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Wang J, Wang G, Gong Y, Qiao X, Li X, Wang G, Zheng Y, Lv J, Li X, Liu Z. Screening of three-way crossbred combination and genetic effect analysis of the SNP in the CLPG gene in meat sheep. Arch Anim Breed 2022; 65:417-426. [PMID: 36756164 PMCID: PMC9901518 DOI: 10.5194/aab-65-417-2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 08/31/2022] [Indexed: 11/18/2022] Open
Abstract
In order to promote the rapid development of the meat sheep industry, a three-way crossbred combination experiment was carried out with Australian White, Dorper, and Charollais sheep as terminal male parents and the elite F1 hybrids of Australian White × Small-tailed Han (Han), Dorper × Han, and Charollais × Han as female parents, which was based on the screening of a two-way crossbred combination in meat sheep. The growth performance of six groups of three-way crossbred combinations and Han lambs was measured and analyzed, and the effect of a polymorphism in the CLPG gene on the growth performance of three-way crossbred lambs was also studied. The results showed that under the same rearing conditions, weight at 3 and 6 months of age and average daily gain from birth to 3 months and from 3 to 6 months of age were all the largest for Australian × (Charollais × Han) crossbred lambs. They were significantly or extremely significant different from the other three-way crossbred combinations and Han lambs ( P < 0.05 , P < 0.01 ). The body height, body length, chest girth, and cannon bone circumference at 3 months of age and body length, chest girth, and cannon bone circumference at 6 months of age were also the largest for Australian × (Charollais × Han) crossbred lambs. Among them, body length, chest girth, and cannon bone circumference at 3 months of age were significantly different from the other three-way crossbred combinations and Han lambs ( P < 0.05 ), and body length, chest girth, and cannon bone circumference at 6 months of age were significantly or extremely significant different from the other three-way crossbred combinations and Han lambs ( P < 0.05 , P < 0.01 ). The potential genetic effects of the CLPG gene on the growth performance indicators of three-way crossbred lambs showed that a mutation site ( g .232 C > T ) of this gene had two genotypes: CC and CT. Among them, the data of body weights and body sizes from CT genotype individuals at birth, 3 months old, and 6 months old were significantly higher than those of CC genotype individuals, and some indicators showed significant or extremely significant differences ( P < 0.05 , P < 0.01 ), suggesting that higher growth performance was observed in individuals with T alleles. To sum up, the crossbred combination of Australian × (Charollais × Han) could be suggested as the optimal choice. The T allele of the CLPG gene showed potential advantages in the performance of meat production in meat sheep. Based on the current results, we recommend that the offspring of Australian × (Charollais × Han) with the T allele should be preferentially utilized for meat sheep production.
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Affiliation(s)
- Jian Tao Wang
- Breeding Livestock and Poultry Management Department, Tangshan Animal Husbandry Technology Promotion Station, Tangshan 063000, China
| | - Guo Sen Wang
- Hebei Key Laboratory of Specialty Animal Germplasm Resources
Exploration and Innovation, College of Animal Science and Technology, Hebei
Normal University of Science & Technology, Qinhuangdao 066004, China
| | - Yuan Fang Gong
- Hebei Key Laboratory of Specialty Animal Germplasm Resources
Exploration and Innovation, College of Animal Science and Technology, Hebei
Normal University of Science & Technology, Qinhuangdao 066004, China
| | - Xian Qiao
- Hebei Key Laboratory of Specialty Animal Germplasm Resources
Exploration and Innovation, College of Animal Science and Technology, Hebei
Normal University of Science & Technology, Qinhuangdao 066004, China
| | - Xiang Li
- Hebei Key Laboratory of Specialty Animal Germplasm Resources
Exploration and Innovation, College of Animal Science and Technology, Hebei
Normal University of Science & Technology, Qinhuangdao 066004, China
| | - Gui Zhu Wang
- Breeding Livestock and Poultry Management Department, Tangshan Animal Husbandry Technology Promotion Station, Tangshan 063000, China
