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Arikawa LM, Mota LFM, Schmidt PI, Frezarim GB, Fonseca LFS, Magalhães AFB, Silva DA, Carvalheiro R, Chardulo LAL, Albuquerque LGD. Genome-wide scans identify biological and metabolic pathways regulating carcass and meat quality traits in beef cattle. Meat Sci 2024; 209:109402. [PMID: 38056170 DOI: 10.1016/j.meatsci.2023.109402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 10/19/2023] [Accepted: 11/28/2023] [Indexed: 12/08/2023]
Abstract
Genome association studies (GWAS) provides knowledge about the genetic architecture of beef-related traits that allow linking the target phenotype to genomic information aiding breeding decision. Thus, the present study aims to uncover the genetic mechanism involved in carcass (REA: rib eye area, BF: backfat thickness, and HCW: hot carcass weight) and meat quality traits (SF: shear-force, MARB: marbling score, and IMF: intramuscular fat content) in Nellore cattle. For this, 6910 young bulls with phenotypic information and 23,859 animals genotyped with 435 k markers were used to perform the weighted single-step GBLUP (WssGBLUP) approach, considering two iterations. The top 10 genomic regions explained 8.13, 11.81, and 9.58% of the additive genetic variance, harboring a total of 119, 143, and 95 positional candidate genes for REA, BF, and HCW, respectively. For meat quality traits, the top 10 windows explained a large proportion of the total genetic variance for SF (14.95%), MARB (17.56%), and IMF (21.41%) surrounding 92, 155, and 111 candidate genes, respectively. Relevant candidate genes (CAST, PLAG1, XKR4, PLAGL2, AQP3/AQP7, MYLK2, WWOX, CARTPT, and PLA2G16) are related to physiological aspects affecting growth, carcass, meat quality, feed intake, and reproductive traits by signaling pathways controlling muscle control, key signal metabolic molecules INS / IGF-1 pathway, lipid metabolism, and adipose tissue development. The GWAS results provided insights into the genetic control of the traits studied and the genes found are potential candidates to be used in the improvement of carcass and meat quality traits.
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Affiliation(s)
- Leonardo Machestropa Arikawa
- São Paulo State University (UNESP), School of Agricultural and Veterinarian Sciences, Department of Animal Science, Via de Acesso Prof. Paulo Donato Castelane, Jaboticabal, SP 14884-900, Brazil.
| | - Lucio Flavio Macedo Mota
- São Paulo State University (UNESP), School of Agricultural and Veterinarian Sciences, Department of Animal Science, Via de Acesso Prof. Paulo Donato Castelane, Jaboticabal, SP 14884-900, Brazil
| | - Patrícia Iana Schmidt
- São Paulo State University (UNESP), School of Agricultural and Veterinarian Sciences, Department of Animal Science, Via de Acesso Prof. Paulo Donato Castelane, Jaboticabal, SP 14884-900, Brazil
| | - Gabriela Bonfá Frezarim
- São Paulo State University (UNESP), School of Agricultural and Veterinarian Sciences, Department of Animal Science, Via de Acesso Prof. Paulo Donato Castelane, Jaboticabal, SP 14884-900, Brazil
| | - Larissa Fernanda Simielli Fonseca
- São Paulo State University (UNESP), School of Agricultural and Veterinarian Sciences, Department of Animal Science, Via de Acesso Prof. Paulo Donato Castelane, Jaboticabal, SP 14884-900, Brazil
| | - Ana Fabrícia Braga Magalhães
- São Paulo State University (UNESP), School of Agricultural and Veterinarian Sciences, Department of Animal Science, Via de Acesso Prof. Paulo Donato Castelane, Jaboticabal, SP 14884-900, Brazil; University of Jequitinhonha and Mucuri Valleys, Department of Animal Science, Rod. MG 367, Diamantina, MG 39100-000, Brazil
| | - Delvan Alves Silva
- São Paulo State University (UNESP), School of Agricultural and Veterinarian Sciences, Department of Animal Science, Via de Acesso Prof. Paulo Donato Castelane, Jaboticabal, SP 14884-900, Brazil; University of Viçosa, Department of Animal Science, Av. PH Rolfs, Viçosa, MG 36570-900, Brazil
| | - Roberto Carvalheiro
- São Paulo State University (UNESP), School of Agricultural and Veterinarian Sciences, Department of Animal Science, Via de Acesso Prof. Paulo Donato Castelane, Jaboticabal, SP 14884-900, Brazil
| | - Luis Artur Loyola Chardulo
- São Paulo State University (UNESP), School of Agricultural and Veterinarian Sciences, Department of Animal Science, Via de Acesso Prof. Paulo Donato Castelane, Jaboticabal, SP 14884-900, Brazil; National Council for Science and Technological Development, Brasilia, DF 71605-001, Brazil
| | - Lucia Galvão de Albuquerque
- São Paulo State University (UNESP), School of Agricultural and Veterinarian Sciences, Department of Animal Science, Via de Acesso Prof. Paulo Donato Castelane, Jaboticabal, SP 14884-900, Brazil; National Council for Science and Technological Development, Brasilia, DF 71605-001, Brazil.
