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Corrêa MSL, Silva EN, Dos Santos TCF, Simielli Fonseca LF, Magalhães AFB, Verardo LL, de Albuquerque LG, Silva DBDS. A network-based approach to understanding gene-biological processes affecting economically important traits of Nelore cattle. Anim Genet 2024; 55:55-65. [PMID: 38112158 DOI: 10.1111/age.13389] [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: 10/07/2023] [Revised: 10/07/2023] [Accepted: 11/29/2023] [Indexed: 12/20/2023]
Abstract
This study aimed to build gene-biological process networks with differentially expressed genes associated with economically important traits of Nelore cattle from 17 previous studies. The genes were clustered into three groups by evaluated traits: group 1, production traits; group 2, carcass traits; and group 3, meat quality traits. For each group, a gene-biological process network analysis was performed with the differentially expressed genes in common. For production traits, 37 genes were found in common, of which 13 genes were enriched for six Gene Ontology (GO) terms; these terms were not functionally grouped. However, the enriched GO terms were related to homeostasis, the development of muscles and the immune system. For carcass traits, four genes were found in common. Thus, it was not possible to functionally group these genes into a network. For meat quality traits, the analysis revealed 222 genes in common. CSRP3 was the only gene differentially expressed in all three groups. Non-redundant biological terms for clusters of genes were functionally grouped networks, reflecting the cross-talk between all biological processes and genes involved. Many biological processes and pathways related to muscles, the immune system and lipid metabolism were enriched, such as striated muscle cell development and triglyceride metabolic processes. This study provides insights into the genetic mechanisms of production, carcass and meat quality traits of Nelore cattle. This information is fundamental for a better understanding of the complex traits and could help in planning strategies for the production and selection systems of Nelore cattle.
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Affiliation(s)
| | - Evandro Neves Silva
- Professor Edson Antônio Velano University (UNIFENAS), Alfenas, Minas Gerais, Brazil
- Federal University of Alfenas (UNIFAL), Alfenas, Minas Gerais, Brazil
| | - Thaís Cristina Ferreira Dos Santos
- Professor Edson Antônio Velano University (UNIFENAS), Alfenas, Minas Gerais, Brazil
- National Center for Research in Energy and Materials (CNPEM), Campinas, São Paulo, Brazil
| | | | - Ana Fabrícia Braga Magalhães
- Department of Animal Science, Federal University of Vales do Jequitinhonha e Mucuri (UFVJM), Diamantina, Minas Gerais, Brazil
| | - Lucas Lima Verardo
- Department of Animal Science, Federal University of Vales do Jequitinhonha e Mucuri (UFVJM), Diamantina, Minas Gerais, Brazil
| | - Lucia Galvão de Albuquerque
- School of Agricultural and Veterinarian Sciences, São Paulo State University (UNESP), Jaboticabal, São Paulo, Brazil
| | - Danielly Beraldo Dos Santos Silva
- Professor Edson Antônio Velano University (UNIFENAS), Alfenas, Minas Gerais, Brazil
- School of Agricultural and Veterinarian Sciences, São Paulo State University (UNESP), Jaboticabal, São Paulo, Brazil
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Genetic Architecture and Signatures of Selection in the Caqueteño Creole (Colombian Native Cattle). DIVERSITY 2022. [DOI: 10.3390/d14100828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Evolutionary mechanisms have shaped the genomic architecture of Colombian Creole cattle breeds. The mating and selection processes have impacted several traits, promoting differences within and between populations. Studies of population structure and selection signatures in Colombian Creole breeds are scarce, and need more attention to better understand genetic differentiation, gene flow, and genetic distance. This study aimed to analyze the population structure and identify selection imprints in the Criollo Caqueteño (CAQ) population. It used 127 CAQ animals genotyped with Chip HD 777,000 SNPs. The population structure analyses used discriminant principal component analysis (DAPC), integrated haplotype scoring (iHS), and index-fixing (Fst) methodologies to detect selection signals. We can highlight SNP regions on the genes TMPRSS15, PGAM2, and EGFR, identified by the Fst method. Additionally, the iHS regions for cluster 1 identified candidate genes on BTA 3 (CMPK1 and FOXD2), BTA 11 (RCAN1), and BTA 22 (ARPP21). In group 2, we can highlight the genes on BTA 4 (SLC13A4, BRAF), BTA 9 (ULBP), BTA 14 (CSMD3) and BTA 19 (KRTAP9-2). These candidate genes have been associated with fertility traits, precocity, growth, and environmental and disease resistance, indicating a genetic potential in CAQ animals. All this promotes a better understanding of the diversity and genetic structure in the CAQ population. Based on that, our study can significantly assist the sustainable development and conservation of the breed in the Colombian Amazon.
