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Chen C, Chen W, Ding H, Zhang G, Xie K, Zhang T. Integrated Metabolomic and Transcriptomic Analysis Reveals Potential Gut-Liver Crosstalks in the Lipogenesis of Chicken. Animals (Basel) 2023; 13:ani13101659. [PMID: 37238090 DOI: 10.3390/ani13101659] [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: 04/22/2023] [Revised: 05/12/2023] [Accepted: 05/15/2023] [Indexed: 05/28/2023] Open
Abstract
Growing evidence has shown the involvement of the gut-liver axis in lipogenesis and fat deposition. However, how the gut crosstalk with the liver and the potential role of gut-liver crosstalk in the lipogenesis of chicken remains largely unknown. In this study, to identify gut-liver crosstalks involved in regulating the lipogenesis of chicken, we first established an HFD-induced obese chicken model. Using this model, we detected the changes in the metabolic profiles of the cecum and liver in response to the HFD-induced excessive lipogenesis using ultra-high-performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS) analysis. The changes in the gene expression profiles of the liver were examined by RNA sequencing. The potential gut-liver crosstalks were identified by the correlation analysis of key metabolites and genes. The results showed that a total of 113 and 73 differentially abundant metabolites (DAMs) between NFD and HFD groups were identified in the chicken cecum and liver, respectively. Eleven DAMs overlayed between the two comparisons, in which ten DAMs showed consistent abundance trends in the cecum and liver after HFD feeding, suggesting their potential as signaling molecules between the gut and liver. RNA sequencing identified 271 differentially expressed genes (DEGs) in the liver of chickens fed with NFD vs. HFD. Thirty-five DEGs were involved in the lipid metabolic process, which might be candidate genes regulating the lipogenesis of chicken. Correlation analysis indicated that 5-hydroxyisourate, alpha-linolenic acid, bovinic acid, linoleic acid, and trans-2-octenoic acid might be transported from gut to liver, and thereby up-regulate the expression of ACSS2, PCSK9, and CYP2C18 and down-regulate one or more genes of CDS1, ST8SIA6, LOC415787, MOGAT1, PLIN1, LOC423719, and EDN2 in the liver to enhance the lipogenesis of chicken. Moreover, taurocholic acid might be transported from the gut to the liver and contribute to HFD-induced lipogenesis by regulating the expression of ACACA, FASN, AACS, and LPL in the liver. Our findings contribute to a better understanding of gut-liver crosstalks and their potential roles in regulating chicken lipogenesis.
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Affiliation(s)
- Can Chen
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Ministry of Education, Yangzhou University, Yangzhou 225009, China
| | - Weilin Chen
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Ministry of Education, Yangzhou University, Yangzhou 225009, China
| | - Hao Ding
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China
| | - Genxi Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Ministry of Education, Yangzhou University, Yangzhou 225009, China
| | - Kaizhou Xie
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Ministry of Education, Yangzhou University, Yangzhou 225009, China
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China
| | - Tao Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Ministry of Education, Yangzhou University, Yangzhou 225009, China
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Matar AM, Alharthi AS, Ayadi M, Al-Garadi MA, Aljummah RS. Identification of Genetic Polymorphisms of PI, PIII, and Exon 53 in the Acetyl-CoA Carboxylase-α (ACACα) Gene and Their Association with Milk Composition Traits of Najdi Sheep. Animals (Basel) 2023; 13:ani13081317. [PMID: 37106880 PMCID: PMC10135350 DOI: 10.3390/ani13081317] [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: 03/03/2023] [Revised: 03/31/2023] [Accepted: 04/08/2023] [Indexed: 04/29/2023] Open
Abstract
Recently, increasing attention has been paid to sheep milk products, which are high in saturated fatty acids (SFA), and the extent of their impact on human health. This study aimed to identify SNPs for PI, PIII, and Exon 53 in the ACACα gene and their association with the MC and FA profiles in Najdi sheep milk. A total of 76 multiparous Najdi ewes were used, and they were maintained using the same feeding system. Milk and blood samples were collected during the first lactation. A genetic polymorphism analysis identified 20 SNPs: 4 SNPs on PI, 6 SNPs on PIII, and 10 SNPs on Exon 53. In PI, the SNP g.4412G > A was associated (p < 0.05) with palmitic acid (C16:0), palmitoleic acid (16:1 n-7) and linoleic acid (LA), while SNP g.4485C > G was associated with CLA and vaccenic acid (VA) (p < 0.05). Furthermore, in PIII, two SNPs (g.1168A > G and g.1331G > T) were associated with milk protein (p < 0.05), while the SNP g.6860G > C in Exon 53 was associated with milk fat (p < 0.05). SNPs in the Najdi breed have been shown to be strongly related to milk fat and EFA contents. This could support a genetic selection program and the control of milk traits in the Najdi breed of high-quality dairy sheep.
