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Kalds P, Zhou S, Gao Y, Cai B, Huang S, Chen Y, Wang X. Genetics of the phenotypic evolution in sheep: a molecular look at diversity-driving genes. Genet Sel Evol 2022; 54:61. [PMID: 36085023 PMCID: PMC9463822 DOI: 10.1186/s12711-022-00753-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Accepted: 08/29/2022] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND After domestication, the evolution of phenotypically-varied sheep breeds has generated rich biodiversity. This wide phenotypic variation arises as a result of hidden genomic changes that range from a single nucleotide to several thousands of nucleotides. Thus, it is of interest and significance to reveal and understand the genomic changes underlying the phenotypic variation of sheep breeds in order to drive selection towards economically important traits. REVIEW Various traits contribute to the emergence of variation in sheep phenotypic characteristics, including coat color, horns, tail, wool, ears, udder, vertebrae, among others. The genes that determine most of these phenotypic traits have been investigated, which has generated knowledge regarding the genetic determinism of several agriculturally-relevant traits in sheep. In this review, we discuss the genomic knowledge that has emerged in the past few decades regarding the phenotypic traits in sheep, and our ultimate aim is to encourage its practical application in sheep breeding. In addition, in order to expand the current understanding of the sheep genome, we shed light on research gaps that require further investigation. CONCLUSIONS Although significant research efforts have been conducted in the past few decades, several aspects of the sheep genome remain unexplored. For the full utilization of the current knowledge of the sheep genome, a wide practical application is still required in order to boost sheep productive performance and contribute to the generation of improved sheep breeds. The accumulated knowledge on the sheep genome will help advance and strengthen sheep breeding programs to face future challenges in the sector, such as climate change, global human population growth, and the increasing demand for products of animal origin.
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Affiliation(s)
- Peter Kalds
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100 China
- Department of Animal and Poultry Production, Faculty of Environmental Agricultural Sciences, Arish University, El-Arish, 45511 Egypt
| | - Shiwei Zhou
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100 China
- College of Veterinary Medicine, Northwest A&F University, Yangling, 712100 China
| | - Yawei Gao
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100 China
| | - Bei Cai
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100 China
| | - Shuhong Huang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100 China
| | - Yulin Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100 China
- International Joint Agriculture Research Center for Animal Bio-Breeding, Ministry of Agriculture and Rural Affairs, Yangling, 712100 China
| | - Xiaolong Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100 China
- International Joint Agriculture Research Center for Animal Bio-Breeding, Ministry of Agriculture and Rural Affairs, Yangling, 712100 China
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Pewan SB, Otto JR, Huerlimann R, Budd AM, Mwangi FW, Edmunds RC, Holman BWB, Henry MLE, Kinobe RT, Adegboye OA, Malau-Aduli AEO. Next Generation Sequencing of Single Nucleotide Polymorphic DNA-Markers in Selecting for Intramuscular Fat, Fat Melting Point, Omega-3 Long-Chain Polyunsaturated Fatty Acids and Meat Eating Quality in Tattykeel Australian White MARGRA Lamb. Foods 2021; 10:foods10102288. [PMID: 34681337 PMCID: PMC8535056 DOI: 10.3390/foods10102288] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 09/13/2021] [Accepted: 09/17/2021] [Indexed: 01/14/2023] Open
Abstract
Meat quality data can only be obtained after slaughter when selection decisions about the live animal are already too late. Carcass estimated breeding values present major precision problems due to low accuracy, and by the time an informed decision on the genetic merit for meat quality is made, the animal is already dead. We report for the first time, a targeted next-generation sequencing (NGS) of single nucleotide polymorphisms (SNP) of lipid metabolism genes in Tattykeel Australian White (TAW) sheep of the MARGRA lamb brand, utilizing an innovative and minimally invasive muscle biopsy sampling technique for directly quantifying the genetic worth of live lambs for health-beneficial omega-3 long-chain polyunsaturated fatty acids (n-3 LC-PUFA), intramuscular fat (IMF), and fat melting point (FMP). NGS of stearoyl-CoA desaturase (SCD), fatty acid binding protein-4 (FABP4), and fatty acid synthase (FASN) genes identified functional SNP with unique DNA marker signatures for TAW genetics. The SCD g.23881050T>C locus was significantly associated with IMF, C22:6n-3, and C22:5n-3; FASN g.12323864A>G locus with FMP, C18:3n-3, C18:1n-9, C18:0, C16:0, MUFA, and FABP4 g.62829478A>T locus with IMF. These add new knowledge, precision, and reliability in directly making early and informed decisions on live sheep selection and breeding for health-beneficial n-3 LC-PUFA, FMP, IMF and superior meat-eating quality at the farmgate level. The findings provide evidence that significant associations exist between SNP of lipid metabolism genes and n-3 LC-PUFA, IMF, and FMP, thus underpinning potential marker-assisted selection for meat-eating quality traits in TAW lambs.
