kept for downstream analysis. Principal component and admixture analyses were applied to assess population structure. The rate of inbreeding within breed was evaluated based on the distribution of runs of homozygosity in the genome and respective coefficients, the genomic relationship matrix, the patterns of linkage disequilibrium, and the historic effective population size. Results showed that both breeds exhibit high levels of genetic diversity. Level of inbreeding between the two breeds estimated by the Wright’s fixation index FST was low (Fst = 0.04362), indicating the existence of a weak genetic differentiation between them. In addition, grouping of farms according to their geographical locations was observed. This study presents for the first time a genome-based analysis on the genetic structure of the two indigenous Greek goat breeds and identifies markers that can be potentially exploited in future selective breeding programs for traceability purposes, targeted genetic improvement schemes and conservation strategies.
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Affiliation(s)
- S. Michailidou
- Laboratory of Animal Husbandry, School of Veterinary Medicine, School of Health Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece
- Institute of Applied Biosciences, Center for Research and Technology Hellas, Thermi, Greece
- * E-mail:
| | - G. Th. Tsangaris
- Proteomics Research Unit, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - A. Tzora
- School of Agriculture, Department of Agriculture, Division of Animal Production, University of Ioannina, Kostakioi Artas, Greece
| | - I. Skoufos
- School of Agriculture, Department of Agriculture, Division of Animal Production, University of Ioannina, Kostakioi Artas, Greece
| | - G. Banos
- Laboratory of Animal Husbandry, School of Veterinary Medicine, School of Health Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece
- Scotland's Rural College and The Roslin Institute University of Edinburgh, Edinburgh, Scotland, United Kingdom
| | - A. Argiriou
- Institute of Applied Biosciences, Center for Research and Technology Hellas, Thermi, Greece
| | - G. Arsenos
- Laboratory of Animal Husbandry, School of Veterinary Medicine, School of Health Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece
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17
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Diniz WJDS, Banerjee P, Regitano LCA. Cross talk between mineral metabolism and meat quality: a systems biology overview. Physiol Genomics 2019; 51:529-538. [PMID: 31545932 DOI: 10.1152/physiolgenomics.00072.2019] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Meat quality has an inherent complexity because of the multiple interrelated causative factors and layers of feedback regulation. Understanding the key factors and their interactions has been challenging, despite the availability of remarkable high-throughput tools and techniques that have provided insights on muscle metabolism and the genetic basis of meat quality. Likewise, we have deepened our knowledge about mineral metabolism and its role in cell functioning. Regardless of these facts, complex traits like mineral content and meat quality have been studied under reductionist approaches. However, as these phenotypes arise from complex interactions among different biological layers (genome, transcriptome, proteome, epigenome, etc.), along with environmental effects, a holistic view and systemic-level understanding of the genetic basis of complex phenotypes are in demand. Based on the state of the art, we addressed some of the questions regarding the interdependence of meat quality traits and mineral content. Furthermore, we sought to highlight potential regulatory mechanisms arising from the genes, miRNAs, and mineral interactions, as well as the pathways modulated by this interplay affecting muscle, mineral metabolism, and meat quality. By answering these questions, we did not intend to give an exhaustive review but to identify the key biological points, the challenges, and benefits of integrative genomic approaches.
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Affiliation(s)
- Wellison J da Silva Diniz
- Center for Biological and Health Sciences (CCBS), Federal University of São Carlos, São Carlos, São Paulo, Brazil
| | - Priyanka Banerjee
- Department of Applied Mathematics and Computer Science, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Luciana C A Regitano
- Embrapa Pecuária Sudeste, Empresa Brasileira de Pesquisa Agropecuária, São Carlos, São Paulo, Brazil
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18
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Afonso J, Coutinho LL, Tizioto PC, da Silva Diniz WJ, de Lima AO, Rocha MIP, Buss CE, Andrade BGN, Piaya O, da Silva JV, Lins LA, Gromboni CF, Nogueira ARA, Fortes MRS, Mourao GB, de Almeida Regitano LC. Muscle transcriptome analysis reveals genes and metabolic pathways related to mineral concentration in Bos indicus. Sci Rep 2019; 9:12715. [PMID: 31481722 PMCID: PMC6722098 DOI: 10.1038/s41598-019-49089-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 08/02/2019] [Indexed: 01/18/2023] Open
Abstract
Mineral content affects the biological processes underlying beef quality. Muscle mineral concentration depends not only on intake-outtake balance and muscle type, but also on age, environment, breed, and genetic factors. To unveil the genetic factors involved in muscle mineral concentration, we applied a pairwise differential gene expression analysis in groups of Nelore steers genetically divergent for nine different mineral concentrations. Here, based on significant expression differences between contrasting groups, we presented candidate genes for the genetic regulation of mineral concentration in muscle. Functional enrichment and protein-protein interaction network analyses were carried out to search for gene regulatory processes concerning each mineral. The core genetic regulation for all minerals studied, except Zn, seems to rest on interactions between components of the extracellular matrix. Regulation of adipogenesis-related pathways was also significant in our results. Antagonistic patterns of gene expression for fatty acid metabolism-related genes may explain the Cu and Zn antagonistic effect on fatty acid accumulation. Our results shed light on the role of these minerals on cell function.