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He W, Fang X, Lu X, Liu Y, Li G, Zhao Z, Li J, Yang R. Function Identification of Bovine ACSF3 Gene and Its Association With Lipid Metabolism Traits in Beef Cattle. Front Vet Sci 2022; 8:766765. [PMID: 35071379 PMCID: PMC8770830 DOI: 10.3389/fvets.2021.766765] [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: 08/30/2021] [Accepted: 12/13/2021] [Indexed: 11/24/2022] Open
Abstract
Acyl-CoA synthetase family member 3 (ACSF3) carries out the first step of mitochondrial fatty acid synthesis II, which is the linkage of malonate and, to a lesser extent, methylmalonate onto CoA. Malonyl-coenzyme A (malonyl-CoA) is a central metabolite in mammalian fatty acid biochemistry that is generated and utilized in the cytoplasm. In this research, we verified the relationship between expression of the ACSF3 and the production of triglycerides (TGs) at the cellular level by silencing and over-expressing ACSF3. Subsequently, through Sanger sequencing, five polymorphisms were found in the functional domain of the bovine ACSF3, and the relationship between ACSF3 polymorphism and the economic traits and fatty acid composition of Chinese Simmental cattle was analyzed by a means of variance analysis and multiple comparison. The results illustrated that the expression of ACSF3 promoted triglyceride synthesis in bovine mammary epithelial cells and bovine fetal fibroblast cells. Further association analysis also indicated that individuals with the AG genotype (g.14211090 G > A) of ACSF3 were significantly associated with the fatty acid composition of intramuscular fat (higher content of linoleic acid, α-linolenic acid, and arachidonic acid), and that CTCAG haplotype individuals were significantly related to the fatty acid composition of intramuscular fat (higher linoleic acid content). Individuals with the AA genotypes of g.14211055 A > G and g.14211090 G > A were substantially associated with a larger eye muscle area in the Chinese Simmental cattle population. ACSF3 played a pivotal role in the regulation of cellular triacylglycerol and long-chain polyunsaturated fatty acid levels, and polymorphism could serve as a useful molecular marker for future marker-assisted selection in the breeding of intramuscular fat deposition traits in beef cattle.