| | - Ying Zhen Zheng
- Tianjin DBN Sci-tech Group, Chang Nong Aquatic Science and Technology Co. Ltd,
Tianjin 301804, China
| | - Jian Guo Lv
- Breeding Livestock and Poultry Management Department, Tangshan Animal Husbandry Technology Promotion Station, Tangshan 063000, China
| | - Xiang Long Li
- Hebei Key Laboratory of Specialty Animal Germplasm Resources
Exploration and Innovation, College of Animal Science and Technology, Hebei
Normal University of Science & Technology, Qinhuangdao 066004, China
| | - Zheng Zhu Liu
- Hebei Key Laboratory of Specialty Animal Germplasm Resources
Exploration and Innovation, College of Animal Science and Technology, Hebei
Normal University of Science & Technology, Qinhuangdao 066004, China
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2
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Ma D, Yu Q, Hedrick VE, Cooper BR, Paschoal Sobreira TJ, Oh JH, Chun H, Kim YHB. Proteomic and metabolomic profiling reveals the involvement of apoptosis in meat quality characteristics of ovine M. longissimus from different callipyge genotypes. Meat Sci 2020; 166:108140. [DOI: 10.1016/j.meatsci.2020.108140] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 03/19/2020] [Accepted: 04/04/2020] [Indexed: 11/16/2022]
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3
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Nietfeld F, Höltig D, Willems H, Valentin-Weigand P, Wurmser C, Waldmann KH, Fries R, Reiner G. Candidate genes and gene markers for the resistance to porcine pleuropneumonia. Mamm Genome 2020; 31:54-67. [PMID: 31960078 PMCID: PMC7060169 DOI: 10.1007/s00335-019-09825-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 12/31/2019] [Indexed: 12/30/2022]
Abstract
Actinobacillus (A.) pleuropneumoniae is one of the most important respiratory pathogens in global pig production. Antimicrobial treatment and vaccination provide only limited protection, but genetic disease resistance is a very promising alternative for sustainable prophylaxis. Previous studies have discovered multiple QTL that may explain up to 30% of phenotypic variance. Based on these findings, the aim of the present study was to use genomic sequencing to identify genetic markers for resistance to pleuropneumonia in a segregating commercial German Landrace line. 163 pigs were infected with A. pleuropneumoniae Serotype 7 through a standardized aerosol infection method. Phenotypes were accurately defined on a clinical, pathological and microbiological basis. The 58 pigs with the most extreme phenotypes were genotyped by sequencing (next-generation sequencing). SNPs were used in a genome-wide association study. The study identified genome-wide associated SNPs on three chromosomes, two of which were chromosomes of QTL which had been mapped in a recent experiment. Each variant explained up to 20% of the total phenotypic variance. Combined, the three variants explained 52.8% of the variance. The SNPs are located in genes involved in the pathomechanism of pleuropneumonia. This study confirms the genetic background for the host's resistance to pleuropneumonia and indicates a potential role of three candidates on SSC2, SSC12 and SSC15. Favorable gene variants are segregating in commercial populations. Further work is needed to verify the results in a controlled study and to identify the functional QTN.
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Affiliation(s)
- Florian Nietfeld
- Department for Veterinary Clinical Sciences, Justus-Liebig-University, Giessen, Germany
| | - Doris Höltig
- Clinic for Swine, Small Ruminants, Forensic Medicine and Ambulatory Service, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - Hermann Willems
- Department for Veterinary Clinical Sciences, Justus-Liebig-University, Giessen, Germany
| | - Peter Valentin-Weigand
- Institute for Microbiology, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - Christine Wurmser
- Chair of Animal Breeding, Technical University of Munich, Freising, Germany
| | - Karl-Heinz Waldmann
- Clinic for Swine, Small Ruminants, Forensic Medicine and Ambulatory Service, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - Ruedi Fries
- Chair of Animal Breeding, Technical University of Munich, Freising, Germany
| | - Gerald Reiner
- Department for Veterinary Clinical Sciences, Justus-Liebig-University, Giessen, Germany.