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Affiliation(s)
- Juliana Afonso
- Department of Evolutionary Genetics and Molecular Biology, Federal University of São Carlos, São Carlos, Brazil
| | | | | | | | - Andressa Oliveira de Lima
- Department of Evolutionary Genetics and Molecular Biology, Federal University of São Carlos, São Carlos, Brazil
| | - Marina Ibelli Pereira Rocha
- Department of Evolutionary Genetics and Molecular Biology, Federal University of São Carlos, São Carlos, Brazil
| | - Carlos Eduardo Buss
- Department of Evolutionary Genetics and Molecular Biology, Federal University of São Carlos, São Carlos, Brazil
| | | | - Otávio Piaya
- Department of Evolutionary Genetics and Molecular Biology, Federal University of São Carlos, São Carlos, Brazil
| | | | - Laura Albuquerque Lins
- Animal Science department, Laboratory of Molecular Genetics. São Paulo State University, Jaboticabal, Brazil
| | | | | | - Marina Rufino Salinas Fortes
- School of Chemistry and Molecular Biosciences, Faculty of Sciences, The University of Queensland, Brisbane, Australia
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19
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Diniz WJS, Mazzoni G, Coutinho LL, Banerjee P, Geistlinger L, Cesar ASM, Bertolini F, Afonso J, de Oliveira PSN, Tizioto PC, Kadarmideen HN, Regitano LCA. Detection of Co-expressed Pathway Modules Associated With Mineral Concentration and Meat Quality in Nelore Cattle. Front Genet 2019; 10:210. [PMID: 30930938 PMCID: PMC6424907 DOI: 10.3389/fgene.2019.00210] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 02/26/2019] [Indexed: 12/14/2022] Open
Abstract
Meat quality is a complex trait that is influenced by genetic and environmental factors, which includes mineral concentration. However, the association between mineral concentration and meat quality, and the specific molecular pathways underlying this association, are not well explored. We therefore analyzed gene expression as measured with RNA-seq in Longissimus thoracis muscle of 194 Nelore steers for association with three meat quality traits (intramuscular fat, meat pH, and tenderness) and the concentration of 13 minerals (Ca, Cr, Co, Cu, Fe, K, Mg, Mn, Na, P, S, Se, and Zn). We identified seven sets of co-expressed genes (modules) associated with at least two traits, which indicates that common pathways influence these traits. From pathway analysis of module hub genes, we further found an over-representation for energy and protein metabolism (AMPK and mTOR signaling pathways) in addition to muscle growth, and protein turnover pathways. Among the identified hub genes FASN, ELOV5, and PDE3B are involved with lipid metabolism and were affected by previously identified eQTLs associated to fat deposition. The reported hub genes and over-represented pathways provide evidence of interplay among gene expression, mineral concentration, and meat quality traits. Future studies investigating the effect of different levels of mineral supplementation in the gene expression and meat quality traits could help us to elucidate the regulatory mechanism by which the genes/pathways are affected.