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Affiliation(s)
- Wei He
- College of Animal Science, Jilin University, Changchun, China
| | - Xibi Fang
- College of Animal Science, Jilin University, Changchun, China
| | - Xin Lu
- College of Animal Science, Jilin University, Changchun, China
| | - Yue Liu
- College of Animal Science, Jilin University, Changchun, China
| | - Guanghui Li
- College of Animal Science, Jilin University, Changchun, China
| | - Zhihui Zhao
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, China
| | - Junya Li
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Runjun Yang
- College of Animal Science, Jilin University, Changchun, China
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Kappeler BIG, Regitano LCA, Poleti MD, Cesar ASM, Moreira GCM, Gasparin G, Coutinho LL. MiRNAs differentially expressed in skeletal muscle of animals with divergent estimated breeding values for beef tenderness. BMC Mol Biol 2019; 20:1. [PMID: 30602381 PMCID: PMC6317189 DOI: 10.1186/s12867-018-0118-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 12/20/2018] [Indexed: 12/16/2022] Open
Abstract
Background MicroRNAs (miRNAs) are small noncoding RNAs of approximately 22 nucleotides, highly conserved among species, which modulate gene expression by cleaving messenger RNA target or inhibiting translation. MiRNAs are involved in the regulation of many processes including cell proliferation, differentiation, neurogenesis, angiogenesis, and apoptosis. Beef tenderness is an organoleptic characteristic of great influence in the acceptance of meat by consumers. Previous studies have shown that collagen level, marbling, apoptosis and proteolysis are among the many factors that affect beef tenderness. Considering that miRNAs can modulate gene expression, this study was designed to identify differentially expressed miRNAs that could be modulating biological processes involved with beef tenderness. Results Deep sequence analysis of miRNA libraries from longissimus thoracis muscle allowed the identification of 42 novel and 308 known miRNAs. Among the known miRNAs, seven were specifically expressed in skeletal muscle. Differential expression analysis between animals with high (H) and low (L) estimated breeding values for shear force (EBVSF) revealed bta-mir-182 and bta-mir-183 are up-regulated (q value < 0.05) in animals with L EBVSF, and bta-mir-338 is up-regulated in animals with H EBVSF. The number of bovine predicted targets for bta-mir-182, bta-mir-183 and bta-mir-338 were 811, 281 and 222, respectively, which correspond to 1204 unique target genes. Among these, four of them, MEF2C, MAP3K2, MTDH and TNRC6B were common targets of the three differentially expressed miRNAs. The functional analysis identified important pathways related to tenderness such as apoptosis and the calpain–calpastatin system. Conclusion The results obtained indicate the importance of miRNAs in the regulatory mechanisms that influence muscle proteolysis and meat tenderness and contribute to our better understanding of the role of miRNAs in biological processes associated with beef tenderness. Electronic supplementary material The online version of this article (10.1186/s12867-018-0118-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Berna I G Kappeler
- Department of Animal Science, "Luiz de Queiroz" College of Agriculture, University of São Paulo, Piracicaba, SP, 13418-900, Brazil
| | | | - Mirele D Poleti
- Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of São Paulo, Pirassununga, SP, 13635-900, Brazil
| | - Aline S M Cesar
- Department of Animal Science, "Luiz de Queiroz" College of Agriculture, University of São Paulo, Piracicaba, SP, 13418-900, Brazil
| | - Gabriel C M Moreira
- Department of Animal Science, "Luiz de Queiroz" College of Agriculture, University of São Paulo, Piracicaba, SP, 13418-900, Brazil
| | - Gustavo Gasparin
- Department of Animal Science, "Luiz de Queiroz" College of Agriculture, University of São Paulo, Piracicaba, SP, 13418-900, Brazil
| | - Luiz L Coutinho
- Department of Animal Science, "Luiz de Queiroz" College of Agriculture, University of São Paulo, Piracicaba, SP, 13418-900, Brazil.
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Sequence and Haplotypes Variation of the Ovine Uncoupling Protein-1 Gene (UCP1) and Their Association with Growth and Carcass Traits in New Zealand Romney Lambs. Genes (Basel) 2018; 9:genes9040189. [PMID: 29601527 PMCID: PMC5924531 DOI: 10.3390/genes9040189] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 03/12/2018] [Accepted: 03/28/2018] [Indexed: 11/21/2022] Open
Abstract
Uncoupling protein-1 gene (UCP1) plays an important role in the regulation of thermogenesis, energy expenditure, and protection against oxidative stress. In this study, six separate UCP1 regions: region-1 and region-2 (two parts of the promoter), region-3 and region-4 (two parts of intron 1), region-5 (spanning part of intron 5 and part of exon 6), and region-6 (spanning part of exon 6 and part of the 3′-UTR) from a variety of sheep breeds, were analysed using polymerase chain reaction-single-stranded conformational polymorphism (PCR-SSCP) analyses. In total, 30 single nucleotide polymorphisms (SNPs) were detected. Of these, 14 were located in the promoter, eight were found in intron 1, six were found in intron 5, and one was found in the 3′-UTR. One substitution in exon 6 (c.910A/G) would putatively result in an amino acid change (p.Thr304Ala). Twenty-eight novel SNPs and nine new haplotypes spanning region-2 to region-5 were identified. Of these nine haplotypes, five were common (B2-A5, C2-A5, C2-C5, A2-A5, and A2-B5) and four were rare (C2-B5, A2-C5, B2-C5, and B2-B5) in the sheep investigated. Of the five common haplotypes found in 314 New Zealand Romney sheep for which growth and carcass trait data were available, the presence of A2-B5 was associated with decreased hot carcass weight (HCW) and loin lean-meat yield (p = 0.006, p = 0.032, respectively), and the presence of C2-C5 was associated with a decreased proportion of leg lean-meat yield (p = 0.047) in the carcasses. No associations were found with growth traits. These results confirm that ovine UCP1 is a variable gene and may have value as a genetic marker for sheep breeding.