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Affiliation(s)
- Shedrach Benjamin Pewan
- Animal Genetics and Nutrition, Veterinary Sciences Discipline, College of Public Health, Medical and Veterinary Sciences, Division of Tropical Health and Medicine, James Cook University, Townsville, QLD 4811, Australia; (S.B.P.); (J.R.O.); (F.W.M.); (R.C.E.); (R.T.K.)
- National Veterinary Research Institute, Private Mail Bag 01 Vom, Plateau State, Nigeria
| | - John Roger Otto
- Animal Genetics and Nutrition, Veterinary Sciences Discipline, College of Public Health, Medical and Veterinary Sciences, Division of Tropical Health and Medicine, James Cook University, Townsville, QLD 4811, Australia; (S.B.P.); (J.R.O.); (F.W.M.); (R.C.E.); (R.T.K.)
| | - Roger Huerlimann
- Marine Climate Change Unit, Okinawa Institute of Science and Technology, 1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan;
- Centre for Sustainable Tropical Fisheries and Aquaculture and Centre for Tropical Bioinformatics and Molecular Biology, College of Science and Engineering, James Cook University, Townsville, QLD 4811, Australia;
| | - Alyssa Maree Budd
- Centre for Sustainable Tropical Fisheries and Aquaculture and Centre for Tropical Bioinformatics and Molecular Biology, College of Science and Engineering, James Cook University, Townsville, QLD 4811, Australia;
| | - Felista Waithira Mwangi
- Animal Genetics and Nutrition, Veterinary Sciences Discipline, College of Public Health, Medical and Veterinary Sciences, Division of Tropical Health and Medicine, James Cook University, Townsville, QLD 4811, Australia; (S.B.P.); (J.R.O.); (F.W.M.); (R.C.E.); (R.T.K.)
| | - Richard Crawford Edmunds
- Animal Genetics and Nutrition, Veterinary Sciences Discipline, College of Public Health, Medical and Veterinary Sciences, Division of Tropical Health and Medicine, James Cook University, Townsville, QLD 4811, Australia; (S.B.P.); (J.R.O.); (F.W.M.); (R.C.E.); (R.T.K.)
| | | | - Michelle Lauren Elizabeth Henry
- Gundagai Meat Processors, 2916 Gocup Road, South Gundagai, NSW 2722, Australia;
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Robert Tumwesigye Kinobe
- Animal Genetics and Nutrition, Veterinary Sciences Discipline, College of Public Health, Medical and Veterinary Sciences, Division of Tropical Health and Medicine, James Cook University, Townsville, QLD 4811, Australia; (S.B.P.); (J.R.O.); (F.W.M.); (R.C.E.); (R.T.K.)
| | - Oyelola Abdulwasiu Adegboye
- Public Health and Tropical Medicine Discipline, College of Public Health, Medical and Veterinary Sciences, Division of Tropical Health and Medicine, James Cook University, Townsville, QLD 4811, Australia;
| | - Aduli Enoch Othniel Malau-Aduli
- Animal Genetics and Nutrition, Veterinary Sciences Discipline, College of Public Health, Medical and Veterinary Sciences, Division of Tropical Health and Medicine, James Cook University, Townsville, QLD 4811, Australia; (S.B.P.); (J.R.O.); (F.W.M.); (R.C.E.); (R.T.K.)