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Affiliation(s)
- Wellison J S Diniz
- Department of Genetics and Evolution, Federal University of São Carlos, São Carlos, Brazil.,Department of Applied Mathematics and Computer Science, Technical University of Denmark, Kongens Lyngby, Denmark.,Embrapa Pecuária Sudeste, Empresa Brasileira de Pesquisa Agropecuária, São Paulo, Brazil
| | - Gianluca Mazzoni
- Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Luiz L Coutinho
- Department of Animal Science, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, Brazil
| | - Priyanka Banerjee
- Department of Applied Mathematics and Computer Science, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Ludwig Geistlinger
- Embrapa Pecuária Sudeste, Empresa Brasileira de Pesquisa Agropecuária, São Paulo, Brazil.,Graduate School of Public Health and Health Policy, The City University of New York, New York, NY, United States
| | - Aline S M Cesar
- Department of Animal Science, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, Brazil
| | - Francesca Bertolini
- Department of Aquaculture, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Juliana Afonso
- Department of Genetics and Evolution, Federal University of São Carlos, São Carlos, Brazil
| | | | - Polyana C Tizioto
- Department of Animal Science, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, Brazil
| | - Haja N Kadarmideen
- Department of Applied Mathematics and Computer Science, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Luciana C A Regitano
- Embrapa Pecuária Sudeste, Empresa Brasileira de Pesquisa Agropecuária, São Paulo, Brazil
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A novel PAX7 10-bp indel variant modulates promoter activity, gene expression and contributes to different phenotypes of Chinese cattle. Sci Rep 2018; 8:1724. [PMID: 29379079 PMCID: PMC5789009 DOI: 10.1038/s41598-018-20177-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Accepted: 01/10/2018] [Indexed: 11/09/2022] Open
Abstract
Paired box 7 (PAX7) gene regulates the conversion of muscle satellite cells into myogenic cells and participates in multi-step processes in myogenesis. Expression levels of PAX7 are decisive for its regulatory function. Previous reports revealed that PAX7 were responsible for the developmental traits of muscle. The relationship of the PAX7 promoter variants and livestock phenotypic traits has not been fully elucidated. We detected a novel 10-bp insertion/deletion (indel) polymorphism in the bovine PAX7 promoter and revealed that the indel altered the binding of the transcriptional factor ZNF219. Luciferase reporter assay showed that deletion-deletion (Del-Del) genotype of the PAX7 gene showed 2.79-fold higher promoter activity than the insertion-insertion (Ins-Ins) genotype (P < 0.05), and ZNF219 overexpression significantly diminished the luciferase activity in Ins-Ins groups. Moreover, the expression of PAX7 and its down-stream genes were detected in fetal skeletal muscle of cattle with different PAX7 genotypes, where the Del-Del genotype also displayed high expression levels. Statistical association analysis demonstrated that this indel had significant effects on early growth traits in cattle. These findings provide a complete overview of the function of the PAX7 10-bp variant, which may have potential as a genetic marker for marker-assisted selection in improving economically significant traits of cattle.
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21
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Widespread modulation of gene expression by copy number variation in skeletal muscle. Sci Rep 2018; 8:1399. [PMID: 29362391 PMCID: PMC5780461 DOI: 10.1038/s41598-018-19782-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Accepted: 01/09/2018] [Indexed: 12/25/2022] Open
Abstract
Copy number variation (CNV) is a frequently observed deviation from the diploid state due to duplication or deletion of genomic regions. Although intensively analyzed for association with diseases and production traits, the specific mechanisms and extent by which such variations affect the phenotype are incompletely understood. We present an integrative study on CNV and genome-wide gene expression in Brazilian Bos indicus cattle. We analyzed CNVs inferred from SNP-chip data for effects on gene expression measured with RNA-seq in skeletal muscle samples of 183 steers. Local effects, where expression changes coincided with CNVs in the respective genes, were restricted to immune genes. Distal effects were attributable to several high-impact CNVs that modulated remote expression in an orchestrated and intertwined fashion. These CNVs were located in the vicinity of major skeletal muscle pathway regulators and associated genes were enriched for proteolysis, autophagy, and muscle structure development. From association analysis between CNVs and several meat quality and production traits, we found CNV-associated expression effects to also manifest at the phenotype level. Based on genome sequences of the population founders, we further demonstrate that CNVs with impact on expression and phenotype are passed on from one generation to another.