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Whole-genome sequencing reveals mutational landscape underlying phenotypic differences between two widespread Chinese cattle breeds. PLoS One 2017; 12:e0183921. [PMID: 28841720 PMCID: PMC5571935 DOI: 10.1371/journal.pone.0183921] [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] [Received: 03/26/2017] [Accepted: 08/10/2017] [Indexed: 12/01/2022] Open
Abstract
Whole-genome sequencing provides a powerful tool to obtain more genetic variability that could produce a range of benefits for cattle breeding industry. Nanyang (Bos indicus) and Qinchuan (Bos taurus) are two important Chinese indigenous cattle breeds with distinct phenotypes. To identify the genetic characteristics responsible for variation in phenotypes between the two breeds, in the present study, we for the first time sequenced the genomes of four Nanyang and four Qinchuan cattle with 10 to 12 fold on average of 97.86% and 98.98% coverage of genomes, respectively. Comparison with the Bos_taurus_UMD_3.1 reference assembly yielded 9,010,096 SNPs for Nanyang, and 6,965,062 for Qinchuan cattle, 51% and 29% of which were novel SNPs, respectively. A total of 154,934 and 115,032 small indels (1 to 3 bp) were found in the Nanyang and Qinchuan genomes, respectively. The SNP and indel distribution revealed that Nanyang showed a genetically high diversity as compared to Qinchuan cattle. Furthermore, a total of 2,907 putative cases of copy number variation (CNV) were identified by aligning Nanyang to Qinchuan genome, 783 of which (27%) encompassed the coding regions of 495 functional genes. The gene ontology (GO) analysis revealed that many CNV genes were enriched in the immune system and environment adaptability. Among several CNV genes related to lipid transport and fat metabolism, Lepin receptor gene (LEPR) overlapping with CNV_1815 showed remarkably higher copy number in Qinchuan than Nanyang (log2 (ratio) = -2.34988; P value = 1.53E-102). Further qPCR and association analysis investigated that the copy number of the LEPR gene presented positive correlations with transcriptional expression and phenotypic traits, suggesting the LEPR CNV may contribute to the higher fat deposition in muscles of Qinchuan cattle. Our findings provide evidence that the distinct phenotypes of Nanyang and Qinchuan breeds may be due to the different genetic variations including SNPs, indels and CNV.