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Allelic and genotypic frequencies for loci associated with meat quality in Mexican Braunvieh cattle. Trop Anim Health Prod 2021; 53:307. [PMID: 33956226 DOI: 10.1007/s11250-021-02757-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 05/02/2021] [Indexed: 10/21/2022]
Abstract
The objective was to estimate allelic and genotypic frequencies for loci associated with meat quality in a Mexican population of Braunvieh cattle. Information was obtained from 300 animals genotyped with the Genomic Profile Bovine LD chip of 30K and 50K SNPs. After the final edition, including quality control, the data contained information for 12 loci of the CAPN1, CAPN3, CAPN5, CAPN14, DGAT1, DGAT2, TG, ANK1, and MADH3 genes. Allelic and genotypic frequencies and Hardy-Weinberg equilibrium were estimated with the Cervus 3.0.7 software. The studied population markers were in Hardy-Weinberg equilibrium, except for those associated with CAPN1, DGAT1, and MADH3. Frequencies higher than those reported for other breeds were found for genotypes associated with meat softness, higher marbling score, lower quantity of saturated fatty acids, and lower shear force (CAPN1 and DGAT2). There were similarities with frequencies reported for Bos taurus breeds for the CAPN3 and TG genes. For the DGAT1 and ANK1 genes, the frequencies of the desired genotypes were low. A marker for DGAT1 and another for MADH3 were monomorphic. The results of this study are encouraging in terms of the potential of the Braunvieh population studied for breeding programs aiming to increase meat quality. The breed has strengths that could be used either by crossbreeding to generate heterozygous animals or by selection to increase frequencies of valuable alleles.
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Kaur M, Kumar A, Siddaraju NK, Fairoze MN, Chhabra P, Ahlawat S, Vijh RK, Yadav A, Arora R. Differential expression of miRNAs in skeletal muscles of Indian sheep with diverse carcass and muscle traits. Sci Rep 2020; 10:16332. [PMID: 33004825 PMCID: PMC7529745 DOI: 10.1038/s41598-020-73071-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 09/03/2020] [Indexed: 12/15/2022] Open
Abstract
The study presents the miRNA profiles of two Indian sheep populations with divergent carcass and muscle traits. The RNA sequencing of longissimus thoracis muscles from the two populations revealed a total of 400 known miRNAs. Myomirs or miRNAs specific to skeletal muscles identified in our data included oar-miR-1, oar-miR-133b, oar-miR-206 and oar-miR-486. Comparison of the two populations led to identification of 100 differentially expressed miRNAs (p < 0.05). A total of 45 miRNAs exhibited a log2 fold change of ≥ ( ±) 3.0. Gene Ontology analysis revealed cell proliferation, epithelial to mesenchymal transition, apoptosis, immune response and cell differentiation as the most significant functions of the differentially expressed miRNAs. The differential expression of some miRNAs was validated by qRT-PCR analysis. Enriched pathways included metabolism of proteins and lipids, PI3K-Akt, EGFR and cellular response to stress. The microRNA-gene interaction network revealed miR-21, miR-155, miR-143, miR-221 and miR-23a as the nodal miRNAs, with multiple targets. MicroRNA-21 formed the focal point of the network with 42 interactions. The hub miRNAs identified in our study form putative regulatory candidates for future research on meat quality traits in Indian sheep. Our results provide insight into the biological pathways and regulatory molecules implicated in muscling traits of sheep.
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Affiliation(s)
- Mandeep Kaur
- ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, 132001, India.,Kurukshetra University, Kurukshetra, Haryana, 136119, India
| | - Ashish Kumar
- ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, 132001, India.,Kurukshetra University, Kurukshetra, Haryana, 136119, India
| | | | | | - Pooja Chhabra
- ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, 132001, India
| | - Sonika Ahlawat
- ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, 132001, India
| | - Ramesh Kumar Vijh
- ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, 132001, India
| | - Anita Yadav
- Kurukshetra University, Kurukshetra, Haryana, 136119, India
| | - Reena Arora
- ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, 132001, India.