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22
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Chen C, Steibel JP, Tempelman RJ. Genome-Wide Association Analyses Based on Broadly Different Specifications for Prior Distributions, Genomic Windows, and Estimation Methods. Genetics 2017; 206:1791-1806. [PMID: 28637709 PMCID: PMC5560788 DOI: 10.1534/genetics.117.202259] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2017] [Accepted: 06/19/2017] [Indexed: 11/18/2022] Open
Abstract
A currently popular strategy (EMMAX) for genome-wide association (GWA) analysis infers association for the specific marker of interest by treating its effect as fixed while treating all other marker effects as classical Gaussian random effects. It may be more statistically coherent to specify all markers as sharing the same prior distribution, whether that distribution is Gaussian, heavy-tailed (BayesA), or has variable selection specifications based on a mixture of, say, two Gaussian distributions [stochastic search and variable selection (SSVS)]. Furthermore, all such GWA inference should be formally based on posterior probabilities or test statistics as we present here, rather than merely being based on point estimates. We compared these three broad categories of priors within a simulation study to investigate the effects of different degrees of skewness for quantitative trait loci (QTL) effects and numbers of QTL using 43,266 SNP marker genotypes from 922 Duroc-Pietrain F2-cross pigs. Genomic regions were based either on single SNP associations, on nonoverlapping windows of various fixed sizes (0.5-3 Mb), or on adaptively determined windows that cluster the genome into blocks based on linkage disequilibrium. We found that SSVS and BayesA lead to the best receiver operating curve properties in almost all cases. We also evaluated approximate maximum a posteriori (MAP) approaches to BayesA and SSVS as potential computationally feasible alternatives; however, MAP inferences were not promising, particularly due to their sensitivity to starting values. We determined that it is advantageous to use variable selection specifications based on adaptively constructed genomic window lengths for GWA studies.
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Affiliation(s)
- Chunyu Chen
- Department of Animal Science, Michigan State University, East Lansing, Michigan 48824
| | - Juan P Steibel
- Department of Animal Science, Michigan State University, East Lansing, Michigan 48824
| | - Robert J Tempelman
- Department of Animal Science, Michigan State University, East Lansing, Michigan 48824
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23
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Macciotta NPP, Biffani S, Bernabucci U, Lacetera N, Vitali A, Ajmone-Marsan P, Nardone A. Derivation and genome-wide association study of a principal component-based measure of heat tolerance in dairy cattle. J Dairy Sci 2017; 100:4683-4697. [PMID: 28365122 DOI: 10.3168/jds.2016-12249] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 02/05/2017] [Indexed: 12/19/2022]
Abstract
Heat stress represents a key factor that negatively affects the productive and reproductive performance of farm animals. In the present work, a new measure of tolerance to heat stress for dairy cattle was developed using principal component analysis. Data were from 590,174 test-day records for milk yield, fat and protein percentages, and somatic cell score of 39,261 Italian Holstein cows. Test-day records adjusted for main systematic factors were grouped into 11 temperature-humidity index (THI) classes. Daughter trait deviations (DTD) were calculated for 1,540 bulls as means of the adjusted test-day records for each THI class. Principal component analysis was performed on the DTD for each bull. The first 2 principal components (PC) explained 42 to 51% of the total variance of the system across the 4 traits. The first PC, a measure of the level at which the curve is located, was interpreted as a measure of the level at which the DTD curve was located. The second PC, which shows the slope of increasing or decreases DTD curves, synthesized the behavior of the DTD pattern. Heritability of the 2 component scores was moderate to high for level across all traits (range = 0.23-0.82) and low to moderate for slope (range = 0.16-0.28). For each trait, phenotypic and genetic correlations between level and slope were equal to zero. A genome-wide association analysis was carried out on a subsample of 423 bulls genotyped with the Illumina 50K bovine bead chip (Illumina, San Diego, CA). Two single nucleotide polymorphisms were significantly associated with slope for milk yield, 4 with level for fat percentage, and 2 with level and slope of protein percentage, respectively. The gene discovery was carried out considering windows of 0.5 Mb surrounding the significant markers and highlighted some interesting candidate genes. Some of them have been already associated with the mechanism of heat tolerance as the heat shock transcription factor (HSF1) and the malonyl-CoA-acyl carrier protein transacylase (MCAT). The 2 PC were able to describe the overall level and the slope of response of milk production traits across increasing levels of THI index. Moreover, they exhibited genetic variability and were genetically uncorrelated. These features suggest their use as measures of thermotolerance in dairy cattle breeding schemes.