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4
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Wang C, Zhang B, Ratliff AC, Arrington J, Chen J, Xiong Y, Yue F, Nie Y, Hu K, Jin W, Tao WA, Hrycyna CA, Sun X, Kuang S. Methyltransferase-like 21e inhibits 26S proteasome activity to facilitate hypertrophy of type IIb myofibers. FASEB J 2019; 33:9672-9684. [PMID: 31162944 DOI: 10.1096/fj.201900582r] [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: 12/24/2022]
Abstract
Skeletal muscles contain heterogeneous myofibers that are different in size and contractile speed, with type IIb myofiber being the largest and fastest. Here, we identify methyltransferase-like 21e (Mettl21e), a member of newly classified nonhistone methyltransferases, as a gene enriched in type IIb myofibers. The expression of Mettl21e was strikingly up-regulated in hypertrophic muscles and during myogenic differentiation in vitro and in vivo. Knockdown (KD) of Mettl21e led to atrophy of cultured myotubes, and targeted mutation of Mettl21e in mice reduced the size of IIb myofibers without affecting the composition of myofiber types. Mass spectrometry and methyltransferase assay revealed that Mettl21e methylated valosin-containing protein (Vcp/p97), a key component of the ubiquitin-proteasome system. KD or knockout of Mettl21e resulted in elevated 26S proteasome activity, and inhibition of proteasome activity prevented atrophy of Mettl21e KD myotubes. These results demonstrate that Mettl21e functions to maintain myofiber size through inhibiting proteasome-mediated protein degradation.-Wang, C., Zhang, B., Ratliff, A. C., Arrington, J., Chen, J., Xiong, Y., Yue, F., Nie, Y., Hu, K., Jin, W., Tao, W. A., Hrycyna, C. A., Sun, X., Kuang, S. Methyltransferase-like 21e inhibits 26S proteasome activity to facilitate hypertrophy of type IIb myofibers.
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Affiliation(s)
- Chao Wang
- Department of Animal Sciences, Purdue University, West Lafayette, Indiana, USA
| | - Bin Zhang
- Institute of Medicinal Plant Development, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Anna C Ratliff
- Department of Chemistry, Purdue University, West Lafayette, Indiana, USA
| | - Justine Arrington
- Department of Chemistry, Purdue University, West Lafayette, Indiana, USA
| | - Jingjuan Chen
- Department of Animal Sciences, Purdue University, West Lafayette, Indiana, USA
| | - Yan Xiong
- Institute of Medicinal Plant Development, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Feng Yue
- Department of Animal Sciences, Purdue University, West Lafayette, Indiana, USA
| | - Yaohui Nie
- Department of Animal Sciences, Purdue University, West Lafayette, Indiana, USA
| | - Keping Hu
- Institute of Medicinal Plant Development, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Wen Jin
- Institute of Medicinal Plant Development, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - W Andy Tao
- Department of Biochemistry, Purdue University, West Lafayette, Indiana, USA.,Center for Cancer Research, Purdue University, West Lafayette, Indiana, USA
| | - Christine A Hrycyna
- Department of Chemistry, Purdue University, West Lafayette, Indiana, USA.,Center for Cancer Research, Purdue University, West Lafayette, Indiana, USA
| | - Xiaobo Sun
- Institute of Medicinal Plant Development, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Shihuan Kuang
- Department of Animal Sciences, Purdue University, West Lafayette, Indiana, USA.,Center for Cancer Research, Purdue University, West Lafayette, Indiana, USA
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A Hearty Dose of Noncoding RNAs: The Imprinted DLK1-DIO3 Locus in Cardiac Development and Disease. J Cardiovasc Dev Dis 2018; 5:jcdd5030037. [PMID: 29996488 PMCID: PMC6162432 DOI: 10.3390/jcdd5030037] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 06/29/2018] [Accepted: 07/04/2018] [Indexed: 12/17/2022] Open
Abstract
The imprinted Dlk1-Dio3 genomic region harbors a noncoding RNA cluster encoding over fifty microRNAs (miRNAs), three long noncoding RNAs (lncRNAs), and a small nucleolar RNA (snoRNA) gene array. These distinct noncoding RNAs (ncRNAs) are thought to arise from a single polycistronic transcript that is subsequently processed into individual ncRNAs, each with important roles in diverse cellular contexts. Considering these ncRNAs are derived from a polycistron, it is possible that some coordinately regulate discrete biological processes in the heart. Here, we provide a comprehensive summary of Dlk1-Dio3 miRNAs and lncRNAs, as they are currently understood in the cellular and organ-level context of the cardiovascular system. Highlighted are expression profiles, mechanistic contributions, and functional roles of these ncRNAs in heart development and disease. Notably, a number of these ncRNAs are implicated in processes often perturbed in heart disease, including proliferation, differentiation, cell death, and fibrosis. However, most literature falls short of characterizing precise mechanisms for many of these ncRNAs, warranting further investigation. Taken together, the Dlk1-Dio3 locus represents a largely unexplored noncoding regulator of cardiac homeostasis, harboring numerous ncRNAs that may serve as therapeutic targets for cardiovascular disease.
