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Wang Y, Yang T, Mo H, Yao M, Song Q, Yu H, Du Y, Li Y, Yu J, Wang L. Identification and functional analysis of six melanocortin-4-receptor-like (MC4R-like) mutations in goldfish (Carassius auratus). Gen Comp Endocrinol 2025; 360:114639. [PMID: 39536983 DOI: 10.1016/j.ygcen.2024.114639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/28/2024] [Revised: 11/05/2024] [Accepted: 11/09/2024] [Indexed: 11/16/2024]
Abstract
Melanocortin receptor-4 (MC4R) belongs to the G protein-coupled receptor family, characterized by a classical structure of seven transmembrane domains (7TMD). They play an important role in food intake and weight regulation. In the present study, we identified melanocortin-4-receptor-like (caMC4RL) mutants of goldfish from the Qian River in the Qin Ling region and characterized their functional properties, including the constitutive activities of the mutants, ligand-induced cAMP and ERK1/2 accumulation, and AMPK activation. The results show that six caMC4RL mutants were identified in goldfish from the Qian River in the Qin Ling region, and are located in the conserved position of the Cyprinidae MC4Rs. The mutations (E57K, P296S, and R302T/K) result in the loss of Gs signaling function. The mutations (P296 and R302T/K) exhibited biased signaling in response to ACTH stimulation in the MAPK/ERK pathway. In addition, the E57K mutant may play a role in weight regulation and could serve as molecular markers for molecular breeding. These data will provide fundamental information for functional studies of teleost GPCR mutants and MC4R isoforms.
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Affiliation(s)
- Ying Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Tianze Yang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Haolin Mo
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Mingxing Yao
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Qingchuan Song
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Huixia Yu
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yuyou Du
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yang Li
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Jiajia Yu
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Lixin Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China.
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2
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Zhao Z, Yang Y, Liu P, Yan T, Li R, Pan C, Li Y, Lan X. A Critical Functional Missense Mutation (T117M) in Sheep MC4R Gene Significantly Leads to Gain-of-Function. Animals (Basel) 2024; 14:2207. [PMID: 39123733 PMCID: PMC11311007 DOI: 10.3390/ani14152207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2024] [Revised: 07/26/2024] [Accepted: 07/27/2024] [Indexed: 08/12/2024] Open
Abstract
The melanocortin 4 receptor (MC4R) gene plays a central role in regulating energy homeostasis and food intake in livestock, thereby affecting their economic worth and growth. In a previous study, the p.T117M mutation in the sheep MC4R gene, which leads to the transition of threonine to methionine, was found to affect the body weight at six months and the average daily gain in Hu sheep. However, there are still limited studies on the frequency of the sheep p.T117M missense mutation globally, and the underlying cellular mechanism remains elusive. Therefore, this study first used WGS to investigate the distribution of the MC4R gene p.T117M mutation in 652 individuals across 22 breeds worldwide. The results showed that the mutation frequency was higher in European breeds compared with Chinese sheep breeds, particularly in Poll Dorset sheep (mutation frequency > 0.5). The p.T117M mutation occurs in the first extracellular loop of MC4R. Mechanistically, the basal activity of the mutated receptor is significantly increased. Specifically, upon treatment with α-MSH and ACTH ligands, the cAMP and MAPK/ERK signaling activation of M117 MC4R is enhanced. These results indicate that the T117M mutation may change the function of the gene by increasing the constitutive activity and signaling activation of cAMP and MAPK/ERK, and, thus, may regulate the growth traits of sheep. In conclusion, this study delved into the global distribution and underlying cellular mechanisms of the T117M mutation of the MC4R gene, establishing a scientific foundation for breeding sheep with superior growth, thereby contributing to the advancement of the sheep industry.
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Affiliation(s)
| | | | | | | | | | | | - Yang Li
- College of Animal Science and Technology, Northwest A&F University, Yangling, Xianyang 712100, China; (Z.Z.); (Y.Y.); (P.L.); (T.Y.); (R.L.); (C.P.)
| | - Xianyong Lan
- College of Animal Science and Technology, Northwest A&F University, Yangling, Xianyang 712100, China; (Z.Z.); (Y.Y.); (P.L.); (T.Y.); (R.L.); (C.P.)