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Associations of CAST, CAPN1 and MSTN Genes Polymorphism with Slaughter Value and Beef Quality – A Review. ANNALS OF ANIMAL SCIENCE 2020. [DOI: 10.2478/aoas-2020-0006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Abstract
The slaughter value of cattle and beef quality are influenced by many factors, which can generally be divided into antemortem (breed, sex, age, housing system, diet, pre-slaughter handling) and postmortem (post-slaughter processing, chilling temperature, packaging). Studies of many authors have shown that meat quality traits can be also influenced by the individual genetic background of an animal. Numerous studies have been conducted worldwide to determine the functions of various genes as well as polymorphisms with potential effects on fattening and slaughter value of cattle and on beef quality. This study reviews the most important research done on the associations of polymorphisms in the calpain, calpastatin and myostatin genes with carcass traits and beef quality. Knowledge about the genes and chromosome regions associated with desired meat quality characteristics may prove very helpful when selecting pairs for mating and estimating the breeding value of offspring, mainly because it is difficult to improve meat quality traits based on conventional selection methods due to their low heritability and polygenic regulation. Furthermore, meat quality evaluation is expensive and can only be carried out after slaughter.
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Manca E, Cesarani A, Gaspa G, Sorbolini S, Macciotta NP, Dimauro C. Use of the Multivariate Discriminant Analysis for Genome-Wide Association Studies in Cattle. Animals (Basel) 2020; 10:ani10081300. [PMID: 32751408 PMCID: PMC7460480 DOI: 10.3390/ani10081300] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 07/23/2020] [Accepted: 07/27/2020] [Indexed: 11/16/2022] Open
Abstract
Simple Summary In the traditional single marker regression approach for genome-wide association studies, if the number of involved individuals is small and the number of single nucleotide polymorphisms (SNPs) to be tested is very large, the probability of getting a significant association simply due to chance becomes enormous. Other techniques, such as the Bayesian methods, require several a priori assumptions, as an a priori posterior inclusion probability threshold, that can limit their effectiveness. In the present study, a multivariate algorithm able to partially overcome this problem was proposed. On simulated data, with 3000 individuals, only 13 and 3 quantitative trait loci (QTLs) were obtained with the single marker regression and the Bayesian approaches, respectively. On the other hand, the multivariate algorithm detected 65 QTLs in the same scenario. The gap between the single marker regression and the multivariate methods slowly decreased as the number of animals increased. This figure was also confirmed on real data. Abstract Genome-wide association studies (GWAS) are traditionally carried out by using the single marker regression model that, if a small number of individuals is involved, often lead to very few associations. The Bayesian methods, such as BayesR, have obtained encouraging results when they are applied to the GWAS. However, these approaches, require that an a priori posterior inclusion probability threshold be fixed, thus arbitrarily affecting the obtained associations. To partially overcome these problems, a multivariate statistical algorithm was proposed. The basic idea was that animals with different phenotypic values of a specific trait share different allelic combinations for genes involved in its determinism. Three multivariate techniques were used to highlight the differences between the individuals assembled in high and low phenotype groups: the canonical discriminant analysis, the discriminant analysis and the stepwise discriminant analysis. The multivariate method was tested both on simulated and on real data. The results from the simulation study highlighted that the multivariate GWAS detected a greater number of true associated single nucleotide polymorphisms (SNPs) and Quantitative trait loci (QTLs) than the single marker model and the Bayesian approach. For example, with 3000 animals, the traditional GWAS highlighted only 29 significantly associated markers and 13 QTLs, whereas the multivariate method found 127 associated SNPs and 65 QTLs. The gap between the two approaches slowly decreased as the number of animals increased. The Bayesian method gave worse results than the other two. On average, with the real data, the multivariate GWAS found 108 associated markers for each trait under study and among them, around 63% SNPs were also found in the single marker approach. Among the top 118 associated markers, 76 SNPs harbored putative candidate genes.
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Affiliation(s)
- Elisabetta Manca
- Dipartimento di Agraria, Università degli Studi di Sassari, 07100 Sassari, Italy; (E.M.); (A.C.); (S.S.); (N.P.P.M.)
| | - Alberto Cesarani
- Dipartimento di Agraria, Università degli Studi di Sassari, 07100 Sassari, Italy; (E.M.); (A.C.); (S.S.); (N.P.P.M.)
| | - Giustino Gaspa
- Dipartimento di Scienze Agrarie, Forestali e Ambientali, Università degli studi di Torino, 10095 Grugliasco, Italy;
| | - Silvia Sorbolini
- Dipartimento di Agraria, Università degli Studi di Sassari, 07100 Sassari, Italy; (E.M.); (A.C.); (S.S.); (N.P.P.M.)
| | - Nicolò P.P. Macciotta
- Dipartimento di Agraria, Università degli Studi di Sassari, 07100 Sassari, Italy; (E.M.); (A.C.); (S.S.); (N.P.P.M.)
| | - Corrado Dimauro
- Dipartimento di Agraria, Università degli Studi di Sassari, 07100 Sassari, Italy; (E.M.); (A.C.); (S.S.); (N.P.P.M.)