- Correspondence: ; Tel.: +61-747-815-339
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Wang Y, Liu W, Hang C, Du Y, Chen Y, Xing J, Gao J, Qiu D. Association of A-FABP gene polymorphism and mRNA expression with intramuscular fat content (IMF) in Baicheng-You chicken. J Anim Physiol Anim Nutr (Berl) 2019; 103:1447-1452. [PMID: 31276245 DOI: 10.1111/jpn.13150] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 06/09/2019] [Accepted: 06/14/2019] [Indexed: 11/28/2022]
Abstract
This study aims to assess the association of polymorphisms and mRNA expression of adipocyte-type fatty acid-binding protein (A-FABP) with intramuscular fat (IMF) in the breast muscle (BM) and leg muscle (LM) of Baicheng-You chickens (BYCs). A total of 180 chickens, including sixty black Baicheng-You chickens (BBYCs), sixty silky Baicheng-You chickens (SBYCs) and sixty white Baicheng-You chickens (WBYCs), were reared from 1 to 120 day. A polymerase chain reaction-single-strand conformation polymorphism strategy (PCR-SSCP) was used to detect the polymorphism of the A-FABP gene in the first exon, and the C51T silent mutational site was found. The IMF content with the AA genotype was significantly higher than that with the AG genotype (p = 0.0473) in the LM of WBYC. Thus, this site could be taken as a molecular marker in selecting a higher IMF content of LM in WBYC. A-FABP gene mRNA expression in the BM and LM of BYCs was detected, and a significant positive correlation was observed in the LM of WBYC. These findings provide fundamental data that might be useful in further study of the role of the A-FABP gene in IMF content and fatty metabolism in chickens.
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Affiliation(s)
- Yong Wang
- College of Animal Science, Tarim University, Alar, China
| | - Wenqiang Liu
- Department of Animal Science and Technology, College of Agriculture, Liaocheng University, Liaocheng, China
| | - Chao Hang
- College of Animal Science, Tarim University, Alar, China
| | - Yiqiang Du
- College of Animal Science, Tarim University, Alar, China
| | - Ying Chen
- College of Animal Science, Tarim University, Alar, China
| | - Jinming Xing
- College of Animal Science, Tarim University, Alar, China
| | - Jun Gao
- College of Animal Science, Tarim University, Alar, China
| | - Dexin Qiu
- College of Animal Science, Tarim University, Alar, China.,State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
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Zhao H, He S, Wang S, Zhu Y, Xu H, Luo R, Lan X, Cai Y, Sun X. Two New Insertion/Deletion Variants of the PITX2 Gene and their Effects on Growth Traits in Sheep. Anim Biotechnol 2017; 29:276-282. [PMID: 29200321 DOI: 10.1080/10495398.2017.1379415] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
In China, Tong sheep (TS) and Lanzhou fat-tailed sheep (LFTS) are two closely relative endanger breeds for low meat production and low fecundity, finding some marker-assisted selected (MAS) is our first priority for improving their growth traits. For this purpose, Hu sheep (HS) and small-tailed Han sheep (STHS) were compared with two endangered breeds (TS and LFTS). Paired-liked homeodomain transcription factor 2 (PITX2) gene was the important member of PITX family, which could adjust animal growth through hypothalamic-pituitary-adrenal axis. During the past years, insertion/deletion (indel) has become increasingly popular in application as MAS. In this study, two novel indel loci were identified, and five significant differences, including chest width, hip width, chest depth, chest circumference, and body height, were found between different breeds. Interestingly, there was no DD genotype and smaller number of ID genotye. All the ID genotypes were significantly greater than II genotype, which was to say the allele of "D" was dominant variation and its frequency was lower, which demonstrated that it has huge space for selection. Briefly, the two indel were potential and useful DNA markers for selecting excellent individuals in relation to growth traits in sheep.