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Kaczor U, Poltowicz K, Kucharski M, Sitarz AM, Nowak J, Wojtysiak D, Zieba DA. Effect of ghrelin and leptin receptors genes polymorphisms on production results and physicochemical characteristics of M. pectoralis superficialis in broiler chickens. ANIMAL PRODUCTION SCIENCE 2017. [DOI: 10.1071/an15152] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Ghrelin and leptin and their receptors GHSR and LEPR regulate food intake, the processes in adipose tissue, and the body’s energy homeostasis in mammals. The aim of the present study was to determine the effect of GHSR/Csp6I and LEPR/Bsh1236I polymorphisms on the meat production parameters of broiler chickens reared to 42 days of age. In 318 fast-growing Hubbard Flex and Ross 308 chickens, g.3051C > T substitution at the GHSR locus and a GGTCAA deletion at positions g.3407_3409del and g.3411_3413del were identified. The use of restriction enzyme Bsh1236I showed the presence of two transitions g.352C > T and g.427G > A in LEPR locus. The chickens were classified into four GHSR/Csp6I and into five LEPR/Bsh1236I diplotypes. GHSR and LEPR polymorphisms were found to influence final bodyweight, daily gain, dressing percentage without giblets, proportion of giblets and the quality characteristics of M. pectoralis superficialis. GHSR/Csp6I and LEPR/Bsh1236I had an effect on pH24 h (P < 0.05) and lightness (L*) of M. pectoralis superficialis (P < 0.05), whereas GHSR/Csp6I influenced shear force (P < 0.05) and thawing loss (P < 0.05). GHSR/Csp6I and LEPR/Bsh1236I were found to have no effect on the abdominal fat content in chicken carcasses. Single nucleotide polymorphisms reported in the present study could be used in breeding programs as selection markers for growth traits and poultry meat quality.
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Juszczuk-Kubiak E, Bujko K, Grześ M, Cymer M, Wicińska K, Szostak A, Pierzchała M. Study of bovine gene: the temporal-spatial expression patterns, polymorphism and association analysis with meat production traits. J Anim Sci 2016; 94:4536-4548. [PMID: 27898947 DOI: 10.2527/jas.2016-0741] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The gene () encodes a transcription factor belonging to the MEF2 family that plays an important role in myogenesis by transcriptional regulation of genes involved in skeletal muscle growth and development. Despite the established importance of the factors in the muscular growth and development, the temporal-spatial expression and biological function of have not been reported in cattle. The aim of this study was to analyze the level of expression in the developing longissimus dorsi muscle (LM) of 4 cattle breeds (Polish Holstein-Friesian [HF], Limousine [LIM], Hereford [HER], Polish Red [PR]), differing in terms of meat production and utility type, at 6, 9, and 12 mo of age. The genetic polymorphism and expression patterns in 6 tissues (heart, spleen, liver, semitendinosus muscle [ST], gluteus medius muscle [GM], and LM) were also investigated. The results showed that mRNA was expressed at a high level in adult skeletal and cardiac muscles. Moreover, expression was markedly greater in the GM than in the LM ( 0.05) and ST ( 0.01). An age-dependent and breed-specific comparison of mRNA level in skeletal muscle of HF, LIM, HER, and PR bulls showed that age was significant differentiating factor of transcript/protein abundance in the LM of HER and LIM ( 0.001) compared to HF and PR, for which the differences in mRNA level were not significant ( > 0.05). Regarding the breed effect on the expression, significantly greater mRNA/protein level was noticed in the LM of 9 and 12 mo-old HER than of LIM ( 0.01), HF ( 0.001), and PR ( 0.001). Four novel SNP, namely, (promoter), (exon 7), (exon 8), and (3'UTR), were identified. We found that 3'UTR variant, situated within the seed region of the miR-5187-3p and miR-6931-5p binding sites, was associated with the level of mRNA/protein in LM of 12-mo-old HF bulls. In addition, we observed a significant association between some carcass quality traits, including meat and carcass fatness quality traits, and various 3'UTR genotypes in the investigated population of HF cattle. Our finding provides new evidence of the significant role in the postnatal muscle growth and development in cattle, and indicates that can be a promising molecular marker for carcass quality-related traits in adult cattle.
