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Ran H, He Q, Han Y, Wang J, Wang H, Yue B, Zhang M, Chai Z, Cai X, Zhong J, Wang H. Functional study and epigenetic targets analyses of SIRT1 in intramuscular preadipocytes via ChIP-seq and mRNA-seq. Epigenetics 2023; 18:2135194. [PMID: 36264146 PMCID: PMC9980681 DOI: 10.1080/15592294.2022.2135194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
The SIRT1 epigenetic regulator is involved in hepatic lipid homoeostasis. However, the role of SIRT1 in regulating intramuscular fat deposition as well as the pathways and potential epigenetic targets involved remain unknown. Herein, we investigate SIRT1 function, its genome-wide epigenetic target profile, and transcriptomic changes under SIRT1 overexpression during yak intramuscular preadipocytes differentiation. To this end, we analysed the relationship between SIRT1 and intramuscular fat content as well as lipid metabolism-related genes in longissimus dorsi tissue. We found that SIRT1 expression negatively correlates with intramuscular fat content as well as with the expression of genes related to lipid synthesis, while positively correlating with that of fatty acid oxidation-involved genes. SIRT1 overexpression in intramuscular preadipocytes significantly reduced adipose differentiation marker expression, intracellular triacylglycerol content, and lipid deposition. Chromatin immunoprecipitation coupled with high-throughput sequencing of H3K4ac (a known direct target of SIRT1) and high-throughput mRNA sequencing results revealed that SIRT1 may regulate intramuscular fat deposition via three potential new transcription factors (NRF1, NKX3.1, and EGR1) and four genes (MAPK1, RXRA, AGPAT1, and HADH) implicated in protein processing within the endoplasmic reticulum pathway and the MAPK signalling pathway in yaks. Our study provides novel insights into the role of SIRT1 in regulating yak intramuscular fat deposition and may help clarify the mechanistic determinants of yak meat characteristics.
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Affiliation(s)
- Hongbiao Ran
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Sichuan Province and Ministry of Education, Institute of Qinghai-Tibetan Plateau, Southwest Minzu University, Chengdu, People's Republic of China
| | - Qiuya He
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling, People's Republic of China
| | - Yuting Han
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Sichuan Province and Ministry of Education, Institute of Qinghai-Tibetan Plateau, Southwest Minzu University, Chengdu, People's Republic of China
| | - Jikun Wang
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Sichuan Province and Ministry of Education, Institute of Qinghai-Tibetan Plateau, Southwest Minzu University, Chengdu, People's Republic of China
| | - Haibo Wang
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Sichuan Province and Ministry of Education, Institute of Qinghai-Tibetan Plateau, Southwest Minzu University, Chengdu, People's Republic of China
| | - Binglin Yue
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Sichuan Province and Ministry of Education, Institute of Qinghai-Tibetan Plateau, Southwest Minzu University, Chengdu, People's Republic of China
| | - Ming Zhang
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Sichuan Province and Ministry of Education, Institute of Qinghai-Tibetan Plateau, Southwest Minzu University, Chengdu, People's Republic of China
| | - Zhixin Chai
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Sichuan Province and Ministry of Education, Institute of Qinghai-Tibetan Plateau, Southwest Minzu University, Chengdu, People's Republic of China
| | - Xin Cai
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Sichuan Province and Ministry of Education, Institute of Qinghai-Tibetan Plateau, Southwest Minzu University, Chengdu, People's Republic of China
| | - Jincheng Zhong
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Sichuan Province and Ministry of Education, Institute of Qinghai-Tibetan Plateau, Southwest Minzu University, Chengdu, People's Republic of China
| | - Hui Wang
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Sichuan Province and Ministry of Education, Institute of Qinghai-Tibetan Plateau, Southwest Minzu University, Chengdu, People's Republic of China
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Helal M, Ali MA, Nadrin AH, Awad YI, Younis NK, Alasyed BM, Jamal M, Eid DH, Soliman HA, Eissa SA, Ragab M. Association between IRS-1, PPAR-γ and LEP genes polymorphisms and growth traits in rabbits. Anim Biotechnol 2023; 34:2391-2399. [PMID: 35767350 DOI: 10.1080/10495398.2022.2092743] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
Single nucleotide polymorphisms are commonly associated with changes in quantitative traits, and have been considered useful markers for improving different traits in livestock. The current study aimed to explore the effect of three SNPs located in Insulin receptor substrate (IRS-1), Peroxisome proliferator-activated receptor γ (PPAR-γ), and Leptin (LEP) genes on the growth traits of rabbits. Individuals from three rabbit breeds were genotyped using RFLP-PCR. The IRS-1 variant (c.189T > G) was associated with post-weaning body weight, and body weight gains, However, the effect on growth rates was insignificant in Baladi Red and V-line rabbits. The PPAR-γ variant (c.207A > C) was significantly associated with 8-wk body weights in V-line rabbits, 10-wk body weights, and growth rates from 8 to 10 weeks of age in New Zealand rabbits. However, the differences between genotypes were insignificant for body weight gains and average daily gain. The LEP gene mutation (g.16079636C > G) had significant effects on body weights at 6 and 8 weeks of age in New Zealand White rabbits and 8 weeks of age in Baladi Red rabbits were associated with the presence of the C allele. Concludingly, the results stressed the importance of the IRS-1 gene in post-weaning growth and suggested the existence of breed-specific effects for PPAR-γ and LEP.