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Affiliation(s)
- Haidong Zhao
- a College of Animal Science and Technology , Northwest A&F University , Yangling , China
| | - Shuai He
- a College of Animal Science and Technology , Northwest A&F University , Yangling , China
| | - Shuhui Wang
- a College of Animal Science and Technology , Northwest A&F University , Yangling , China
| | - Yanjiao Zhu
- a College of Animal Science and Technology , Northwest A&F University , Yangling , China
| | - Hongwei Xu
- b Science Experimental Center , Northwest University for Nationalities , Lanzhou , China
| | - Renyun Luo
- c Ruilin Sci-Tech Culture and Breeding Limit Company , Yongjing , China
| | - Xianyong Lan
- a College of Animal Science and Technology , Northwest A&F University , Yangling , China
| | - Yong Cai
- c Ruilin Sci-Tech Culture and Breeding Limit Company , Yongjing , China.,d College of Life Science and Engineering , Northwest University for Nationalities , Lanzhou , China
| | - Xiuzhu Sun
- a College of Animal Science and Technology , Northwest A&F University , Yangling , China
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Wang Y, Chen H, Han D, Chen Y, Muhatai G, Kurban T, Xing J, He J. Correlation of the A-FABP Gene Polymorphism and mRNA Expression with Intramuscular Fat Content in Three-Yellow Chicken and Hetian-Black Chicken. Anim Biotechnol 2016; 28:37-43. [DOI: 10.1080/10495398.2016.1194288] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Yong Wang
- Key Laboratory of Tarim Animal Husbandry Science & Technology of Xinjiang Production and Construction Groups, College of Animal Science, Tarim University, Alar, Xinjiang Uygur Autonomous Region, China
| | - Hongwei Chen
- Key Laboratory of Tarim Animal Husbandry Science & Technology of Xinjiang Production and Construction Groups, College of Animal Science, Tarim University, Alar, Xinjiang Uygur Autonomous Region, China
| | - Diangang Han
- Kunming Airport Entry-Exit Inspection and Quarantine Bureau, Kunming, China
| | - Ying Chen
- Key Laboratory of Tarim Animal Husbandry Science & Technology of Xinjiang Production and Construction Groups, College of Animal Science, Tarim University, Alar, Xinjiang Uygur Autonomous Region, China
| | - Gemingguli Muhatai
- Key Laboratory of Tarim Animal Husbandry Science & Technology of Xinjiang Production and Construction Groups, College of Animal Science, Tarim University, Alar, Xinjiang Uygur Autonomous Region, China
| | - Tursunjan Kurban
- Key Laboratory of Tarim Animal Husbandry Science & Technology of Xinjiang Production and Construction Groups, College of Animal Science, Tarim University, Alar, Xinjiang Uygur Autonomous Region, China
| | - Jinming Xing
- Key Laboratory of Tarim Animal Husbandry Science & Technology of Xinjiang Production and Construction Groups, College of Animal Science, Tarim University, Alar, Xinjiang Uygur Autonomous Region, China
| | - Jianzhong He
- Key Laboratory of Tarim Animal Husbandry Science & Technology of Xinjiang Production and Construction Groups, College of Animal Science, Tarim University, Alar, Xinjiang Uygur Autonomous Region, China
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Wang Y, He J, Yang W, Muhantay G, Chen Y, Xing J, Liu J. Correlation between Heart-type Fatty Acid-binding Protein Gene Polymorphism and mRNA Expression with Intramuscular Fat in Baicheng-oil Chicken. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2015; 28:1380-7. [PMID: 26323394 PMCID: PMC4554844 DOI: 10.5713/ajas.14.0886] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Revised: 02/03/2015] [Accepted: 03/12/2015] [Indexed: 01/19/2023]
Abstract