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3
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Sha Y, He Y, Liu X, Shao P, Wang F, Xie Z, Li W, Wang J, Li S, Zhao S, Chen G. Interactions of rumen microbiota and metabolites with meat quality-related genes to regulate meat quality and flavor of Tibetan sheep under nutrient stress in the cold season. J Appl Microbiol 2023; 134:lxad182. [PMID: 37567778 DOI: 10.1093/jambio/lxad182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 07/26/2023] [Accepted: 08/10/2023] [Indexed: 08/13/2023]
Abstract
AIM The meat of Tibetan sheep has a unique flavor, delicious taste, and superior nutritional value. However, the change of grass will lead to a change in meat quality. This study aimed to explore the potential regulatory mechanisms of microbial metabolites with respect to meat quality traits of Tibetan sheep under nutrient stress in the cold season. METHODS AND RESULTS We determined and analyzed the longissimus dorsi quality, fatty acid composition, expression of genes, and rumen microbial metabolites of Tibetan sheep in cold and warm seasons. The shear force was decreased (P < .05), the meat color a*24 h value was increased (P < .05), and the contents of crude fat (EE) and protein (CP) were decreased in the cold season. Polyunsaturated fatty acids (PUFAs)-linoleic acid and docosahexaenoic acid increased significantly in the cold season (P < .05). The expressions of meat quality genes MC4R, CAPN1, H-FABP, and LPL were significantly higher in the warm season (P < .05), and the CAST gene was significantly expressed in the cold season (P < .01). The different microbial metabolites of Tibetan sheep in the cold and warm seasons were mainly involved in amino acid metabolism, lipid metabolism, and digestive system pathway, and there was some correlation between microbiota and meat quality traits. There are similarities between microbial metabolites enriched in the lipid metabolism pathway and muscle metabolites. CONCLUSION Under nutritional stress in the cold season, the muscle tenderness of Tibetan sheep was improved, and the fat deposition capacity was weakened, but the levels of beneficial fatty acids were higher than those in the warm season, which was more conducive to healthy eating.
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Affiliation(s)
- Yuzhu Sha
- College of Animal Science and Technology/Gansu Key Laboratory of Herbivorous Animal Biotechnology, Gansu Agricultural University, Lanzhou 730070, China
| | - Yanyu He
- School of Fundamental Sciences, Massey University, Palmerston North 4410, New Zealand
| | - Xiu Liu
- College of Animal Science and Technology/Gansu Key Laboratory of Herbivorous Animal Biotechnology, Gansu Agricultural University, Lanzhou 730070, China
| | - Pengyang Shao
- College of Animal Science and Technology/Gansu Key Laboratory of Herbivorous Animal Biotechnology, Gansu Agricultural University, Lanzhou 730070, China
| | - Fanxiong Wang
- College of Animal Science and Technology/Gansu Key Laboratory of Herbivorous Animal Biotechnology, Gansu Agricultural University, Lanzhou 730070, China
| | - Zhuanhui Xie
- College of Animal Science and Technology/Gansu Key Laboratory of Herbivorous Animal Biotechnology, Gansu Agricultural University, Lanzhou 730070, China
| | - Wenhao Li
- Academy of Animal Science and Veterinary medicine, Qinghai University, Xining 810000, China
| | - Jiqing Wang
- College of Animal Science and Technology/Gansu Key Laboratory of Herbivorous Animal Biotechnology, Gansu Agricultural University, Lanzhou 730070, China
| | - Shaobin Li
- College of Animal Science and Technology/Gansu Key Laboratory of Herbivorous Animal Biotechnology, Gansu Agricultural University, Lanzhou 730070, China
| | - Shengguo Zhao
- College of Animal Science and Technology/Gansu Key Laboratory of Herbivorous Animal Biotechnology, Gansu Agricultural University, Lanzhou 730070, China
| | - Guoshun Chen
- College of Animal Science and Technology/Gansu Key Laboratory of Herbivorous Animal Biotechnology, Gansu Agricultural University, Lanzhou 730070, China
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Tao YX. Mutations in melanocortin-4 receptor: From fish to men. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2022; 189:215-257. [PMID: 35595350 DOI: 10.1016/bs.pmbts.2022.03.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Melanocortin-4 receptor (MC4R), expressed abundantly in the hypothalamus, is a critical regulator of energy homeostasis, including both food intake and energy expenditure. Shortly after the publication in 1997 of the Mc4r knockout phenotypes in mice, including increased food intake and severe obesity, the first mutations in MC4R were reported in humans in 1998. Studies in the subsequent two decades have established MC4R mutation as the most common monogenic form of obesity, especially in early-onset severe obesity. Studies in animals, from fish to mammals, have established the conserved physiological roles of MC4R in all vertebrates in regulating energy balance. Drug targeting MC4R has been recently approved for treating morbid genetic obesity. How the MC4R can be exploited for animal production is highly worthy of active investigation.