- Correspondence: ; Tel.: +39079229298
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Boudon S, Ounaissi D, Viala D, Monteils V, Picard B, Cassar-Malek I. Label free shotgun proteomics for the identification of protein biomarkers for beef tenderness in muscle and plasma of heifers. J Proteomics 2020; 217:103685. [DOI: 10.1016/j.jprot.2020.103685] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 01/15/2020] [Accepted: 02/08/2020] [Indexed: 12/21/2022]
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Christensen S, Monteavaro C, Purslow PP. Single-nucleotide polymorphisms for matrix metalloprotease-1 can affect perimysial strength and intramuscular fat content but not growth rate of cattle. ANIMAL PRODUCTION SCIENCE 2020. [DOI: 10.1071/an18789] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Context
Single-nucleotide polymorphisms (SNPs) in the gene coding for matrix metalloprotease-1 (MMP-1) are known to affect the level of intramuscular fat found in cattle. As well as a signalling molecule affecting adipogenesis, MMP-1 is a major collagenase involved in the turnover of connective tissue.
Aims
The aim of the work was to assess whether SNPs in the gene for MMP-1 may affect the mechanical properties of intramuscular connective tissue, and therefore meat texture.
Methods
Allelic frequencies of three SNPs for MMP-1 were determined in a group of black Aberdeen Angus cattle whose growth characteristics had been traced for 450 days before slaughter. Associations between the alleles of each of the three SNPs and growth rate, killing out percentage, half-carcass weight, intramuscular fat content, cooking loss, strength of perimysium in cooked M. semitendinosus and Warner–Bratzler peak force of cooked M. longissimus dorsi were studied.
Key results
None of the SNPs studied had any effect on growth curves, and only one SNP (ss77831914) showed differences in half-carcass weight between alleles. Carcass yield and killing out percentage showed a small difference between alleles of ss7783924. No effects were found on the Warner–Bratzler peak force of M. longissimus dorsi cooked to 70°C. Two SNPs (ss77831914 and ss77831924) showed significant differences between alleles in the raw strength of perimysium in M. semitendinosus and the amount of intramuscular fat.
Conclusions
Commonly occurring SNPs of the major collagenase MMP-1 can affect the strength of intramuscular connective tissue as well as intramuscular fat content. Although these differences in connective tissue strength do not influence Warner–Bratzler measures of toughness at a cooking temperature of 70°C, they may contribute to differences in toughness in low-temperature, long-time cooking.
Implications
Because none of the SNPs had effects on the growth curves of the cattle studied, selection of animals with the relevant alleles of SNPs ss77831914 ss77831924 could be used to produce more tender meat without affecting carcass yield.
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Wang Z, Ma H, Xu L, Zhu B, Liu Y, Bordbar F, Chen Y, Zhang L, Gao X, Gao H, Zhang S, Xu L, Li J. Genome-Wide Scan Identifies Selection Signatures in Chinese Wagyu Cattle Using a High-Density SNP Array. Animals (Basel) 2019; 9:ani9060296. [PMID: 31151238 PMCID: PMC6617538 DOI: 10.3390/ani9060296] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 05/23/2019] [Accepted: 05/24/2019] [Indexed: 12/31/2022] Open
Abstract
Selective breeding can lead to genetic diversity and diverse phenotypes in farm animals. Analysis of the genomic regions under selection can provide important insights into the genetic basis of complex traits. In this study, a high-density SNP array was used for analysis of genome selection signatures in Chinese Wagyu cattle. In total, we obtained 478,903 SNPs and 24,820 no-overlap regions for |iHS| (integrated haplotype score) estimations. Under the threshold of the top 1%, 239 regions were finally identified as candidate selected regions and 162 candidate genes were found based on the UMD3.1 genome assembly. These genes were reported to be associated with fatty acids, such as Bos taurus nitric oxide synthase 1 adaptor protein (NOS1AP), Bos taurus hydroxysteroid 17-beta dehydrogenase 7 (HSD17B7), Bos taurus WD repeat domain 7 (WDR7), Bos taurus ELOVL fatty acid elongase 2 (ELOVL2), Bos taurus calpain 1 (CAPN1), Bos taurus parkin RBR E3 ubiquitin protein ligase (PRKN, also known as PARK2), Bos taurus mitogen-activated protein kinase kinase 6 (MAP2K6), meat quality, including Bos taurus ADAM metallopeptidase domain 12 (ADAM12), Bos taurus 5'-aminolevulinate synthase 1 (ALAS1), Bos taurus small integral membrane protein 13 (SMIM13) and Bos taurus potassium two pore domain channel subfamily K member 2 (KCNK2), growth, and developmental