This study aims to determine the polymorphism and mRNA expression pattern of the heart-type fatty acid-binding protein (H-FABP) gene and their association with intramuscular fat (IMF) content in the breast and leg muscles of Baicheng oil chicken (BOC). A total of 720 chickens, including 240 black Baicheng oil chicken (BBOC), 240 silky Baicheng oil chicken (SBOC), and 240 white Baicheng oil chicken (WBOC) were raised. Three genotypes of H-FABP gene second extron following AA, AB, and BB were detected by polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP) strategy. The G939A site created AA genotype and G956A site created BB genotype. The content of IMF in AA genotype in breast muscle of BBOC was significantly higher than that of AB (p = 0.0176) and the genotype in leg muscle of WBOC was significantly higher than that of AB (p = 0.0145). The G939A site could be taken as genetic marker for higher IMF content selecting for breast muscle of BBOC and leg muscle of WBOC. The relative mRNA expression of H-FABP was measured by real-time PCR at 30, 60, 90, and 120 d. The IMF content significantly increased with age in both muscles. The mRNA expression level of H-FABP significantly decreased with age in both muscles of the three types of chickens. Moreover, a significant negative correlation between H-FABP abundance and IMF content in the leg muscles of WBOC (p = 0.035) was observed. The mRNA expression of H-FABP negatively correlated with the IMF content in both breast and leg muscles of BOC sat slaughter time.
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Affiliation(s)
- Yong Wang
- Inspection Center for the Quality of Agricultural and Sideline Products of Shandong, Zoucheng 273500, China
| | - Jianzhong He
- Inspection Center for the Quality of Agricultural and Sideline Products of Shandong, Zoucheng 273500, China
| | - Wenxuan Yang
- Inspection Center for the Quality of Agricultural and Sideline Products of Shandong, Zoucheng 273500, China
| | - Gemenggul Muhantay
- Inspection Center for the Quality of Agricultural and Sideline Products of Shandong, Zoucheng 273500, China
| | - Ying Chen
- Inspection Center for the Quality of Agricultural and Sideline Products of Shandong, Zoucheng 273500, China
| | - Jinming Xing
- Inspection Center for the Quality of Agricultural and Sideline Products of Shandong, Zoucheng 273500, China
| | - Jianzhu Liu
- College of Veterinary Medicine, Research Center for Animal Disease Control Engineering Shandong, Shandong Agricultural University, Tai'an 271018, China
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Transcriptome profile analysis of adipose tissues from fat and short-tailed sheep. Gene 2014; 549:252-7. [PMID: 25088569 DOI: 10.1016/j.gene.2014.07.072] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2014] [Revised: 07/21/2014] [Accepted: 07/30/2014] [Indexed: 11/20/2022]
Abstract
Recent studies in domestic animals have used RNA-seq to explore the transcriptome of different tissues in a limited number of individuals. In the present study, de novo transcriptome sequencing was used to compare sheep adipose tissue transcriptome profiles between a fat-tailed breed (Kazak sheep; KS) and a short-tailed (Tibetan sheep; TS). The RNA-seq data from these two groups revealed that 646 genes were differentially expressed between the KS and TS groups, including 280 up-regulated and 366 down-regulated genes. We identified genes relevant to fat metabolism in adipose tissues, including two top genes with the largest fold change (NELL1 and FMO3). Pathway analysis revealed that the differentially expressed genes between the KS and TS breeds belong to fatty acid metabolism relevant pathways (e.g. fat digestion and absorption, glycine, serine, and threonine metabolism) and cell junction-related pathways (e.g. cell adhesion molecules) which contribute to fat deposition. This work highlighted potential genes and gene networks that affect fat deposition and meat quality in sheep.
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Zhang Y, Liu Y, Song J, Cheng S, Dong L. Effects of dietary energy level on the transcription of the H-FABP gene in different tissues of sheep. Small Rumin Res 2013. [DOI: 10.1016/j.smallrumres.2013.09.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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