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Affiliation(s)
- Ya-Xiong Tao
- Department of Anatomy, Physiology and Pharmacology, College of Veterinary Medicine, Auburn University, Auburn, AL, United States.
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5
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Exploring single nucleotide polymorphisms in GH, IGF-I, MC4R and DGAT1 genes as predictors for growth performance in dromedary camel using multiple linear regression analysis. Small Rumin Res 2022. [DOI: 10.1016/j.smallrumres.2022.106619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Gorlov IF, Shirokova NV, Anisimova EY, Slozhenkina MI, Kolosov YA, Natyrov AK, Kolosov AY, Mosolova NI, Kolosova MA, Tarchokov TT, Mosolov AA, Mosolova DA, Karpenko EV. MC4R gene polymorphism and its association with meat traits of Karachai sheep grown in Russian Federation. JOURNAL OF APPLIED ANIMAL RESEARCH 2021. [DOI: 10.1080/09712119.2021.1883624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Ivan Fiodorovich Gorlov
- Volga Region Research Institute of Manufacture and Processing of Meat-And-Milk Production, Volgograd, Russian Federation
- Volgograd State Technical University, Volgograd, Russian Federation
| | - Nadezhda Vasilievna Shirokova
- Don State Agrarian University, Laboratory of Molecular Diagnostics and Biotechnology of Farm Animals, Persianovsky, Russian Federation
| | - Elena Yurievna Anisimova
- Volga Region Research Institute of Manufacture and Processing of Meat-And-Milk Production, Volgograd, Russian Federation
- Volgograd State University, Volgograd, Russian Federation
| | - Marina Ivanovna Slozhenkina
- Volga Region Research Institute of Manufacture and Processing of Meat-And-Milk Production, Volgograd, Russian Federation
- Volgograd State Technical University, Volgograd, Russian Federation
| | - Yuriy Anatolievich Kolosov
- Don State Agrarian University, Laboratory of Molecular Diagnostics and Biotechnology of Farm Animals, Persianovsky, Russian Federation
| | | | - Anatoliy Yurievich Kolosov
- Don State Agrarian University, Laboratory of Molecular Diagnostics and Biotechnology of Farm Animals, Persianovsky, Russian Federation
| | - Natalia Ivanovna Mosolova
- Volga Region Research Institute of Manufacture and Processing of Meat-And-Milk Production, Volgograd, Russian Federation
- Volgograd State Technical University, Volgograd, Russian Federation
| | - Maria Anatolievna Kolosova
- Don State Agrarian University, Laboratory of Molecular Diagnostics and Biotechnology of Farm Animals, Persianovsky, Russian Federation
| | | | - Aleksandr Anatolievich Mosolov
- Volga Region Research Institute of Manufacture and Processing of Meat-And-Milk Production, Volgograd, Russian Federation
| | - Daria Aleksandrovna Mosolova
- Volga Region Research Institute of Manufacture and Processing of Meat-And-Milk Production, Volgograd, Russian Federation
- Plekhanov Russian University of Economics, Moscow, Russian Federation
| | - Ekaterina Vladimirovna Karpenko
- Volga Region Research Institute of Manufacture and Processing of Meat-And-Milk Production, Volgograd, Russian Federation
- Volgograd State Technical University, Volgograd, Russian Federation
- Volgograd State University, Volgograd, Russian Federation
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7
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Al-Thuwaini TM, Al-Shuhaib MBS, Lepretre F, Dawud HH. Two co-inherited novel SNPs in the MC4R gene related to live body weight and hormonal assays in Awassi and Arabi sheep breeds of Iraq. Vet Med Sci 2020; 7:897-907. [PMID: 33369226 PMCID: PMC8136946 DOI: 10.1002/vms3.421] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 11/10/2020] [Accepted: 12/09/2020] [Indexed: 12/27/2022] Open
Abstract
Melanocortin‐4 receptor (MC4R) gene plays a key role in the regulation of body weight and energy homeostasis. This study aims to evaluate the association of single nucleotide polymorphisms (SNPs) of the MC4R gene with live body weight and hormonal assays in two breeds of sheep that differ in productive performance, Awassi and Arabi. All known coding sequences of the MC4R gene were covered in this study. DNA samples from 150 animals (Awassi and Arabi breed) were genotyped by PCR‐single‐strand conformation polymorphism (PCR‐SSCP) to assess their pattern of genetic variation. Concerning exon 1, clear heterogeneity was detected with three different SSCP‐banding patterns. The sequencing reactions confirmed these variations by detecting the presence of the two novel SNPs, 107G/C and 138A/C, and three genotypes, GC, AC and AA. The 107G/C SNP was detected in GC genotype, while the 138A/C was detected on both GC and AC genotypes. The other SSCP‐banding pattern (AA genotype) did not show any detectable unique variation. Both SNPs were closely and strongly linked in both breeds (D' and r2 values were 1.00), which signifies that both loci were co‐inherited as one unit. Association analysis indicated that both breeds with GC/AC haplotype showed higher live body weight (37.250 ± 0.790) relative to the GG/AA (30.244 ± 0.968) and CC/CC (47.231 ± 1.230) haplotypes (p < .05). Concerning the genotyping of exon 2, only 362 bp showed heterogeneity with a missense mutation, with no significant association (p > .05) with the measured traits. In conclusion, the two novel SNPs (107G/C and 138 A/C) were highly associated with live body weight in both breeds. Haplotype analysis confirmed that these two novel SNPs were in strong linkage disequilibrium (LD) and could be used as genetic markers for sheep phenotypic trait improvement.