traits, such as Bos taurus insulin like growth factor 2 receptor (IGF2R), Bos taurus RAR related orphan receptor A (RORA), Bos taurus fibroblast growth factor 14 (FGF14), Bos taurus paired box 6 (PAX6) and Bos taurus LIM homeobox 6 (LHX6). In addition, we identified several genes that are associated with body size and weight, including Bos taurus sorting nexin 29 (SNX29), Bos taurus zinc finger imprinted 2 (ZIM2), Bos taurus family with sequence similarity 110 member A (FAM110A), immune system, including Bos taurus toll like receptor 9 (TLR9), Bos taurus TAFA chemokine like family member 1 (TAFA1), Bos taurus glutathione peroxidase 8 (putative) (GPX8), Bos taurus interleukin 5 (IL5), Bos taurus PR domain containing 9 (PRDM9), Bos taurus glutamate ionotropic receptor kainate type subunit 2 (GRIK2) and feed intake efficiency, Bos taurus sodium voltage-gated channel alpha subunit 9 (SCN9A), Bos taurus relaxin family peptide/INSL5 receptor 4 (RXFP4), Bos taurus RNA polymerase II associated protein 3 (RPAP3). Moreover, four GO terms of biological regulation (GO:0009987, GO:0008152) and metabolic process (GO:0003824, GO:0005488) were found based on these genes. In addition, we found that 232 candidate regions (~18 Mb) overlapped with the Quantitative trait loci (QTL)regions extracted from cattle QTLdb. Our findings imply that many genes were selected for important traits in Chinese Wagyu cattle. Moreover, these results can contribute to the understanding of the genetic basis of the studied traits during the formation of this population.
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Affiliation(s)
- Zezhao Wang
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
| | - Haoran Ma
- College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
| | - Lei Xu
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
- Institute of Animal Husbandry and Veterinary Research, Anhui Academy of Agricultural Sciences, Hefei 230031, China.
| | - Bo Zhu
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Ying Liu
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Farhad Bordbar
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Yan Chen
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Lupei Zhang
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Xue Gao
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Huijiang Gao
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Shengli Zhang
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
| | - Lingyang Xu
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Junya Li
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
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Braz CU, Taylor JF, Decker JE, Bresolin T, Espigolan R, Garcia DA, Gordo DGM, Magalhães AFB, de Albuquerque LG, de Oliveira HN. Polymorphism analysis in genes associated with meat tenderness in Nelore cattle. Meta Gene 2018. [DOI: 10.1016/j.mgene.2018.08.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
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11
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Ripoll G, Albertí P, Panea B, Failla S, Hocquette JF, Dunner S, Sañudo C, Olleta JL, Christensen M, Ertbjerg P, Richardson I, Concetti S, Williams JL. Colour variability of beef in young bulls from fifteen European breeds. Int J Food Sci Technol 2018. [DOI: 10.1111/ijfs.13890] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Guillermo Ripoll
- Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA); Instituto Agroalimentario de Aragón - IA2 (CITA-Universidad de Zaragoza); Avda, Montañana, 930 Zaragoza 50059 Spain
| | - Pere Albertí
- Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA); Instituto Agroalimentario de Aragón - IA2 (CITA-Universidad de Zaragoza); Avda, Montañana, 930 Zaragoza 50059 Spain
| | - Begoña Panea
- Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA); Instituto Agroalimentario de Aragón - IA2 (CITA-Universidad de Zaragoza); Avda, Montañana, 930 Zaragoza 50059 Spain
| | - Sebastiana Failla
- Research Centre for Animal Production and Aquaculture; CREA; Monterotondo 00015 Italy
| | - Jean F. Hocquette
- VetAgro Sup, UMR1213; Unité de Recherches sur les Herbivores; Theix; INRA; Saint-Genès Champanelle F-63122 France
| | - Susana Dunner
- Departamento de Producción Animal; Facultad de Veterinaria; Universidad Complutense; Madrid 28040 Spain
| | - Carlos Sañudo
- Instituto Agroalimentario de Aragón - IA2 (CITA-Universidad de Zaragoza); Universidad de Zaragoza; Zaragoza 50013 Spain
| | - José L. Olleta
- Instituto Agroalimentario de Aragón - IA2 (CITA-Universidad de Zaragoza); Universidad de Zaragoza; Zaragoza 50013 Spain
| | | | - Per Ertbjerg
- Department of Food and Environmental Sciences; University of Helsinki; Helsinki FI-00014 Finland