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Affiliation(s)
- Mostafa Helal
- Department of Animal Production, Faculty of Agriculture, Cairo University, Giza, Egypt
| | - Mahmoud A Ali
- Biotechnology Program, Faculty of Agriculture, Cairo University, Giza, Egypt
| | - Amira H Nadrin
- Biotechnology Program, Faculty of Agriculture, Cairo University, Giza, Egypt
| | - Yomna I Awad
- Biotechnology Program, Faculty of Agriculture, Cairo University, Giza, Egypt
| | - Nada K Younis
- Biotechnology Program, Faculty of Agriculture, Cairo University, Giza, Egypt
| | - Basant M Alasyed
- Biotechnology Program, Faculty of Agriculture, Cairo University, Giza, Egypt
| | - Mohnad Jamal
- Biotechnology Program, Faculty of Agriculture, Cairo University, Giza, Egypt
| | - Dima H Eid
- Biotechnology Program, Faculty of Agriculture, Cairo University, Giza, Egypt
| | - Hagar A Soliman
- Biotechnology Program, Faculty of Agriculture, Cairo University, Giza, Egypt
| | - Sara A Eissa
- Biotechnology Program, Faculty of Agriculture, Cairo University, Giza, Egypt
| | - Mohamed Ragab
- Department of Poultry Production, Kafr El-Sheikh University, Kafr EL-Sheikh, Egypt
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Lyu Y, Ren Y, Qu K, Quji S, Zhuzha B, Lei C, Chen N. Local ancestry and selection in admixed Sanjiang cattle. STRESS BIOLOGY 2023; 3:30. [PMID: 37676416 PMCID: PMC10441984 DOI: 10.1007/s44154-023-00101-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 06/29/2023] [Indexed: 09/08/2023]
Abstract
The majority of native cattle are taurine × indicine cattle of diverse phenotypes in the central region of China. Sanjiang cattle, a typical breed in the central region, play a central role in human livelihood and have good adaptability, including resistance to dampness, heat, roughage, and disease, and are thus regarded as an important genetic resource. However, the genetic history of the successful breed remains unknown. Here, we sequenced 10 Sanjiang cattle genomes and compared them to the 70 genomes of 5 representative populations worldwide. We characterized the genomic diversity and breed formation process of Sanjiang cattle and found that Sanjiang cattle have a mixed ancestry of indicine (55.6%) and taurine (33.2%) dating to approximately 30 generations ago, which has shaped the genome of Sanjiang cattle. Through ancestral fragment inference, selective sweep and transcriptomic analysis, we identified several genes linked to lipid metabolism, immune regulation, and stress reactions across the mosaic genome of Sanjiang cattle showing an excess of taurine or indicine ancestry. Taurine ancestry might contribute to meat quality, and indicine ancestry is more conducive to adaptation to hot climate conditions, making Sanjiang cattle a valuable genetic resource for the central region of China. Our results will help us understand the evolutionary history and ancestry components of Sanjiang cattle, which will provide a reference for resource conservation and selective breeding of Chinese native cattle.
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Affiliation(s)
- Yang Lyu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Yaxuan Ren
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Kaixing Qu
- Academy of Science and Technology, Chuxiong Normal University, Chuxiong, China
| | - Suolang Quji
- Institute of Animal Husbandry and Veterinary Science, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China
| | - Basang Zhuzha
- Institute of Animal Husbandry and Veterinary Science, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China
| | - Chuzhao Lei
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China.
| | - Ningbo Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China.