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Growth, carcass and meat quality traits in beef from Angus, Hereford and cross-breed grazing steers, and their association with SNPs in genes related to fat deposition metabolism. Meat Sci 2016; 114:121-129. [DOI: 10.1016/j.meatsci.2015.12.018] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Revised: 12/11/2015] [Accepted: 12/23/2015] [Indexed: 11/18/2022]
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Tissue expression and predicted protein structures of the bovine ANGPTL3 and association of novel SNPs with growth and meat quality traits. Animal 2015; 9:1285-97. [DOI: 10.1017/s1751731115000658] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
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10
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Feng X, Yu X, Tong J. Novel single nucleotide polymorphisms of the insulin-like growth factor-I gene and their associations with growth traits in common carp (Cyprinus carpio L.). Int J Mol Sci 2014; 15:22471-82. [PMID: 25486058 PMCID: PMC4284719 DOI: 10.3390/ijms151222471] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Revised: 11/08/2014] [Accepted: 11/10/2014] [Indexed: 11/16/2022] Open
Abstract
Insulin-like growth factor-I (IGF-I) plays an important role in the growth and development of vertebrates. To study polymorphisms of IGF-I, we screened a total of 4555 bp of genomic sequences in four exons and partial introns for the discovery of single nucleotide polymorphism (SNP) in common carp (Cyprinus carpio). Three SNPs (g.3759T>G, g.7627T>A and g.7722T>C) in intron 2 and a nonsynonymous SNP (g.7892C>T) in exon 3 were identified in a pilot population including random parents and their progenies. 289 progenies were further genotyped for studying possible associations between genotypes or combined genotypes and growth traits. The results showed that the locus g.7627T>A was significantly associated with body weight and body length, and fish with genotype AA had a mean body weight 5.9% higher than those with genotype TT. No significant associations were observed between genotypes of other loci and growth traits. However, when both g.7627T>A and g.7722T>C were considered, the combined genotype TT/TT was extremely associated with the lowest values of body length and body weight and the highest K value in comparison with other diplotypes (p < 0.01). These results suggest that genotype AA at g.7627T>A and its combined genotypes with alleles from another locus have positive effects on growth traits, which would be a candidate molecular marker for further studies in marker-assisted selection in common carp.
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Affiliation(s)
- Xiu Feng
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, the Chinese Academy of Sciences, Wuhan 430072, China.
| | - Xiaomu Yu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, the Chinese Academy of Sciences, Wuhan 430072, China.
| | - Jingou Tong
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, the Chinese Academy of Sciences, Wuhan 430072, China.
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Meirelles FV, Bressan FF, Smith LC, Perecin F, Chiaratti MR, Ferraz JBS. Cytoplasmatic inheritance, epigenetics and reprogramming DNA as tools in animal breeding. Livest Sci 2014. [DOI: 10.1016/j.livsci.2014.05.024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Juszczuk-Kubiak E, Wicińska K, Starzyński RR. Postnatal expression patterns and polymorphism analysis of the bovine myocyte enhancer factor 2C (Mef2C) gene. Meat Sci 2014; 98:753-8. [PMID: 25108515 DOI: 10.1016/j.meatsci.2014.06.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Accepted: 06/13/2014] [Indexed: 10/25/2022]
Abstract
The aim of this study was to analyze the level of expression of the Mef2C gene in the developing bovine longissimus dorsi (LD) muscle (at 6, 9 and 12months of age) and to evaluate differences in expression among Polish Holstein-Friesian (HO) and Limousine (LM) bulls. Moreover, the expression patterns of Mef2C in different tissues were determined. The results showed that Mef2C mRNA was expressed at a high level in adult skeletal and cardiac muscles. Moreover, Mef2C expression was markedly lower in the semitendinosus (ST) than in the gluteus medius (GM) and LD muscles. A relatively higher Mef2C mRNA and MEF2C protein level was estimated in the muscles of HO bulls at the age of 12months in comparison with its lower expression in LM bulls. Furthermore, we found that the Mef2C promoter variant (GU211004:g.-1606C>T) does not affect the level of mRNA in the LD and ST muscles of 12-month-old HO bulls.
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Affiliation(s)
- E Juszczuk-Kubiak
- Department of Molecular Cytogenetics, Institute of Genetics and Animal Breeding of the Polish Academy of Sciences, Jastrzębiec, Poland.