| | - Ian Richardson
- Division of Farm Animal Science; University of Bristol; Bristol BS40 5DU UK
| | - Serafino Concetti
- Research Centre for Animal Production and Aquaculture; CREA; Monterotondo 00015 Italy
| | - John L. Williams
- Davies Research Centre; School of Animal and Veterinary Sciences; University of Adelaide; Roseworthy SA 5371 Australia
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Kowalewska-Łuczak I, Głosińska JI, Czerniawska-Piątkowska E. Effect of UCP2 and UCP3 Genes Polymorphisms on Functional Traits in Dairy Cattle. RUSS J GENET+ 2018. [DOI: 10.1134/s1022795418070074] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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13
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Ekine-Dzivenu C, Vinsky M, Basarab JA, Aalhus JL, Dugan MER, Li C. Phenotypic and genetic correlations of fatty acid composition in subcutaneous adipose tissue with carcass merit and meat tenderness traits in Canadian beef cattle. J Anim Sci 2017; 95:5184-5196. [PMID: 29293784 PMCID: PMC6292258 DOI: 10.2527/jas2017.1966] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 09/20/2017] [Indexed: 01/11/2023] Open
Abstract
Bivariate animal models were used to estimate phenotypic and genetic correlations between 9 carcass merit and meat tenderness traits with 25 individual and grouped fatty acids in the subcutaneous adipose tissue of a population of 1,366 Canadian beef cattle finishing heifers and steers. In general, phenotypic correlations were low (<0.25 in magnitude) except for moderate phenotypic correlations of 9-17:1 (-0.29 ± 0.16), 18:0 (0.26 ± 0.14), 11-18:1 (-0.33 ± 0.15), 11-18:1 (0.35 ± 0.14) with Warner-Bratzler shear force measured 3 d postmortem and between 14:0 (-0.36 ± 0.1), 9-14:1 (-0.34 ± 0.08), 9-16:1 (-0.36 ± 0.08), 9-18:1 (0.26 ± 0.07), and sum of branched-chain fatty acids (BCFA; -0.27 ± 0.06) and back fat thickness (BFAT). Genetic correlations were also low for most of the traits. However, moderate to moderately high genetic correlations (0.25 to 0.50 in magnitude) were detected for some traits, including 17:0 (0.4 ± 0.11), 18:0 (0.44 ± 0.12), 9-14:1 (-0.47 ± 0.11), 9-16:1 (-0.43 ± 0.11), and the -6:-3 PUFA ratio (-0.5 ± 0.15) with HCW; 9-14:1 (-0.41 ± 0.13) and 9-16:1 (-0.42 ± 0.13) with BFAT; 17:0 (0.43 ± 0.19) and BCFA (0.45 ± 0.19) with lean meat yield; 13-18:1 (0.40 ± 0.15) with carcass marbling score; sum of CLA (0.45 ± 0.22), 18:2-6 (0.47 ± 0.17), and sum of PUFA (0.48 ± 0.17) with overall tenderness measured 3 d postmortem; the -6:-3 PUFA ratio (0.41 ± 0.22) and sum of CLA (0.42 ± 0.25) with overall tenderness measured 29 d postmortem; and BCFA (0.41 ± 0.27) with Warner-Bratzler shear force measured 29 d postmortem. The genetic correlations observed in this study suggest that contents of some fatty acids in beef tissue and carcass merit and meat tenderness traits are likely influenced by a subset of the same genes in beef cattle. Due to some antagonistic genetic correlations, multiple-trait economic indexes are recommended when fatty acid composition, carcass merit, and meat tenderness traits are included in the breeding objective.
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Integrating genome and transcriptome profiling for elucidating the mechanism of muscle growth and lipid deposition in Pekin ducks. Sci Rep 2017. [PMID: 28630415 PMCID: PMC5476626 DOI: 10.1038/s41598-017-04178-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Muscle growth and lipid deposition are co-ordinately regulated processes. Cherry Valley Pekin duck is a lean-type duck breed with high growth rate, whereas the native Pekin duck of China has high lipid deposition. Phenotypic analysis showed that native Pekin ducks have smaller fibre diameter and larger density in the breast muscle at 3 weeks of age and higher intramuscular fat content at 6 weeks of age than those in Cherry Valley Pekin ducks. We detected 17 positively selected genes (PSGs) by comparing genes mainly involved with muscle organ development, muscle contraction, peroxisome proliferator activated receptor signalling pathway, and fatty acid metabolism. In all, 52 and 206 differentially expressed genes (DEGs) were identified in transcriptomic comparisons between the two breeds at 3 and 6 weeks of age, respectively, which could potentially affect muscle growth and lipid deposition. Based on the integration of PSGs and DEGs and their functional annotations, we found that 11 and 10 genes were correlated with muscle growth and lipid deposition, respectively. Identification of candidate genes controlling quantitative traits of duck muscle might aid in elucidating the mechanisms of muscle growth and lipid deposition and could help in improving duck breeding.