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Abdelrahman M, Wang W, Shaukat A, Kulyar MFEA, Lv H, Abulaiti A, Yao Z, Ahmad MJ, Liang A, Yang L. Nutritional Modulation, Gut, and Omics Crosstalk in Ruminants. Animals (Basel) 2022; 12:ani12080997. [PMID: 35454245 PMCID: PMC9029867 DOI: 10.3390/ani12080997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 03/31/2022] [Accepted: 04/05/2022] [Indexed: 11/30/2022] Open
Abstract
Simple Summary Over the last decade, animal nutrition science has been significantly developed, supported by the great advancements in molecular technologies. For scientists, the present "feedomics and nutrigenomics" era continues to evolve and shape how research is designed, performed, and understood. The new omics interpretations have established a new point of view for the nutrition–gene interaction, integrating more comprehensive findings from animal physiology, molecular genetics, and biochemistry. In the ruminant model, this modern approach addresses rumen microbes as a critical intermediate that can deepen the studies of diet–gut interaction with host genomics. The present review discusses nutrigenomics’ and feedomics’ potential contribution to diminishing the knowledge gap about the DNA cellular activities of different nutrients. It also presents how nutritional management can influence the epigenetic pathway, considering the production type, life stage, and species for more sustainable ruminant nutrition strategies. Abstract Ruminant nutrition has significantly revolutionized a new and prodigious molecular approach in livestock sciences over the last decade. Wide-spectrum advances in DNA and RNA technologies and analysis have produced a wealth of data that have shifted the research threshold scheme to a more affluent level. Recently, the published literature has pointed out the nutrient roles in different cellular genomic alterations among different ruminant species, besides the interactions with other factors, such as age, type, and breed. Additionally, it has addressed rumen microbes within the gut health and productivity context, which has made interpreting homogenous evidence more complicated. As a more systematic approach, nutrigenomics can identify how genomics interacts with nutrition and other variables linked to animal performance. Such findings should contribute to crystallizing powerful interpretations correlating feeding management with ruminant production and health through genomics. This review will present a road-mapping discussion of promising trends in ruminant nutrigenomics as a reference for phenotype expression through multi-level omics changes.
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Affiliation(s)
- Mohamed Abdelrahman
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agriculture University, Wuhan 430070, China; (M.A.); (W.W.); (A.S.); (H.L.); (A.A.); (Z.Y.); (M.J.A.); (A.L.)
- Animal Production Department, Faculty of Agriculture, Assuit University, Asyut 71515, Egypt
| | - Wei Wang
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agriculture University, Wuhan 430070, China; (M.A.); (W.W.); (A.S.); (H.L.); (A.A.); (Z.Y.); (M.J.A.); (A.L.)
| | - Aftab Shaukat
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agriculture University, Wuhan 430070, China; (M.A.); (W.W.); (A.S.); (H.L.); (A.A.); (Z.Y.); (M.J.A.); (A.L.)
| | | | - Haimiao Lv
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agriculture University, Wuhan 430070, China; (M.A.); (W.W.); (A.S.); (H.L.); (A.A.); (Z.Y.); (M.J.A.); (A.L.)
| | - Adili Abulaiti
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agriculture University, Wuhan 430070, China; (M.A.); (W.W.); (A.S.); (H.L.); (A.A.); (Z.Y.); (M.J.A.); (A.L.)
| | - Zhiqiu Yao
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agriculture University, Wuhan 430070, China; (M.A.); (W.W.); (A.S.); (H.L.); (A.A.); (Z.Y.); (M.J.A.); (A.L.)
| | - Muhammad Jamil Ahmad
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agriculture University, Wuhan 430070, China; (M.A.); (W.W.); (A.S.); (H.L.); (A.A.); (Z.Y.); (M.J.A.); (A.L.)
| | - Aixin Liang
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agriculture University, Wuhan 430070, China; (M.A.); (W.W.); (A.S.); (H.L.); (A.A.); (Z.Y.); (M.J.A.); (A.L.)
- National Center for International Research on Animal Genetics, Breeding and Reproduction (NCIRAGBR), Huazhong Agricultural University, Wuhan 430070, China
| | - Liguo Yang
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agriculture University, Wuhan 430070, China; (M.A.); (W.W.); (A.S.); (H.L.); (A.A.); (Z.Y.); (M.J.A.); (A.L.)