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Affiliation(s)
- Tahreer M Al-Thuwaini
- Department of Animal Production, College of Agriculture, Al-Qasim Green University, Babil, Iraq
| | | | - Frederic Lepretre
- University of Lille, Plateau de Genomique Fonctionnelle et Structurale, Lille, France
| | - Halla Hassan Dawud
- Department of Animal Production, College of Agriculture, Al-Qasim Green University, Babil, Iraq
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8
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Shan H, Song X, Cao Y, Xiong P, Wu J, Jiang J, Jiang Y. Association of the melanocortin 4 receptor (MC4R) gene polymorphism with growth traits of Hu sheep. Small Rumin Res 2020. [DOI: 10.1016/j.smallrumres.2020.106206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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9
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The genetic polymorphisms of melanocortin-4 receptor gene are associated with carcass quality traits in a Chinese indigenous beef cattle breed. Res Vet Sci 2020; 132:202-206. [PMID: 32604043 DOI: 10.1016/j.rvsc.2020.06.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 05/19/2020] [Accepted: 06/10/2020] [Indexed: 11/24/2022]
Abstract
Melanocortin-4 receptor (MC4R) was considered as an essential modifiers in feelings intake, the regulation of metabolism and body weight. This study aimed at identifying polymorphisms in MC4R gene that might associate with carcass quality traits in Chinese indigenous beef cattle breed. qPCR analysis showed that the MC4R gene was widely expressed in various tissues, with predominantly expression levels in heart. Three single-nucleotide polymorphisms (SNPs) were identified, including a mutation (g.85A > G) in 5'untranslated regions (UTR) and two mutations (g.927C > T and g.1069C > G) in exon 1. Based on the χ2 test, both g.927C > T and g.1069C > G loci fitted with Hardy-Weinberg equilibrium (P > .05). Population genetic analysis showed that except for g.85A > G, the other detected SNPs strongly affected the bovine back fat thickness and intramuscular fat content (P < .05). The individuals with Hap1/4 diplotypes (ACC-ATG) were highly significantly associated with carcass quality traits than the other diplotypes (P < .01 or P < .05). Results indicated that the bovine MC4R gene polymorphisms were implicated as genetic markers of potential importance in marker-assisted selection (MAS) strategies to improve carcass quality in Chinese Qinchuan cattle.
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10
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Yu DY, Wu RZ, Zhao Y, Nie ZH, Wei L, Wang TY, Liu ZP. Polymorphisms of four candidate genes and their correlations with growth traits in blue fox (Alopex lagopus). Gene 2019; 717:143987. [PMID: 31362037 DOI: 10.1016/j.gene.2019.143987] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2018] [Revised: 07/16/2019] [Accepted: 07/16/2019] [Indexed: 11/16/2022]
Abstract
To improve the accuracy and genetic progress of blue fox breeding, the relationships between genetic polymorphisms and growth and reproductive traits of the blue fox were investigated. MC4R, MC3R, INHA and INHBA were selected as candidate genes for molecular evolution and statistical analyses. Single-factor variance analyses showed that the MC4R (g.267C > T, g.423C > T, and g.731C > A) and MC3R (g.677C > T) genotypes had significant impacts on body weight, chest circumference, abdominal perimeter and body mass index (BMI) (P < 0.05) in blue fox. The MC4R and MC3R combined genotypes had significant effects on the body weight and abdominal circumference. The different genotypes of INHA g.75G > A had significant effects on female fecundity, whereas the different genotypes of INHBA g.404G > T and g.467G > T and the INHA and INHBA combined genotypes had significant effects on male fecundity. The proteins encoded by the open reading frames (ORFs) of different polymorphic loci were predicted and analysed. The aims of this study were to identify genetic markers related to growth and reproduction in the blue fox and to provide an efficient, economical and accurate theoretical approach for auxiliary fox breeding.