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15
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Christensen S, Purslow PP. The role of matrix metalloproteinases in muscle and adipose tissue development and meat quality: A review. Meat Sci 2016; 119:138-46. [PMID: 27180222 DOI: 10.1016/j.meatsci.2016.04.025] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Revised: 04/18/2016] [Accepted: 04/19/2016] [Indexed: 11/29/2022]
Abstract
Matrix metalloproteinases (MMPs) are a group of enzymes that degrade extracellular matrix components but are also important signaling molecules that regulate many biological processes including muscle, adipose and connective tissue development. Most recently it has been discovered that MMPs act as intracellular signaling molecules inducing gene expression and altering related proteins in the nucleus. Several single nucleotide polymorphisms of MMPs and their inhibitors are known to exist and most of the research on MMPs to date has focused on their activity in relation to human health and disease. Nevertheless there is a growing body of evidence identifying important roles of MMPs as regulators of myogenesis, fibrogenesis and adipogenesis. The aim of this review is to highlight the currently known functions of the MMPs that have a direct bearing on the deposition of meat components and their relationship with meat quality. Some central pathways by which these enzymes can affect the tenderness, the amount and type of fatty acids are highlighted.
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Affiliation(s)
- Sara Christensen
- Departamento de Tecnología y Calidad de los Alimentos, Facultad de Ciencias Veterinarias, Universidad Nacional del Centro de la Provincia de Buenos Aires, Tandil, Argentina
| | - Peter P Purslow
- Departamento de Tecnología y Calidad de los Alimentos, Facultad de Ciencias Veterinarias, Universidad Nacional del Centro de la Provincia de Buenos Aires, Tandil, Argentina.
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16
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Kim W, Park H, Seo S. Global Metabolic Reconstruction and Metabolic Gene Evolution in the Cattle Genome. PLoS One 2016; 11:e0150974. [PMID: 26992093 PMCID: PMC4798299 DOI: 10.1371/journal.pone.0150974] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Accepted: 02/22/2016] [Indexed: 11/23/2022] Open
Abstract
The sequence of cattle genome provided a valuable opportunity to systematically link genetic and metabolic traits of cattle. The objectives of this study were 1) to reconstruct genome-scale cattle-specific metabolic pathways based on the most recent and updated cattle genome build and 2) to identify duplicated metabolic genes in the cattle genome for better understanding of metabolic adaptations in cattle. A bioinformatic pipeline of an organism for amalgamating genomic annotations from multiple sources was updated. Using this, an amalgamated cattle genome database based on UMD_3.1, was created. The amalgamated cattle genome database is composed of a total of 33,292 genes: 19,123 consensus genes between NCBI and Ensembl databases, 8,410 and 5,493 genes only found in NCBI or Ensembl, respectively, and 266 genes from NCBI scaffolds. A metabolic reconstruction of the cattle genome and cattle pathway genome database (PGDB) was also developed using Pathway Tools, followed by an intensive manual curation. The manual curation filled or revised 68 pathway holes, deleted 36 metabolic pathways, and added 23 metabolic pathways. Consequently, the curated cattle PGDB contains 304 metabolic pathways, 2,460 reactions including 2,371 enzymatic reactions, and 4,012 enzymes. Furthermore, this study identified eight duplicated genes in 12 metabolic pathways in the cattle genome compared to human and mouse. Some of these duplicated genes are related with specific hormone biosynthesis and detoxifications. The updated genome-scale metabolic reconstruction is a useful tool for understanding biology and metabolic characteristics in cattle. There has been significant improvements in the quality of cattle genome annotations and the MetaCyc database. The duplicated metabolic genes in the cattle genome compared to human and mouse implies evolutionary changes in the cattle genome and provides a useful information for further research on understanding metabolic adaptations of cattle.