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6
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Mackin SJ, Thakur A, Walsh CP. Imprint stability and plasticity during development. Reproduction 2018; 156:R43-R55. [PMID: 29743259 DOI: 10.1530/rep-18-0051] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 05/08/2018] [Indexed: 12/20/2022]
Abstract
There have been a number of recent insights in the area of genomic imprinting, the phenomenon whereby one of two autosomal alleles is selected for expression based on the parent of origin. This is due in part to a proliferation of new techniques for interrogating the genome that are leading researchers working on organisms other than mouse and human, where imprinting has been most studied, to become interested in looking for potential imprinting effects. Here, we recap what is known about the importance of imprints for growth and body size, as well as the main types of locus control. Interestingly, work from a number of labs has now shown that maintenance of the imprint post implantation appears to be a more crucial step than previously appreciated. We ask whether imprints can be reprogrammed somatically, how many loci there are and how conserved imprinted regions are in other species. Finally, we survey some of the methods available for examining DNA methylation genome-wide and look to the future of this burgeoning field.
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Affiliation(s)
- Sarah-Jayne Mackin
- Genomic Medicine Research GroupSchool of Biomedical Sciences, Ulster University, Northern Ireland, UK
| | - Avinash Thakur
- Genomic Medicine Research GroupSchool of Biomedical Sciences, Ulster University, Northern Ireland, UK
| | - Colum P Walsh
- Genomic Medicine Research GroupSchool of Biomedical Sciences, Ulster University, Northern Ireland, UK
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7
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Yu H, Waddell JN, Kuang S, Tellam RL, Cockett NE, Bidwell CA. Identification of genes directly responding to DLK1 signaling in Callipyge sheep. BMC Genomics 2018; 19:283. [PMID: 29690867 PMCID: PMC5937834 DOI: 10.1186/s12864-018-4682-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2018] [Accepted: 04/16/2018] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND In food animal agriculture, there is a need to identify the mechanisms that can improve the efficiency of muscle growth and protein accretion. Callipyge sheep provide excellent machinery since the up-regulation of DLK1 and RTL1 results in extreme postnatal muscle hypertrophy in distinct muscles. The aim of this study is to distinguish the genes that directly respond to DLK1 and RTL1 signaling from the genes that change as the result of muscle specific effects. RESULTS The quantitative PCR results indicated that DLK1 expression was significantly increased in hypertrophied muscles but not in non-hypertrophied muscles. However, RTL1 was up-regulated in both hypertrophied and non-hypertrophied muscles. Five genes, including PARK7, DNTTIP1, SLC22A3, METTL21E and PDE4D, were consistently co-expressed with DLK1, and therefore were possible transcriptional target genes responding to DLK1 signaling. Treatment of myoblast and myotubes with DLK1 protein induced an average of 1.6-fold and 1.4-fold increase in Dnttip1 and Pde4d expression respectively. Myh4 expression was significantly elevated in DLK1-treated myotubes, whereas the expression of Mettl21e was significantly increased in the DLK1-treated myoblasts but reduced in DLK1-treated myotubes. DLK1 treatment had no impact on Park7 expression. In addition, Park7 and Dnttip1 increased Myh4 and decreased Myh7 promoter activity, resemble to the effects of Dlk1. In contrast, expression of Mettl21e increased Myh7 and decreased Myh4 luciferase activity. CONCLUSION The study provided additional supports that RTL1 alone was insufficient to induce muscle hypertrophy and concluded that DLK1 was likely the primary effector of the hypertrophy phenotype. The results also suggested that DNTTIP1 and PDE4D were secondary effector genes responding to DLK1 signaling resulting in muscle fiber switch and muscular hypertrophy in callipyge lamb.