- National Center for International Research on Animal Genetics, Breeding and Reproduction (NCIRAGBR), Huazhong Agricultural University, Wuhan 430070, China
- Correspondence: ; Tel.: +86-138-7105-6592
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Ma J, Gao X, Li J, Gao H, Wang Z, Zhang L, Xu L, Gao H, Li H, Wang Y, Zhu B, Cai W, Wang C, Chen Y. Assessing the Genetic Background and Selection Signatures of Huaxi Cattle Using High-Density SNP Array. Animals (Basel) 2021; 11:ani11123469. [PMID: 34944246 PMCID: PMC8698132 DOI: 10.3390/ani11123469] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 11/24/2021] [Accepted: 12/02/2021] [Indexed: 11/16/2022] Open
Abstract
Huaxi cattle, a specialized beef cattle breed in China, has the characteristics of fast growth, high slaughter rate, and net meat rate, good reproductive performance, strong stress resistance, and wide adaptability. In this study, we evaluated the genetic diversity, population structure, and genetic relationships of Huaxi cattle and its ancestor populations at the genome-wide level, as well as detecting the selection signatures of Huaxi cattle. Principal component analysis (PCA) and phylogenetic analysis revealed that Huaxi cattle were obviously separated from other cattle populations. The admixture analysis showed that Huaxi cattle has distinct genetic structures among all populations at K = 4. It can be concluded that Huaxi cattle has formed its own unique genetic features. Using integrated haplotype score (iHS) and composite likelihood ratio (CLR) methods, we identified 143 and 199 potentially selected genes in Huaxi cattle, respectively, among which nine selected genes (KCNK1, PDLIM5, CPXM2, CAPN14, MIR2285D, MYOF, PKDCC, FOXN3, and EHD3) related to ion binding, muscle growth and differentiation, and immunity were detected by both methods. Our study sheds light on the unique genetic feature and phylogenetic relationship of Huaxi cattle, provides a basis for the genetic mechanism analysis of important economic traits, and guides further intensive breeding improvement of Huaxi cattle.
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Affiliation(s)
- Jun Ma
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (J.M.); (X.G.); (J.L.); (H.G.); (Z.W.); (L.Z.); (L.X.); (H.G.); (H.L.); (Y.W.); (B.Z.); (W.C.)
| | - Xue Gao
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (J.M.); (X.G.); (J.L.); (H.G.); (Z.W.); (L.Z.); (L.X.); (H.G.); (H.L.); (Y.W.); (B.Z.); (W.C.)
| | - Junya Li
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (J.M.); (X.G.); (J.L.); (H.G.); (Z.W.); (L.Z.); (L.X.); (H.G.); (H.L.); (Y.W.); (B.Z.); (W.C.)
| | - Huijiang Gao
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (J.M.); (X.G.); (J.L.); (H.G.); (Z.W.); (L.Z.); (L.X.); (H.G.); (H.L.); (Y.W.); (B.Z.); (W.C.)
| | - Zezhao Wang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (J.M.); (X.G.); (J.L.); (H.G.); (Z.W.); (L.Z.); (L.X.); (H.G.); (H.L.); (Y.W.); (B.Z.); (W.C.)
| | - Lupei Zhang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (J.M.); (X.G.); (J.L.); (H.G.); (Z.W.); (L.Z.); (L.X.); (H.G.); (H.L.); (Y.W.); (B.Z.); (W.C.)
| | - Lingyang Xu
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (J.M.); (X.G.); (J.L.); (H.G.); (Z.W.); (L.Z.); (L.X.); (H.G.); (H.L.); (Y.W.); (B.Z.); (W.C.)
| | - Han Gao
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (J.M.); (X.G.); (J.L.); (H.G.); (Z.W.); (L.Z.); (L.X.); (H.G.); (H.L.); (Y.W.); (B.Z.); (W.C.)
| | - Hongwei Li
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (J.M.); (X.G.); (J.L.); (H.G.); (Z.W.); (L.Z.); (L.X.); (H.G.); (H.L.); (Y.W.); (B.Z.); (W.C.)
| | - Yahui Wang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (J.M.); (X.G.); (J.L.); (H.G.); (Z.W.); (L.Z.); (L.X.); (H.G.); (H.L.); (Y.W.); (B.Z.); (W.C.)
| | - Bo Zhu
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (J.M.); (X.G.); (J.L.); (H.G.); (Z.W.); (L.Z.); (L.X.); (H.G.); (H.L.); (Y.W.); (B.Z.); (W.C.)
| | - Wentao Cai
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (J.M.); (X.G.); (J.L.); (H.G.); (Z.W.); (L.Z.); (L.X.); (H.G.); (H.L.); (Y.W.); (B.Z.); (W.C.)
| | - Congyong Wang
- Beijing Lianyu Beef Cattle Breeding Technology Limited Company, Beijing 100193, China;
| | - Yan Chen
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (J.M.); (X.G.); (J.L.); (H.G.); (Z.W.); (L.Z.); (L.X.); (H.G.); (H.L.); (Y.W.); (B.Z.); (W.C.)