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Affiliation(s)
- N P P Macciotta
- Dipartimento di Agraria, Università di Sassari, 07100 Sassari, Italy.
| | - S Biffani
- Associazione Italiana Allevatori, 00161 Roma, Italy
| | - U Bernabucci
- Dipartimento di Scienze Agrarie e Forestali, Università degli Studi della Tuscia-Viterbo, 01100 Viterbo, Italy
| | - N Lacetera
- Dipartimento di Scienze Agrarie e Forestali, Università degli Studi della Tuscia-Viterbo, 01100 Viterbo, Italy
| | - A Vitali
- Dipartimento di Scienze Agrarie e Forestali, Università degli Studi della Tuscia-Viterbo, 01100 Viterbo, Italy
| | - P Ajmone-Marsan
- Istituto di Zootecnica, Università Cattolica del Sacro Cuore, 29122 Piacenza, Italy
| | - A Nardone
- Dipartimento di Scienze Agrarie e Forestali, Università degli Studi della Tuscia-Viterbo, 01100 Viterbo, Italy.
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24
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Brito LF, Kijas JW, Ventura RV, Sargolzaei M, Porto-Neto LR, Cánovas A, Feng Z, Jafarikia M, Schenkel FS. Genetic diversity and signatures of selection in various goat breeds revealed by genome-wide SNP markers. BMC Genomics 2017; 18:229. [PMID: 28288562 PMCID: PMC5348779 DOI: 10.1186/s12864-017-3610-0] [Citation(s) in RCA: 91] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 03/07/2017] [Indexed: 01/08/2023] Open
Abstract
Background The detection of signatures of selection has the potential to elucidate the identities of genes and mutations associated with phenotypic traits important for livestock species. It is also very relevant to investigate the levels of genetic diversity of a population, as genetic diversity represents the raw material essential for breeding and has practical implications for implementation of genomic selection. A total of 1151 animals from nine goat populations selected for different breeding goals and genotyped with the Illumina Goat 50K single nucleotide polymorphisms (SNP) Beadchip were included in this investigation. Results The proportion of polymorphic SNPs ranged from 0.902 (Nubian) to 0.995 (Rangeland). The overall mean HO and HE was 0.374 ± 0.021 and 0.369 ± 0.023, respectively. The average pairwise genetic distance (D) ranged from 0.263 (Toggenburg) to 0.323 (Rangeland). The overall average for the inbreeding measures FEH, FVR, FLEUT, FROH and FPED was 0.129, −0.012, −0.010, 0.038 and 0.030, respectively. Several regions located on 19 chromosomes were potentially under selection in at least one of the goat breeds. The genomic population tree constructed using all SNPs differentiated breeds based on selection purpose, while genomic population tree built using only SNPs in the most significant region showed a great differentiation between LaMancha and the other breeds. We hypothesized that this region is related to ear morphogenesis. Furthermore, we identified genes potentially related to reproduction traits, adult body mass, efficiency of food conversion, abdominal fat deposition, conformation traits, liver fat metabolism, milk fatty acids, somatic cells score, milk protein, thermo-tolerance and ear morphogenesis. Conclusions In general, moderate to high levels of genetic variability were observed for all the breeds and a characterization of runs of homozygosity gave insights into the breeds’ development history. The information reported here will be useful for the implementation of genomic selection and other genomic studies in goats. We also identified various genome regions under positive selection using smoothed FST and hapFLK statistics and suggested genes, which are potentially under selection. These results can now provide a foundation to formulate biological hypotheses related to selection processes in goats. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3610-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Luiz F Brito
- Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, Ontario, Canada.
| | - James W Kijas
- CSIRO Agriculture & Food, Brisbane, Queensland, Australia
| | - Ricardo V Ventura
- Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, Ontario, Canada.,Beef Improvement Opportunities, Guelph, Ontario, Canada
| | - Mehdi Sargolzaei
- Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, Ontario, Canada.,The Semex Alliance, Guelph, Ontario, Canada
| | | | - Angela Cánovas
- Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, Ontario, Canada
| | - Zeny Feng
- Department of Mathematics and Statistics, University of Guelph, Guelph, Ontario, Canada
| | - Mohsen Jafarikia
- Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, Ontario, Canada.,Canadian Centre for Swine Improvement Inc., Ottawa, Ontario, Canada
| | - Flávio S Schenkel
- Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, Ontario, Canada
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25
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Diniz WJDS, Coutinho LL, Tizioto PC, Cesar ASM, Gromboni CF, Nogueira ARA, de Oliveira PSN, de Souza MM, Regitano LCDA. Iron Content Affects Lipogenic Gene Expression in the Muscle of Nelore Beef Cattle. PLoS One 2016; 11:e0161160. [PMID: 27532424 PMCID: PMC4988672 DOI: 10.1371/journal.pone.0161160] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 08/01/2016] [Indexed: 12/16/2022] Open
Abstract
Iron (Fe) is an essential mineral for metabolism and plays a central role in a range of biochemical processes. Therefore, this study aimed to identify differentially expressed (DE) genes and metabolic pathways in Longissimus dorsi (LD) muscle from cattle with divergent iron content, as well as to investigate the likely role of these DE genes in biological processes underlying beef quality parameters. Samples for RNA extraction for sequencing and iron, copper, manganese, and zinc determination were collected from LD muscles at slaughter. Eight Nelore steers, with extreme genomic estimated breeding values for iron content (Fe-GEBV), were selected from a reference population of 373 animals. From the 49 annotated DE genes (FDR<0.05) found between the two groups, 18 were up-regulated and 31 down-regulated for the animals in the low Fe-GEBV group. The functional enrichment analyses identified several biological processes, such as lipid transport and metabolism, and cell growth. Lipid metabolism was the main pathway observed in the analysis of metabolic and canonical signaling pathways for the genes identified as DE, including the genes FASN, FABP4, and THRSP, which are functional candidates for beef quality, suggesting reduced lipogenic activities with lower iron content. Our results indicate metabolic pathways that are partially influenced by iron, contributing to a better understanding of its participation in skeletal muscle physiology.