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Affiliation(s)
- Hui Yu
- Department of Animal Sciences, Purdue University, 270 South Russell Street, West Lafayette, IN, 47907, USA. .,Department of Molecular and Integrative Physiology, University of Michigan, 1000 Wall Street, Ann Arbor, MI, 48105, USA.
| | - Jolena N Waddell
- Department of Animal Sciences, Purdue University, 270 South Russell Street, West Lafayette, IN, 47907, USA.,Department of Animal Science & Veterinary Technology, Tarleton State University, Stephenville, TX, USA
| | - Shihuan Kuang
- Department of Animal Sciences, Purdue University, 270 South Russell Street, West Lafayette, IN, 47907, USA.,Center for Cancer Research, Purdue University, West Lafayette, IN, USA
| | - Ross L Tellam
- CSIRO Animal, Food and Health Sciences, St. Lucia, QLD, Australia
| | - Noelle E Cockett
- Department of Animal, Dairy and Veterinary Sciences, Utah State University, Logan, UT, USA
| | - Christopher A Bidwell
- Department of Animal Sciences, Purdue University, 270 South Russell Street, West Lafayette, IN, 47907, USA.
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Chao T, Ji Z, Hou L, Wang J, Zhang C, Wang G, Wang J. Sheep skeletal muscle transcriptome analysis reveals muscle growth regulatory lncRNAs. PeerJ 2018; 6:e4619. [PMID: 29666768 PMCID: PMC5899421 DOI: 10.7717/peerj.4619] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 03/25/2018] [Indexed: 01/06/2023] Open
Abstract
As widely distributed domestic animals, sheep are an important species and the source of mutton. In this study, we aimed to evaluate the regulatory lncRNAs associated with muscle growth and development between high production mutton sheep (Dorper sheep and Qianhua Mutton Merino sheep) and low production mutton sheep (Small-tailed Han sheep). In total, 39 lncRNAs were found to be differentially expressed. Using co-expression analysis and functional annotation, 1,206 co-expression interactions were found between 32 lncRNAs and 369 genes, and 29 of these lncRNAs were found to be associated with muscle development, metabolism, cell proliferation and apoptosis. lncRNA–mRNA interactions revealed 6 lncRNAs as hub lncRNAs. Moreover, three lncRNAs and their associated co-expressed genes were demonstrated by cis-regulatory gene analyses, and we also found a potential regulatory relationship between the pseudogene lncRNA LOC101121401 and its parent gene FTH1. This study provides a genome-wide resolution of lncRNA and mRNA regulation in muscles from mutton sheep.