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Affiliation(s)
- Dong-Yue Yu
- College of Wildlife Resources, Northeast Forestry University, Harbin, China
| | - Ru-Zi Wu
- College of Wildlife Resources, Northeast Forestry University, Harbin, China
| | - Yao Zhao
- College of Wildlife Resources, Northeast Forestry University, Harbin, China
| | - Zi-Han Nie
- College of Wildlife Resources, Northeast Forestry University, Harbin, China
| | - Lai Wei
- Hualong Blue Fox Breeding Company, Harbin, China
| | - Tian-Yi Wang
- Hualong Blue Fox Breeding Company, Harbin, China
| | - Zhi-Ping Liu
- College of Wildlife Resources, Northeast Forestry University, Harbin, China.
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11
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Shishay G, Liu G, Jiang X, Yu Y, Teketay W, Du D, Jing H, Liu C. Variation in the Promoter Region of the MC4R Gene Elucidates the Association of Body Measurement Traits in Hu Sheep. Int J Mol Sci 2019; 20:E240. [PMID: 30634446 PMCID: PMC6358852 DOI: 10.3390/ijms20020240] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 12/24/2018] [Accepted: 12/30/2018] [Indexed: 12/15/2022] Open
Abstract
The melanocortin 4 receptor (MC4R) gene is expressed in the appetite-regulating areas of the brain and is engaged in the leptin signaling pathway. Although previous studies have identified variants in the coding region of the sheep MC4R gene showing significant associations with birth weight, weaning weight, and backfat thickness, no such associations have been reported for the promoter region. Besides, the essential promoter region of the sheep MC4R has not been delineated. In this study, to better understand the transcriptional regulation of MC4R and to elucidate the association between regulatory variants and haplotypes with body measurement traits in sheep, we cloned and characterized the MC4R promoter. We found that the minimal promoter of the gene is located within the region -1207/-880 bp upstream of the first exon. Real-time quantitative PCR (RT-qPCR) data revealed the mRNA expression of the MC4R gene had a significant difference between sex and age. In the association analysis, eight single nucleotide polymorphisms (SNPs) had a significant association with one or more traits (p < 0.05); of these, two SNPs were novel. Notably, individuals with haplotype H1H2 (CT-GA-GT-GA-GT-GA-GA-CG) were heavier in body weight than other haplotypes. Altogether, variations in the MC4R gene promoter, most notably haplotype H1H2, may greatly benefit marker-assisted selection in sheep.
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Affiliation(s)
- Girmay Shishay
- Laboratory of Small Ruminant Genetics, Breeding and Reproduction, Huazhong Agricultural University, Wuhan 430070, China.
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China.
| | - Guiqiong Liu
- Laboratory of Small Ruminant Genetics, Breeding and Reproduction, Huazhong Agricultural University, Wuhan 430070, China.
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China.
| | - Xunping Jiang
- Laboratory of Small Ruminant Genetics, Breeding and Reproduction, Huazhong Agricultural University, Wuhan 430070, China.
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China.
| | - Yun Yu
- Laboratory of Small Ruminant Genetics, Breeding and Reproduction, Huazhong Agricultural University, Wuhan 430070, China.
| | - Wassie Teketay
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China.
| | - Dandan Du
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China.
| | - Huang Jing
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China.
| | - Chenghui Liu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China.