- Correspondence:
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6
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Li Z, Liu X, Li Y, Wang W, Wang N, Xiao F, Gao H, Guo H, Li H, Wang S. Chicken C/EBPζ gene: Expression profiles, association analysis, and identification of functional variants for abdominal fat. Domest Anim Endocrinol 2021; 76:106631. [PMID: 33979717 DOI: 10.1016/j.domaniend.2021.106631] [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: 11/15/2020] [Revised: 04/06/2021] [Accepted: 04/06/2021] [Indexed: 10/21/2022]
Abstract
CCAAT enhancer binding protein ζ (C/EBPζ) plays an important role in adipose proliferation and differentiation in humans. However, very little is known about the effect of C/EBPζ on the growth and development of adipose tissues in domesticated animals. The present study attempted to investigate the mRNA expression profiles of chicken C/EBPζ in a variety of tissues; analyze the association of its variants with abdominal fat; and identify the functional variants for abdominal fat. The tissue expression profiles revealed that C/EBPζ was highly expressed in 19 tissues obtained from broilers. The expression level of C/EBPζ in fat broilers was significantly lower than that in lean broilers in the duodenum, ileum, cecum, kidney, pectoral muscle, and liver (P < 0.05). Among 170 polymorphic loci of C/EBPζ, 9 single nucleotide polymorphisms (SNPs) demonstrated a significant association with chicken abdominal fat traits (P < 0.05) as well as significant discrepancies in their allelic frequencies between fat and lean birds. Particularly, only C/EBPζ g.7085A>C exhibited significant correlation with abdominal fat traits (P < 0.00015) using the Bonferroni method. The results revealed that, in preadipocyte immortalized cells (ICPI), the luciferase activity of the A allele of g.7085A>C locus was remarkably stronger than that of the C allele (P < 0.05). In silico analysis showed that g.7085A>C locus was located in the binding region of the transcription factor SOX5, which possesses the ability to transform C/EBPζ transcription efficiency through binding with SOX5. In summary, the data obtained from this study suggested that C/EBPζ is a potential candidate gene responsible for abdominal fat deposition in chicken and that g.7085A>C is a functional SNP that can be promisingly leveraged for marker assisted selection (MAS) in future chicken breeding programs.
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Affiliation(s)
- Z Li
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin 150030, China; Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin 150030, China; College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, China
| | - X Liu
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin 150030, China; Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin 150030, China; College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, China
| | - Y Li
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin 150030, China; Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin 150030, China; College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, China
| | - W Wang
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin 150030, China; Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin 150030, China; College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, China
| | - N Wang
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin 150030, China; Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin 150030, China; College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, China
| | - F Xiao
- Fujian Sunnzer Biotechnology Development Co., Ltd, 354100, Guangze, Fujian Province, China
| | - H Gao
- Fujian Sunnzer Biotechnology Development Co., Ltd, 354100, Guangze, Fujian Province, China
| | - H Guo
- Fujian Sunnzer Biotechnology Development Co., Ltd, 354100, Guangze, Fujian Province, China
| | - H Li
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin 150030, China; Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin 150030, China; College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, China
| | - S Wang
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin 150030, China; Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin 150030, China; College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, China.
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7
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Cao H, Wen Y, Xu X, Liu K, Liu H, Tan Y, Zhou W, Mao H, Dong X, Xu N, Yin Z. Investigation of the CEBPA gene expression pattern and association analysis of its polymorphisms with meat quality traits in chickens. Anim Biotechnol 2020; 33:448-456. [PMID: 32776801 DOI: 10.1080/10495398.2020.1803343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Meat quality is closely related to the fat deposition which is regulated by a cascade of transcription factors. As a transcription factor, the CCAAT/enhancer binding protein alpha (CEBPA) is considered as one of the key molecules regulating adipogenesis. Therefore, the objective of this study was to detect the expression pattern of the CEBPA gene and evaluate whether its single nucleotide polymorphisms (SNPs) were associated with the meat quality traits in Wuliang Mountain Black-bone (WLMB) chickens. The results showed that the chicken CEBPA mRNA was widely expressed in the 11 tissues, and the expression pattern of it might be tissue- and time-specific different. The locus of g.74C > G was not significantly associated with chicken meat quality. For the locus of g.552G > A, chickens with the GG genotype showed higher pH (p < 0.01), lower drip loss (p < 0.01) and higher intramuscular fat (p < 0.05) than those with other genotypes. It suggested that polymorphisms of the CEBPA gene were significantly associated with the meat quality traits of WLMB chickens. The results of this study contribute to the functional research of the CEBPA gene and lay the foundation for improving meat quality based on the marker-assisted selection in chickens.