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Affiliation(s)
- Tianle Chao
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Taian, Shandong, China
| | - Zhibin Ji
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Taian, Shandong, China
| | - Lei Hou
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Taian, Shandong, China
| | - Jin Wang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Taian, Shandong, China
| | - Chunlan Zhang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Taian, Shandong, China
| | - Guizhi Wang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Taian, Shandong, China
| | - Jianmin Wang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Taian, Shandong, China
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9
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Freking BA, King DA, Shackelford SD, Wheeler TL, Smith TPL. Effects and interactions of myostatin and callipyge mutations: I. Growth and carcass traits. J Anim Sci 2018; 96:454-461. [PMID: 29401324 DOI: 10.1093/jas/skx055] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Objectives were to document effects of the Texel myostatin mutation (MSTN) on growth and carcass traits and also test whether or not interactions with the callipyge mutation (CLPG) could be detected. Twelve rams heterozygous at both loci on the two different chromosomes were mated to 215 terminal-sire type composite crossbred ewes genotyped as non-carriers for both loci. A total of 365 lambs were born, 362 of those were genotyped and 236 lambs contributed carcass data to estimate effects and interactions among the four genotype combinations produced. The four genotype combinations were defined as follows: ++/++ for wild-type at both loci; ++/C+ for wild-type at MSTN and heterozygous at CLPG; M+/++ for heterozygous at MSTN and wild-type at CLPG; and M+/C+ for heterozygous at both loci. The two independently segregating sire-derived alleles represent different breed-of-origin contrasts at each locus (Texel vs. composite origin for MSTN and Dorset vs. Texel origin for CLPG). Birth weight was recorded on all lambs, and subsequent body weights were adjusted to 56 (weaning), 70, and 140 d of age. Within sire-sex-genotype subgroups, naturally reared lambs were assigned to one of eight slaughter groups accounting for variation in birth date. Lambs were serially slaughtered at weekly intervals, 30 lambs per group, from roughly 26 to 33 wk of age. In addition to standard carcass traits, subjective leg scores were assigned and widths of carcasses were measured at the widest points of the shoulder and rump. Differences in birth weight were detected (P < 0.01) for the combination of the two loci and birth type, with single-born differences among genotypes exceeding differences among twin born progeny. Those interaction differences among genotypes were not as important at weaning (P = 0.36). Impact on growth rate differences among the genotypes during the post-weaning period were variable and dependent on sex of the lamb (P < 0.01). A synergistic interaction between MSTN and CLPG was observed for leg muscling scores (P < 0.05) but no other measures of carcass shape were affected. One copy of MSTN had a more modest impact on fat deposition and muscle conformation than did CLPG and did not interact (all values P > 0.20). Although some non-additive interactions that vary by trait and sex were detected, in general the data are consistent with the two mutations acting on muscle growth through independent pathways.
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Affiliation(s)
- Brad A Freking
- USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE
| | - David A King
- USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE
| | | | - Tommy L Wheeler
- USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE
| | - Tim P L Smith
- USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE
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10
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Weikard R, Demasius W, Kuehn C. Mining long noncoding RNA in livestock. Anim Genet 2016; 48:3-18. [DOI: 10.1111/age.12493] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/16/2016] [Indexed: 02/01/2023]
Affiliation(s)
- R. Weikard
- Institute Genome Biology; Leibniz Institute for Farm Animal Biology (FBN); 18196 Dummerstorf Germany
| | - W. Demasius
- Institute Genome Biology; Leibniz Institute for Farm Animal Biology (FBN); 18196 Dummerstorf Germany
| | - C. Kuehn
- Institute Genome Biology; Leibniz Institute for Farm Animal Biology (FBN); 18196 Dummerstorf Germany
- Faculty of Agricultural and Environmental Sciences; University Rostock; 18059 Rostock Germany
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11
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Parent-of-origin effects of A1CF and AGO2 on testicular germ-cell tumors, testicular abnormalities, and fertilization bias. Proc Natl Acad Sci U S A 2016; 113:E5425-33. [PMID: 27582469 DOI: 10.1073/pnas.1604773113] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Testicular tumors, the most common cancer in young men, arise from abnormalities in germ cells during fetal development. Unconventional inheritance for testicular germ cell tumor (TGCT) risk both in humans and mice implicates epigenetic mechanisms. Apolipoprotein B mRNA-editing enzyme complex 1 (APOBEC1) cytidine deaminase and Deadend-1, which are involved in C-to-U RNA editing and microRNA-dependent mRNA silencing, respectively, are potent epigenetic modifiers of TGCT susceptibility in the genetically predisposed 129/Sv inbred mouse strain. Here, we show that partial loss of either APOBEC1 complementation factor (A1CF), the RNA-binding cofactor of APOBEC1 in RNA editing, or Argonaute 2 (AGO2), a key factor in the biogenesis of certain noncoding RNAs, modulates risk for TGCTs and testicular abnormalities in both parent-of-origin and conventional genetic manners. In addition, non-Mendelian inheritance was found among progeny of A1cf and Ago2 mutant intercrosses but not in backcrosses and without fetal loss. Together these findings suggest nonrandom union of gametes rather than meiotic drive or preferential lethality. Finally, this survey also suggested that A1CF contributes to long-term reproductive performance. These results directly implicate the RNA-binding proteins A1CF and AGO2 in the epigenetic control of germ-cell fate, urogenital development, and gamete functions.