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Affiliation(s)
| | | | | | | | | | | | | | - Marcela Maria de Souza
- Department of Genetic and Evolution, Federal University of São Carlos, São Carlos, Brazil
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26
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Cohen-Zinder M, Asher A, Lipkin E, Feingersch R, Agmon R, Karasik D, Brosh A, Shabtay A. FABP4 is a leading candidate gene associated with residual feed intake in growing Holstein calves. Physiol Genomics 2016; 48:367-76. [PMID: 26993365 DOI: 10.1152/physiolgenomics.00121.2015] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Accepted: 03/09/2016] [Indexed: 01/08/2023] Open
Abstract
Ecological and economic concerns drive the need to improve feed utilization by domestic animals. Residual feed intake (RFI) is one of the most acceptable measures for feed efficiency (FE). However, phenotyping RFI-related traits is complex and expensive and requires special equipment. Advances in marker technology allow the development of various DNA-based selection tools. To assimilate these technologies for the benefit of RFI-based selection, reliable phenotypic measures are prerequisite. In the current study, we identified single nucleotide polymorphisms (SNPs) associated with RFI phenotypic consistency across different ages and diets (named RFI 1-3), using DNA samples of high or low RFI ranked Holstein calves. Using targeted sequencing of chromosomal regions associated with FE- and RFI-related traits, we identified 48 top SNPs significantly associated with at least one of three defined RFIs. Eleven of these SNPs were harbored by the fatty acid binding protein 4 (FABP4). While 10 significant SNPs found in FABP4 were common for RFI 1 and RFI 3, one SNP (FABP4_5; A<G substitution), in the promoter region of the gene, was significantly associated with all three RFIs. As the three RFI classes reflect changing diets and ages with concomitant RFI phenotypic consistency, the above polymorphisms and in particular FABP4_5, might be considered possible markers for RFI-based selection for FE in the Holstein breed, following a larger-scale validation.
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Affiliation(s)
- Miri Cohen-Zinder
- Beef cattle section, Newe-Ya'ar Research Center, Agricultural Research Organization, Ramat Yishay, Israel;
| | - Aviv Asher
- Beef cattle section, Newe-Ya'ar Research Center, Agricultural Research Organization, Ramat Yishay, Israel; Israeli Center for Interdisciplinary Research in Chronobiology, University of Haifa, Haifa, Israel
| | - Ehud Lipkin
- Department of Genetics, The Hebrew University of Jerusalem, Jerusalem, Israel; and
| | - Roi Feingersch
- Faculty of Medicine in the Galilee, Bar-Ilan University, Safed, Israel
| | - Rotem Agmon
- Beef cattle section, Newe-Ya'ar Research Center, Agricultural Research Organization, Ramat Yishay, Israel
| | - David Karasik
- Faculty of Medicine in the Galilee, Bar-Ilan University, Safed, Israel
| | - Arieh Brosh
- Beef cattle section, Newe-Ya'ar Research Center, Agricultural Research Organization, Ramat Yishay, Israel
| | - Ariel Shabtay
- Beef cattle section, Newe-Ya'ar Research Center, Agricultural Research Organization, Ramat Yishay, Israel
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