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Affiliation(s)
- Haiyue Cao
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yaya Wen
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - XiuLi Xu
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Ke Liu
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Honghua Liu
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yuge Tan
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Wei Zhou
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Haiguang Mao
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Xinyang Dong
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Ningying Xu
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Zhaozheng Yin
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China
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8
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Wang X, Cheng J, Qin W, Chen H, Chen G, Shang X, Zhang M, Balsai N, Chen H. Polymorphisms in 5' proximal regulating region of THRSP gene are associated with fat production in pigs. 3 Biotech 2020; 10:267. [PMID: 32509500 DOI: 10.1007/s13205-020-02266-6] [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: 04/16/2020] [Accepted: 05/18/2020] [Indexed: 01/17/2023] Open
Abstract
Chinese and imported pig breeds differ in fat production potential, which is associated with the polymorphisms in the 5' proximal regulating region (5'PRR) of thyroid hormone responsive gene (THRSP). In three Chinese breeds (Dingyuan, CDY; Wannanhua, CWH; and Jixi, CJX) and one introduced breed (Yorkshire, YKS), three variant sites were located at T/C-400, A/G-376, and G/A-98 in the 5'PRR. Chinese pig breeds had higher C-400 allele frequencies than YKS. The frequencies of A-376 in CDY and G-376 in CWH were about 0.8. G-98 allele frequencies in CWH and YKS were 0.8617 and 0.8149, respectively. TGG was the dominant haplotype in YKS, CGG in CWH and CJX, and CAA in CDY. According to haplotype frequency, four breeds were clustered into three types, which was consistent with the geographical distribution of the breeds. In CDY, the average backfat thickness (BFT) was the highest with the CC-400 genotype, followed by CT-400 and TT-400 genotypes. In YKS, the pigs with CC-400 or CT-400 genotypes had higher BFT and average daily weight gain, whereas those with CC-400 or TT-400 genotypes had larger lion-eye area. No significant difference was observed in carcass traits among different genotypes at the A/G-376 and G/A-98 loci. The mRNA abundance of THRSP expression for the CCAGAG genotype was significantly higher than that for CTAGAG or TTAGAG genotype. These results indicated that the polymorphisms and genotype distribution of THRSP were closely related to the potential for fat production in pig breeds, which were the result of adaptation to artificial selection and natural selection.
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Affiliation(s)
- Xiaohong Wang
- School of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036 China
- Experimental Animal Center of Anhui Medical University, Hefei, 230032 China
| | - Jin Cheng
- School of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036 China
| | - Wenjuan Qin
- School of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036 China
- Anhui Agricultural University International Immunization Center, Hefei, 230036 China
| | - Hua Chen
- School of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036 China
| | - Gongwei Chen
- School of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036 China
| | - Xuanjian Shang
- School of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036 China
| | - Mengting Zhang
- School of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036 China
| | - Nyamsuren Balsai
- School of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036 China
| | - Hongquan Chen
- School of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036 China
- Key Laboratory of Local Livestock and Poultry Genetic Resources Conservation and Biobreeding of Anhui Province, Hefei, 230036 China
- Anhui Agricultural University International Immunization Center, Hefei, 230036 China
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9
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Grigoletto L, Ferraz JBS, Oliveira HR, Eler JP, Bussiman FO, Abreu Silva BC, Baldi F, Brito LF. Genetic Architecture of Carcass and Meat Quality Traits in Montana Tropical ® Composite Beef Cattle. Front Genet 2020; 11:123. [PMID: 32180796 PMCID: PMC7057717 DOI: 10.3389/fgene.2020.00123] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 02/03/2020] [Indexed: 12/16/2022] Open
Abstract
The Montana Tropical® Composite is a recently developed beef cattle population that is rapidly expanding in Brazil and other tropical countries. This is mainly due to its improved meat quality and adaptation to tropical climate conditions compared to Zebu and Taurine cattle breeds, respectively. This study aimed to investigate the genetic architecture of ultrasound-based carcass and meat quality traits in Montana Tropical® Composite beef cattle. Therefore, we estimated variance components and genetic parameters and performed genome-wide association studies using the weighted single-step Genomic Best Linear Unbiased Prediction (GBLUP) approach. A pedigree dataset containing 28,480 animals was used, in which 1,436 were genotyped using a moderate-density Single Nucleotide Polymorphism panel (30K; 30,105 SNPs). A total of 9,358, 5,768, 7,996, and 1,972 phenotypic records for the traits Longissimus muscle area (LMA), backfat thickness (BFT), rump fat thickness (RFT), and for marbling score (MARB), respectively, were used for the analyses. Moderate to high heritability estimates were obtained and ranged from 0.16 ± 0.03 (RFT) to 0.33 ± 0.05 (MARB). A high genetic correlation was observed between BFT and RFT (0.97 ± 0.02), suggesting that a similar set of genes affects both traits. The most relevant genomic regions associated with LMA, BFT, RFT, and MARB were found on BTA10 (5.4–5.8 Mb), BTA27 (25.2–25.5 Mb), BTA18 (60.6–61.0 Mb), and BTA21 (14.8–15.4 Mb). Two overlapping genomic regions were identified for RFT and MARB (BTA13:47.9–48.1 Mb) and for BFT and RFT (BTA13:61.5–62.3 Mb). Candidate genes identified in this study, including PLAG1, LYN, WWOX, and PLAGL2, were previously reported to be associated with growth, stature, skeletal muscle growth, fat thickness, and fatty acid composition. Our results indicate that ultrasound-based carcass and meat quality traits in the Montana Tropical® Composite beef cattle are heritable, and therefore, can be improved through selective breeding. In addition, various novel and already known genomic regions related to these traits were identified, which contribute to a better understanding of the underlying genetic background of LMA, BFT, RFT, and MARB in the Montana Tropical Composite population.