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12
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O'Doherty AM, MacHugh DE, Spillane C, Magee DA. Genomic imprinting effects on complex traits in domesticated animal species. Front Genet 2015; 6:156. [PMID: 25964798 PMCID: PMC4408863 DOI: 10.3389/fgene.2015.00156] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2014] [Accepted: 04/06/2015] [Indexed: 11/13/2022] Open
Abstract
Monoallelically expressed genes that exert their phenotypic effect in a parent-of-origin specific manner are considered to be subject to genomic imprinting, the most well understood form of epigenetic regulation of gene expression in mammals. The observed differences in allele specific gene expression for imprinted genes are not attributable to differences in DNA sequence information, but to specific chemical modifications of DNA and chromatin proteins. Since the discovery of genomic imprinting some three decades ago, over 100 imprinted mammalian genes have been identified and considerable advances have been made in uncovering the molecular mechanisms regulating imprinted gene expression. While most genomic imprinting studies have focused on mouse models and human biomedical disorders, recent work has highlighted the contributions of imprinted genes to complex trait variation in domestic livestock species. Consequently, greater understanding of genomic imprinting and its effect on agriculturally important traits is predicted to have major implications for the future of animal breeding and husbandry. In this review, we discuss genomic imprinting in mammals with particular emphasis on domestic livestock species and consider how this information can be used in animal breeding research and genetic improvement programs.
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Affiliation(s)
- Alan M O'Doherty
- UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield Ireland
| | - David E MacHugh
- UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield Ireland ; Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Belfield Ireland
| | - Charles Spillane
- Genetics and Biotechnology Laboratory, Plant and AgriBiosciences Research Centre, School of Natural Sciences, National University of Ireland Galway, Galway Ireland
| | - David A Magee
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Belfield Ireland ; Department of Animal Science, University of Connecticut, Storrs, CT USA
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Cheng H, Xu X, Hadfield T, Cockett N, Charlier C, Georges M, Takeda H. Experimental evaluation does not reveal a direct effect of microRNA from the callipyge locus on DLK1 expression. BMC Genomics 2014; 15:944. [PMID: 25359221 PMCID: PMC4226911 DOI: 10.1186/1471-2164-15-944] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2014] [Accepted: 10/16/2014] [Indexed: 01/10/2023] Open
Abstract
Background Polar overdominance at the ovine callipyge (CLPG) locus involves the post-transcriptional trans-inhibition of DLK1 in skeletal muscle of CLPG/CLPG sheep. The abundant maternally expressed microRNAs (miRNAs) mapping to the imprinted DLK1-GTL2 domain are prime candidate mediators of this trans-effect. Results We have tested the affinity of 121 miRNAs processed from this locus for DLK1 by co-transfecting COS1 cells with a vector expressing the full-length ovine DLK1 with corresponding mimic miRNAs. None of the tested miRNAs was able to down regulate DLK1 to the extent observed in vivo. Conclusions This suggests that other factors, with or without these miRNAs, are involved in mediating the observed trans-effect. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-944) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | | | - Haruko Takeda
- Unit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of Liège (B34), 1 Avenue de l'Hôpital, 4000 Liège, Belgium.
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