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Affiliation(s)
- Abdulkareem M Matar
- Department of Animal Production, College of Food and Agriculture Sciences, King Saud University, P.O. Box 2460, Riyadh 11451, Saudi Arabia
| | - Abdulrahman S Alharthi
- Department of Animal Production, College of Food and Agriculture Sciences, King Saud University, P.O. Box 2460, Riyadh 11451, Saudi Arabia
| | - Moez Ayadi
- Department of Animal Production, College of Food and Agriculture Sciences, King Saud University, P.O. Box 2460, Riyadh 11451, Saudi Arabia
| | - Maged A Al-Garadi
- Department of Animal Production, College of Food and Agriculture Sciences, King Saud University, P.O. Box 2460, Riyadh 11451, Saudi Arabia
| | - Riyadh S Aljummah
- Department of Animal Production, College of Food and Agriculture Sciences, King Saud University, P.O. Box 2460, Riyadh 11451, Saudi Arabia
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Selionova M, Aibazov M, Mamontova T, Malorodov V, Sermyagin A, Zinovyeva N, Easa AA. Genome-wide association study of live body weight and body conformation traits in young Karachai goats. Small Rumin Res 2022. [DOI: 10.1016/j.smallrumres.2022.106836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
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Wu X, Zhen H, Liu Y, Li L, Luo Y, Liu X, Li S, Hao Z, Li M, Hu L, Qiao L, Wang J. Tissue-Specific Expression of Circ_015343 and Its Inhibitory Effect on Mammary Epithelial Cells in Sheep. Front Vet Sci 2022; 9:919162. [PMID: 35836501 PMCID: PMC9275140 DOI: 10.3389/fvets.2022.919162] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 05/16/2022] [Indexed: 02/06/2023] Open
Abstract
Circular RNAs (circRNAs) are a kind of non-coding RNA that have an important molecular function in mammary gland development and lactation of mammals. In our previous study, circ_015343 was found to be highly expressed in the ovine mammary gland tissue at the peak-lactation period by using RNA sequencing (RNA-seq). In the present study, the authenticity of circ_015343 was confirmed by using reverse transcriptase-polymerase chain reaction (RT-PCR) analysis and Sanger sequencing. The circ_015343 was derived from the complete 10 exons of aminoadipic semialdehyde synthase (AASS), ranging from exon 2 to exon 11 and mainly located in cytoplasm of ovine mammary epithelial cells. The circRNA was found to be expressed in eight ovine tissues, with the highest expression level in the mammary gland and the least expression in Longissimus dorsi muscle. The circ_015343 had a lower level of expression in a sheep breed with higher milk yield and milk fat content. The disturbed circ_015343 increased the viability and proliferation of the ovine mammary epithelial cells. The inhibition of circ_015343 also increased the expression levels of three milk fat synthesis marker genes: acetyl-coenzyme A carboxylase alpha (ACACA), fatty acid-binding protein 4 (FABP4), and sterol regulatory element-binding protein 1 (SREBP1), as well as three proliferation-related genes: cyclin dependent kinase 2 (CDK2), cyclin dependent kinase 4 (CDK4) and proliferating cell nuclear antigen (PCNA), but decreased the expression level of its parent gene AASS. A circRNA-miRNA-mRNA interaction network showed that circ_015343 would bind some microRNAs (miRNAs) to regulate the expression of functional genes related to the development of mammary gland and lactation. This study contributes to a better understanding of the roles of circ_015343 in the mammary gland of sheep.