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Affiliation(s)
- Laís Grigoletto
- Department of Animal Sciences, College of Animal Sciences and Food Engineering, University of São Paulo, Pirassununga, Brazil.,Department of Animal Sciences, Purdue University, West Lafayette, IN, United States
| | - José B S Ferraz
- Department of Animal Sciences, College of Animal Sciences and Food Engineering, University of São Paulo, Pirassununga, Brazil
| | - Hinayah R Oliveira
- Department of Animal Sciences, Purdue University, West Lafayette, IN, United States
| | - Joanir P Eler
- Department of Animal Sciences, College of Animal Sciences and Food Engineering, University of São Paulo, Pirassununga, Brazil
| | - Fernando O Bussiman
- Department of Animal Sciences, College of Animal Sciences and Food Engineering, University of São Paulo, Pirassununga, Brazil
| | - Barbara C Abreu Silva
- Department of Animal Sciences, College of Animal Sciences and Food Engineering, University of São Paulo, Pirassununga, Brazil
| | - Fernando Baldi
- Department of Animal Sciences, College of Agricultural and Veterinary Sciences, São Paulo State University, Jaboticabal, Brazil
| | - Luiz F Brito
- Department of Animal Sciences, Purdue University, West Lafayette, IN, United States
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10
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Do DN, Schenkel F, Miglior F, Zhao X, Ibeagha-Awemu EM. Targeted genotyping to identify potential functional variants associated with cholesterol content in bovine milk. Anim Genet 2020; 51:200-209. [PMID: 31913546 DOI: 10.1111/age.12901] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 12/03/2019] [Accepted: 12/10/2019] [Indexed: 01/04/2023]
Abstract
High blood cholesterol concentration, mainly caused by high dietary cholesterol, is a potential risk factor for human health. Dairy products are important sources of human dietary cholesterol intake. Therefore, monitoring bovine milk cholesterol concentration is important for human health benefit. Genetic selection for improvement of cow milk cholesterol content requires understanding of the genetics of milk cholesterol. For this purpose, we performed analyses of additive and dominance effects of 126 potentially functional SNPs within 43 candidate genes with milk cholesterol content [expressed as mg of cholesterol in 100 g of fat (CHL_fat) or in 100 mg of milk (CHL_milk)]. The additive and dominance effects of SNPs rs380643365 in AGPAT1 (P = 0.04) and rs134357240 in SOAT1 (P = 0.035) genes associated significantly with CHL_fat. Moreover, five (rs109326954 and rs523413537 in DGAT1, rs109376747 in LDLR, rs42781651 in FAM198B and rs109967779 in ACAT2) and four (rs137347384 in RBM19, rs109376747 in LDLR, rs42016945 in PPARG and rs110862179 in SCAP) SNPs were significantly associated with CHL_milk (P < 0.05) based on additive and dominance effect analyses respectively. Rs109326954 and rs523413537 in DGAT1 explained a considerable portion of the phenotypic variance of CHL_milk (7.54 and 6.84% respectively), and might be useful in selection programs for reduced milk cholesterol content. Several significantly associated SNPs were in genes (such as ACAT2 and LDLR) involved in cholesterol metabolism in the liver or cholesterol transport, suggesting multiple mechanisms regulating milk cholesterol content. Nine and seven SNPs identified by additive or dominance effect analyses associated significantly with milk yield and fat yield respectively. Further analyses are required to better understand the consequences of these variants and their potential use in genomic selection of the studied traits.