| | - K Wicińska
- Department of Molecular Cytogenetics, Institute of Genetics and Animal Breeding of the Polish Academy of Sciences, Jastrzębiec, Poland
| | - R R Starzyński
- Department of Molecular Biology, Institute of Genetics and Animal Breeding of the Polish Academy of Sciences, Jastrzębiec, Poland
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Mohammadi H, Shahrebabak MM, Sadeghi M. Association between single nucleotide polymorphism in the ovine DGAT1 gene and carcass traits in two Iranian sheep breeds. Anim Biotechnol 2013; 24:159-67. [PMID: 23777346 DOI: 10.1080/10495398.2013.763816] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
The aim of the study was to investigate the single nucleotide polymorphisms (SNPs) at 16-17 exon of DGAT1 gene in Lori-Bakhtiari sheep (LB) and Zel sheep (Z) breeds and provide a foundation for studying the relationship of DGAT1 gene with some carcass traits and the genetic relationship between LB sheep and Z sheep breeds. A total of 309 sheep were slaughtered and the carcass weight, backfat thickness, fat-tail weight, fat-tail percentage, dressing percentage, and dressing percentage adjusted to fat-tail weight were measured. Single nucleotide polymorphism was detected by comparing sequences of PCR products, and the restriction fragment length polymorphism (RFLP) technique was adopted for genotyping. The results of PCR-RFLP analysis showed that the SNP had three genotypes of TT (272 and 37 bp), TC (309, 272, and 37 bp), and CC (309 bp), in which TT was the predominant genotype and allele T was predominant allele in LB and Z sheep breeds. At the DGAT1 locus, CC sheep showed the significantly greater fat-tail weight (P < 0.05) and backfat thickness (P < 0.01). The results of this study demonstrate novel associations in which the C allele had a positive effect on fat-tail weight and backfat thickness in fat-tailed sheep.
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Affiliation(s)
- Hossein Mohammadi
- Department of Animal Science, University College of Agriculture & Natural Resources UTCAN, University of Tehran, Karaj, Tehran, Iran.
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da Silva RCG, Ferraz JBS, Meirelles FV, Eler JP, Balieiro JCC, Cucco DC, Mattos EC, Rezende FM, Silva SL. Association of single nucleotide polymorphisms in the bovine leptin and leptin receptor genes with growth and ultrasound carcass traits in Nellore cattle. GENETICS AND MOLECULAR RESEARCH 2012; 11:3721-8. [PMID: 22930433 DOI: 10.4238/2012.august.17.10] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Given the important role of leptin in metabolism, we looked for a possible association of leptin and leptin receptor polymorphisms with carcass and growth traits in Nellore cattle. We examined associations of leptin and leptin receptor SNPs with ultrasound carcass (longissimus dorsi muscle area (ribeye area), backfat thickness and rump fat thickness and growth traits (weaning weight adjusted to 210 days of age, yearling weight adjusted to 550 days of age, weight gain of weaning to yearling and scrotal circumference adjusted to 550 days of age) of 2162 Bos primigenius indicus (Nellore) animals. Allele and genotypic frequencies were calculated for each marker. Allele substitution, additive and dominance effects of the polymorphisms were also evaluated. Some alleles of the molecular markers had low frequencies, lower than 1%, in the sample analyzed, although the same polymorphisms described for B. p. taurus cattle were found. Due to very low allelic frequencies, the E2JW, A59V and UASMS2 markers were not included in the analysis, because they were almost fixed. E2FB was found to be significantly associated with weight gain, ribeye area and backfat thickness. The promoter region markers, C963T and UASMS1, were also found to be significantly associated with ribeye area. T945M was significantly associated with weight gain. We conclude that the leptin and receptor gene markers would be useful for marker-assisted selection.
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Pinto LFB, Ferraz JBS, Pedrosa VB, Eler JP, Meirelles FV, Bonin MN, Rezende FM, Carvalho ME, Cucco DC, Silva RCG. Single nucleotide polymorphisms in CAPN and leptin genes associated with meat color and tenderness in Nellore cattle. GENETICS AND MOLECULAR RESEARCH 2011; 10:2057-64. [PMID: 21968622 DOI: 10.4238/vol10-3gmr1263] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
We analyzed single nucleotide polymorphisms in calpain, leptin, leptin receptor, and growth hormone receptor genes and their association with color, drip and cooking losses of longissimus muscle at 7, 14 and 21 days postmortem in 638 purebred Nellore bulls slaughtered between 22 and 26 months of age. Meat samples were vacuum-packed and aged at 4°C. The single nucleotide polymorphisms T945M, GHR2, E2FB, and CAPN4751 were evaluated. All genotypic classes were observed; however, the T/T genotype of T945M and E2FB was found at a low frequency. A significant association of E2FB with drip loss (a measure of water-holding capacity) was detected at seven days of meat aging. CAPN4751 had an additive effect on red and yellow color intensities. The T allele of CAPN4751 was found to be positively associated with improved meat color, but not with meat tenderness, differing from a previous report indicating that it is associated with meat tenderness. We conclude that the potential for use of CAPN4751 as a marker for these meat quality traits requires further research.