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Du L, Li K, Chang T, An B, Liang M, Deng T, Cao S, Du Y, Cai W, Gao X, Xu L, Zhang L, Li J, Gao H. Integrating genomics and transcriptomics to identify candidate genes for subcutaneous fat deposition in beef cattle. Genomics 2022; 114:110406. [PMID: 35709924 DOI: 10.1016/j.ygeno.2022.110406] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 05/31/2022] [Accepted: 06/09/2022] [Indexed: 02/07/2023]
Abstract
Fat deposition is a complex economic trait regulated by polygenic genetic basis and environmental factors. Therefore, integrating multi-omics data to uncover its internal regulatory mechanism has attracted extensive attention. Here, we performed genomics and transcriptomics analysis to detect candidates affecting subcutaneous fat (SCF) deposition in beef cattle. The association of 770K SNPs with the backfat thickness captured nine significant SNPs within or near 11 genes. Additionally, 13 overlapping genes regarding fat deposition were determined via the analysis of differentially expressed genes and weighted gene co-expression network analysis (WGCNA). We then calculated the correlations of these genes with BFT and constructed their interaction network. Finally, seven biomarkers including ACACA, SCD, FASN, ACOX1, ELOVL5, HACD2, and HSD17B12 were screened. Notably, ACACA, identified by the integration of genomics and transcriptomics, was more likely to exert profound effects on SCF deposition. These findings provided novel insights into the regulation mechanism underlying bovine fat accumulation.
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Affiliation(s)
- Lili Du
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Keanning Li
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Tianpeng Chang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Bingxing An
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Mang Liang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Tianyu Deng
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Sheng Cao
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; Tianjin Agricultural University, Tianjin 300000, China
| | - Yueying Du
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; Qingdao Agricultural University, Shandong 266000, China
| | - Wentao Cai
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Xue Gao
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Lingyang Xu
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Lupei Zhang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Junya Li
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Huijiang Gao
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
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Brzáková M, Rychtářová J, Čítek J, Sztankóová Z. A Candidate Gene Association Study for Economically Important Traits in Czech Dairy Goat Breeds. Animals (Basel) 2021; 11:ani11061796. [PMID: 34208578 PMCID: PMC8234603 DOI: 10.3390/ani11061796] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 06/09/2021] [Accepted: 06/10/2021] [Indexed: 12/25/2022] Open
Abstract
Milk production is influenced by many factors, including genetic and environmental factors and their interactions. Animal health, especially udder health, is usually evaluated by the number of somatic cells. The present study described the effect of polymorphisms in the ACACA, BTN1A1, LPL, and SCD genes on the daily milk yield, fat, and protein percentages and somatic cell count. In this study, 590 White Shorthaired (WSH) and Brown Shorthaired (BSH) goats were included. SNP genotyping was performed by PCR-RFLP and multiplex PCR followed by SNaPshot minisequencing analysis. The linear mixed model with repeated measurement was used to identify the genetic associations between the studied genes/SNPs and chosen traits. All selected genes were polymorphic in the tested goat populations and showed significant associations with milk traits. Only BTN1A1 (SNP g.599 A > G) showed a significant association with the somatic cell score. After Bonferroni correction, a significant effect of LPL g.300G > A on daily milk yield and fat percentage, LPL g.185G > T on protein percentage, and LPL G50C, SCD EX3_15G > A, and SCD EX3_68A > G on fat percentage was found. The importance of environmental factors, such as the herd-year effect, month of milking, and lactation order on all milk performance indicators was confirmed.