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12
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Purfield DC, McParland S, Wall E, Berry DP. The distribution of runs of homozygosity and selection signatures in six commercial meat sheep breeds. PLoS One 2017; 12:e0176780. [PMID: 28463982 PMCID: PMC5413029 DOI: 10.1371/journal.pone.0176780] [Citation(s) in RCA: 160] [Impact Index Per Article: 22.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 04/17/2017] [Indexed: 11/18/2022] Open
Abstract
Domestication and the subsequent selection of animals for either economic or morphological features can leave a variety of imprints on the genome of a population. Genomic regions subjected to high selective pressures often show reduced genetic diversity and frequent runs of homozygosity (ROH). Therefore, the objective of the present study was to use 42,182 autosomal SNPs to identify genomic regions in 3,191 sheep from six commercial breeds subjected to selection pressure and to quantify the genetic diversity within each breed using ROH. In addition, the historical effective population size of each breed was also estimated and, in conjunction with ROH, was used to elucidate the demographic history of the six breeds. ROH were common in the autosomes of animals in the present study, but the observed breed differences in patterns of ROH length and burden suggested differences in breed effective population size and recent management. ROH provided a sufficient predictor of the pedigree inbreeding coefficient, with an estimated correlation between both measures of 0.62. Genomic regions under putative selection were identified using two complementary algorithms; the fixation index and hapFLK. The identified regions under putative selection included candidate genes associated with skin pigmentation, body size and muscle formation; such characteristics are often sought after in modern-day breeding programs. These regions of selection frequently overlapped with high ROH regions both within and across breeds. Multiple yet uncharacterised genes also resided within putative regions of selection. This further substantiates the need for a more comprehensive annotation of the sheep genome as these uncharacterised genes may contribute to traits of interest in the animal sciences. Despite this, the regions identified as under putative selection in the current study provide an insight into the mechanisms leading to breed differentiation and genetic variation in meat production.
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Affiliation(s)
- Deirdre C. Purfield
- Animal & Grassland Research and Innovation Center, Teagasc, Moorepark, Fermoy, Co. Cork, Ireland
- * E-mail:
| | - Sinead McParland
- Animal & Grassland Research and Innovation Center, Teagasc, Moorepark, Fermoy, Co. Cork, Ireland
| | - Eamon Wall
- Sheep Ireland, Bandon, Co. Cork, Ireland
| | - Donagh P. Berry
- Animal & Grassland Research and Innovation Center, Teagasc, Moorepark, Fermoy, Co. Cork, Ireland
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Zhang L, Ma X, Xuan J, Wang H, Yuan Z, Wu M, Liu R, Zhu C, Wei C, Zhao F, Du L. Identification of MEF2B and TRHDE Gene Polymorphisms Related to Growth Traits in a New Ujumqin Sheep Population. PLoS One 2016; 11:e0159504. [PMID: 27472808 PMCID: PMC4966928 DOI: 10.1371/journal.pone.0159504] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 07/05/2016] [Indexed: 11/21/2022] Open
Abstract
2 SNPs were discovered in our previous genome-wide association study (GWAS): s58995.1 (rs420767326 A>G) in MEF2B gene and OAR3_115712045.1 (rs401775061 A>C) in TRHDE gene, which were significantly associated with post-weaning gain in sheep. Herein, we performed a replication experiment to investigate single nucleotide polymorphisms (SNPs) within the MEF2B and TRHDE gene exons, the 5′untranslated regions (within 1000bp), the 3′ untranslated regions (within 1000bp) and their associations with Ujumqin sheep growth traits in 4-month age and 6-month age, respectively. Finally,3 SNPs were selected to be investigated including 1 SNP in 3′untranslated regions in MEF2B gene (rs417014745 A>G) and 2 SNPs in TRHDE gene (rs426980328 T>C and rs430810656 G>A).The χ2 test showed all the 3 variations were in Hardy–Weinberg equilibrium (P>0.05) status. Association analysis suggested that rs426980328 T>C was significantly associated with body weight and chest girth in 4-month age (P<0.05). rs430810656 G>A exhibited extremely significant association with body weight and chest girth in 4-month age (P<0.01). rs417014745 A>G was extremely significantly associated with body weight and chest girth in 4-month age and chest girth in 6-month age (P<0.01), and it was also significantly associated with body weight in 6-month age (P<0.05). Combined effect analysis indicated significant associations between the combinations of rs426980328-rs417014745, rs430810656-rs417014745 and several growth traits (P<0.05). These results suggested MEF2B and TRHDE genes affected growth traits in Ujumqin sheep and the combination effect of the two genes also played a significant effective role. These SNPs might have potential value as genetic markers for growth traits and it could be used in Ujumqin sheep breeding in future. Further studies are necessary to confirm our findings.
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Affiliation(s)
- Li Zhang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Xiaomeng Ma
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Junli Xuan
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Huihua Wang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Zehu Yuan
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Mingming Wu
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Ruizao Liu
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Caiye Zhu
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Caihong Wei
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Fuping Zhao
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Lixin Du
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
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