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Affiliation(s)
- L F B Pinto
- Departamento de Produção Animal, Escola de Medicina Veterinária e Zootecnia, Universidade Federal da Bahia, Salvador, BA, Brasil
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Association of bovine carcass phenotypes with genes in an adaptive thermogenesis pathway. Mol Biol Rep 2011; 39:1441-5. [PMID: 21617946 DOI: 10.1007/s11033-011-0880-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2010] [Accepted: 05/14/2011] [Indexed: 10/18/2022]
Abstract
Associations of carcass phenotypes with genes regulating fat and energy metabolism involved in adaptive thermogenesis were examined in beef cattle. Carcass weight (CW) was found to be associated with MAP2K6 and UCP2 genes; back fat thickness (BFT) was found to be associated with PPARGC1A, MAP2K6, and UCP2 genes; marbling score (MS) was found to be associated with PPARGC1A and MAP2K6 genes; and eye-muscle area (EMA) was found to be associated only with UCP2 gene (P < 0.05). Further analyses found significant associations of interactions between PPARGC1A and MAP2K6 genes with CW and MS. Especially, interactive genetic associations were identified between c.424 and 222 G>A in PPARGC1A and c.17-10118 T>G in MAP2K6 and between c.228+28619 A>G in PPARGC1A and c.17-10118 T>G in MAP2K6, and they were both detected for CW and MS at a significant level (P < 0.05). The current study suggested that the individual and interactive associations of PPARGC1A, MAP2K6, and UCP2 genes with carcass phenotypes might be resulted from the pathway with fat and energy metabolism through the adaptive thermogenesis.
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Kawahara-Miki R, Tsuda K, Shiwa Y, Arai-Kichise Y, Matsumoto T, Kanesaki Y, Oda SI, Ebihara S, Yajima S, Yoshikawa H, Kono T. Whole-genome resequencing shows numerous genes with nonsynonymous SNPs in the Japanese native cattle Kuchinoshima-Ushi. BMC Genomics 2011; 12:103. [PMID: 21310019 PMCID: PMC3048544 DOI: 10.1186/1471-2164-12-103] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2010] [Accepted: 02/10/2011] [Indexed: 01/03/2023] Open
Abstract
Background Because the Japanese native cattle Kuchinoshima-Ushi have been isolated in a small island and their lineage has been intensely protected, it has been assumed to date that numerous and valuable genomic variations are conserved in this cattle breed. Results In this study, we evaluated genetic features of this breed, including single nucleotide polymorphism (SNP) information, by whole-genome sequencing using a Genome Analyzer II. A total of 64.2 Gb of sequence was generated, of which 86% of the obtained reads were successfully mapped to the reference sequence (Btau 4.0) with BWA. On an average, 93% of the genome was covered by the reads and the number of mapped reads corresponded to 15.8-fold coverage across the covered region. From these data, we identified 6.3 million SNPs, of which more than 5.5 million (87%) were found to be new. Out of the SNPs annotated in the bovine sequence assembly, 20,432 were found in protein-coding regions containing 11,713 nonsynonymous SNPs in 4,643 genes. Furthermore, phylogenetic analysis using sequence data from 10 genes (more than 10 kbp) showed that Kuchinoshima-Ushi is clearly distinct from European domestic breeds of cattle. Conclusions These results provide a framework for further genetic studies in the Kuchinoshima-Ushi population and research on functions of SNP-containing genes, which would aid in understanding the molecular basis underlying phenotypic variation of economically important traits in cattle and in improving intrinsic defects in domestic cattle breeds.
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Affiliation(s)
- Ryouka Kawahara-Miki
- Genome Research Center, NODAI Research Institute, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo, Japan
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