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Affiliation(s)
- Woonsu Kim
- Department of Animal Biosystem Sciences, Chungnam National University, Daejeon, Republic of Korea
| | - Hyesun Park
- Department of Animal Biosystem Sciences, Chungnam National University, Daejeon, Republic of Korea
| | - Seongwon Seo
- Department of Animal Biosystem Sciences, Chungnam National University, Daejeon, Republic of Korea
- * E-mail:
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17
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Modzelewska-Kapituła M, Nogalski Z, Kwiatkowska A. The influence of crossbreeding on collagen solubility and tenderness of Infraspinatus and Semimembranosus muscles of semi-intensively reared young bulls. Anim Sci J 2016; 87:1312-1321. [DOI: 10.1111/asj.12581] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Revised: 09/18/2015] [Accepted: 10/29/2015] [Indexed: 11/29/2022]
Affiliation(s)
- Monika Modzelewska-Kapituła
- Department of Industrial Commodity, Basics of Techniques and Energy Management, Faculty of Food Sciences; University of Warmia and Mazury in Olsztyn; Olsztyn Poland
| | - Zenon Nogalski
- Department of Cattle Breeding and Milk Evaluation, Faculty of Animal Bioengineering; University of Warmia and Mazury in Olsztyn; Olsztyn Poland
| | - Aleksandra Kwiatkowska
- Department of Meat Technology and Chemistry, Faculty of Food Sciences; University of Warmia and Mazury in Olsztyn; Olsztyn Poland
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18
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Mazzetto A, Feigl B, Schils R, Cerri C, Cerri C. Improved pasture and herd management to reduce greenhouse gas emissions from a Brazilian beef production system. Livest Sci 2015. [DOI: 10.1016/j.livsci.2015.02.014] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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19
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Dang CG, Cho SH, Sharma A, Kim HC, Jeon GJ, Yeon SH, Hong SK, Park BY, Kang HS, Lee SH. Genome-wide Association Study for Warner-Bratzler Shear Force and Sensory Traits in Hanwoo (Korean Cattle). ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2014; 27:1328-35. [PMID: 25178377 PMCID: PMC4150200 DOI: 10.5713/ajas.2013.13690] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2013] [Revised: 03/02/2014] [Accepted: 04/11/2014] [Indexed: 01/23/2023]
Abstract
Significant SNPs associated with Warner-Bratzler (WB) shear force and sensory traits were confirmed for Hanwoo beef (Korean cattle). A Bonferroni-corrected genome-wide significant association (p<1.3×10−6) was detected with only one single nucleotide polymorphism (SNP) on chromosome 5 for WB shear force. A slightly higher number of SNPs was significantly (p<0.001) associated with WB shear force than with other sensory traits. Further, 50, 25, 29, and 34 SNPs were significantly associated with WB shear force, tenderness, juiciness, and flavor likeness, respectively. The SNPs between p = 0.001 and p = 0.0001 thresholds explained 3% to 9% of the phenotypic variance, while the most significant SNPs accounted for 7% to 12% of the phenotypic variance. In conclusion, because WB shear force and sensory evaluation were moderately affected by a few loci and minimally affected by other loci, further studies are required by using a large sample size and high marker density.
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Affiliation(s)
- C G Dang
- Animal Product Research and Development Division, National Institute of Animal Science, Rural Development Administration, Suwon 441-706, Korea
| | - S H Cho
- Animal Product Research and Development Division, National Institute of Animal Science, Rural Development Administration, Suwon 441-706, Korea
| | - A Sharma
- Animal Product Research and Development Division, National Institute of Animal Science, Rural Development Administration, Suwon 441-706, Korea
| | - H C Kim
- Animal Product Research and Development Division, National Institute of Animal Science, Rural Development Administration, Suwon 441-706, Korea
| | - G J Jeon
- Animal Product Research and Development Division, National Institute of Animal Science, Rural Development Administration, Suwon 441-706, Korea
| | - S H Yeon
- Animal Product Research and Development Division, National Institute of Animal Science, Rural Development Administration, Suwon 441-706, Korea
| | - S K Hong
- National Institute of Animal Science, Rural Development Administration, Suwon 441-706, Korea
| | - B Y Park
- Animal Product Research and Development Division, National Institute of Animal Science, Rural Development Administration, Suwon 441-706, Korea
| | - H S Kang
- Animal Product Research and Development Division, National Institute of Animal Science, Rural Development Administration, Suwon 441-706, Korea
| | - S H Lee
- Animal Product Research and Development Division, National Institute of Animal Science, Rural Development Administration, Suwon 441-706, Korea
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Polymorphisms in twelve candidate genes are associated with growth, muscle lipid profile and meat quality traits in eleven European cattle breeds. Mol Biol Rep 2014; 41:4721-31. [DOI: 10.1007/s11033-014-3343-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2013] [Accepted: 03/21/2014] [Indexed: 10/25/2022]
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21
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Sevane N, Nute G, Sañudo C, Cortes O, Cañon J, Williams J, Dunner S. Muscle lipid composition in bulls from 15 European breeds. Livest Sci 2014. [DOI: 10.1016/j.livsci.2013.11.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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