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Affiliation(s)
- D N Do
- Agriculture and Agri-Food Canada, Sherbrooke Research and Development Centre, Sherbrooke, QC,, J1M 0C8, Canada.,Department of Animal Science and Aquaculture, Dalhousie University, 58 River Road, Truro, NS, B2N 5E3, Canada
| | - F Schenkel
- Department of Animal Biosciences, Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - F Miglior
- Department of Animal Biosciences, Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - X Zhao
- Department of Animal Science, McGill University, Ste-Anne-de-Bellevue, Montreal, QC, H9X 3V9, Canada
| | - E M Ibeagha-Awemu
- Agriculture and Agri-Food Canada, Sherbrooke Research and Development Centre, Sherbrooke, QC,, J1M 0C8, Canada
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11
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Fonseca PADS, Id-Lahoucine S, Reverter A, Medrano JF, Fortes MS, Casellas J, Miglior F, Brito L, Carvalho MRS, Schenkel FS, Nguyen LT, Porto-Neto LR, Thomas MG, Cánovas A. Combining multi-OMICs information to identify key-regulator genes for pleiotropic effect on fertility and production traits in beef cattle. PLoS One 2018; 13:e0205295. [PMID: 30335783 PMCID: PMC6193631 DOI: 10.1371/journal.pone.0205295] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 09/21/2018] [Indexed: 12/21/2022] Open
Abstract
The identification of biological processes related to the regulation of complex traits is a difficult task. Commonly, complex traits are regulated through a multitude of genes contributing each to a small part of the total genetic variance. Additionally, some loci can simultaneously regulate several complex traits, a phenomenon defined as pleiotropy. The lack of understanding on the biological processes responsible for the regulation of these traits results in the decrease of selection efficiency and the selection of undesirable hitchhiking effects. The identification of pleiotropic key-regulator genes can assist in developing important tools for investigating biological processes underlying complex traits. A multi-breed and multi-OMICs approach was applied to study the pleiotropic effects of key-regulator genes using three independent beef cattle populations evaluated for fertility traits. A pleiotropic map for 32 traits related to growth, feed efficiency, carcass and meat quality, and reproduction was used to identify genes shared among the different populations and breeds in pleiotropic regions. Furthermore, data-mining analyses were performed using the Cattle QTL database (CattleQTLdb) to identify the QTL category annotated in the regions around the genes shared among breeds. This approach allowed the identification of a main gene network (composed of 38 genes) shared among breeds. This gene network was significantly associated with thyroid activity, among other biological processes, and displayed a high regulatory potential. In addition, it was possible to identify genes with pleiotropic effects related to crucial biological processes that regulate economically relevant traits associated with fertility, production and health, such as MYC, PPARG, GSK3B, TG and IYD genes. These genes will be further investigated to better understand the biological processes involved in the expression of complex traits and assist in the identification of functional variants associated with undesirable phenotypes, such as decreased fertility, poor feed efficiency and negative energetic balance.
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Affiliation(s)
- Pablo Augusto de Souza Fonseca
- University of Guelph, Department of Animal Biosciences, Centre for Genetic Improvement of Livestock, Guelph, Ontario, Canada
- Universidade Federal de Minas Gerais, Departamento de Biologia Geral, Belo Horizonte, Minas Gerais, Brazil
| | - Samir Id-Lahoucine
- University of Guelph, Department of Animal Biosciences, Centre for Genetic Improvement of Livestock, Guelph, Ontario, Canada
| | - Antonio Reverter
- CSIRO Agriculture and Food, Queensland Bioscience Precinct, Brisbane, Queensland, Australia
| | - Juan F. Medrano
- University of California-Davis, Department of Animal Science, Davis, California, United States of America
| | - Marina S. Fortes
- The University of Queensland, School of Chemistry and Molecular Biosciences, Brisbane, Queensland, Australia
| | - Joaquim Casellas
- Universitat Autònoma de Barcelona, Departament de Ciència Animal i dels Aliments, Barcelona, Bellaterra, Barcelona, Spain
| | - Filippo Miglior
- University of Guelph, Department of Animal Biosciences, Centre for Genetic Improvement of Livestock, Guelph, Ontario, Canada
- Canadian Dairy Network, Guelph, Ontario, Canada
| | - Luiz Brito
- University of Guelph, Department of Animal Biosciences, Centre for Genetic Improvement of Livestock, Guelph, Ontario, Canada
| | - Maria Raquel S. Carvalho
- Universidade Federal de Minas Gerais, Departamento de Biologia Geral, Belo Horizonte, Minas Gerais, Brazil
| | - Flávio S. Schenkel
- University of Guelph, Department of Animal Biosciences, Centre for Genetic Improvement of Livestock, Guelph, Ontario, Canada
| | - Loan T. Nguyen
- The University of Queensland, School of Chemistry and Molecular Biosciences, Brisbane, Queensland, Australia
| | - Laercio R. Porto-Neto
- CSIRO Agriculture and Food, Queensland Bioscience Precinct, Brisbane, Queensland, Australia
| | - Milton G. Thomas
- Colorado State University, Department of Animal Science, Fort-Colins, Colorado, United States of America
| | - Angela Cánovas
- University of Guelph, Department of Animal Biosciences, Centre for Genetic Improvement of Livestock, Guelph, Ontario, Canada
- * E-mail:
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