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Affiliation(s)
- Michaela Brzáková
- Department of Genetics and Breeding of Farm Animals, Institute of Animal Science, 104 00 Prague, Czech Republic;
- Correspondence: ; Tel.: +420-606-794059
| | - Jana Rychtářová
- Department of Biology of Reproduction, Institute of Animal Science, 104 00 Prague, Czech Republic;
| | - Jindřich Čítek
- Department of Genetics and Agricultural Biotechnologies, Faculty of Agriculture, University of South Bohemia, 370 05 Ceske Budejovice, Czech Republic;
- Department of Infectious Diseases and Preventive Medicine, Veterinary Research Institute, 621 00 Brno, Czech Republic
| | - Zuzana Sztankóová
- Department of Genetics and Breeding of Farm Animals, Institute of Animal Science, 104 00 Prague, Czech Republic;
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Ge P, Ma H, Li Y, Ni A, Isa AM, Wang P, Bian S, Shi L, Zong Y, Wang Y, Jiang L, Hagos H, Yuan J, Sun Y, Chen J. Identification of microRNA-Associated-ceRNA Networks Regulating Crop Milk Production in Pigeon ( Columba livia). Genes (Basel) 2020; 12:genes12010039. [PMID: 33396684 PMCID: PMC7824448 DOI: 10.3390/genes12010039] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 12/27/2020] [Accepted: 12/28/2020] [Indexed: 12/18/2022] Open
Abstract
Pigeon belongs to altrices. Squab cannot forage independently. Nutrition can only be obtained from crop milk secreted by male and female pigeon. miRNA could regulate many biological events. However, the roles of miRNA and ceRNA in regulating crop milk production are still unknown. In this study, we investigated the miRNAs expression profile of female pigeon crop, explored the potential key genes, and found the regulatory mechanisms of crop milk production. A total of 71 miRNAs were identified differentially expressed significantly. Meanwhile, miR-20b-5p, miR-146b-5p, miR-21-5p, and miR-26b-5p were found to be the key miRNAs regulating lactation. Target genes of these miRNAs participated mainly in cell development; protein and lipid synthesis; and ion signaling processes, such as cell-cell adhesion, epithelial cell morphogenesis, calcium signaling pathway, protein digestion, and absorption. In the ceRNA network, miR-193-5p was located in the central position, and miR-193-5p/CREBRF/LOC110355588, miR-460b-5p/GRHL2/MSTRG.132954, and miR-193-5p/PIK3CD/LOC110355588 regulatory axes were believed to affect lactation. Collectively, our findings enriched the miRNA expression profile of pigeon and provided novel insights into the microRNA-associated-ceRNA networks regulating crop milk production in pigeon.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | - Jilan Chen
- Correspondence: ; Tel.: +86-10-628-160-05
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Analysis of Whole Genome Resequencing Datasets from a Worldwide Sample of Sheep Breeds to Identify Potential Causal Mutations Influencing Milk Composition Traits. Animals (Basel) 2020; 10:ani10091542. [PMID: 32882861 PMCID: PMC7552124 DOI: 10.3390/ani10091542] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 08/21/2020] [Accepted: 08/28/2020] [Indexed: 01/30/2023] Open
Abstract
Different studies have shown that polymorphisms in the sequence of genes coding for the milk proteins and milk fatty acids are associated with milk composition traits as well as with cheese-making traits. However, the lack of coincident results across sheep populations has prevented the use of this information in sheep breeding programs. The main objective of this study was to exploit the information derived from a total of 175 whole genome resequencing (WGR) datasets from 43 domestic sheep breeds and three wild sheep to evaluate the genetic diversity of 24 candidate genes for milk composition and identify genetic variants with a potential phenotypic effect. The functional annotation of the identified variants highlighted five single nucleotide polymorphisms (SNPs) predicted to have a high impact on the protein function and 42 missense SNPs with a putative deleterious effect. When comparing the allelic frequencies at these 47 polymorphisms with relevant functional effects between the genomes of Assaf and Churra sheep breeds, two missense deleterious variants were identified as potential markers associated to the milk composition differences found between the Churra and Assaf: XDH:92215727C>T and LALBA:137390760T>C. Future research is required to confirm the effect of the potential functionally relevant variants identified in the present study on milk composition and cheese-making traits.
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Zhang H, Liu T, Li B, Zhang K, Wang D, Liu Y, Ge L, Jiang Y, Su F. Establishment of a Stable β-Casein Protein-Secreted Laoshan Dairy Goat Mammary Epithelial Cell Line. Front Vet Sci 2020; 7:501. [PMID: 32903554 PMCID: PMC7438409 DOI: 10.3389/fvets.2020.00501] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Accepted: 07/02/2020] [Indexed: 12/15/2022] Open
Abstract
Mammary epithelial cells are widely used as models in mastitis research and as tools for mammalian bioreactors; however, the short lifespan of these cells limits their utility. Several mammal epithelial cell line models have been established; however, the secretion capacity and the bacterial sensitivity of these lines have not been effectively evaluated. In this study, a stable immortalized goat mammary epithelial cell (GMEC) line was constructed by transfection with the SV40 gene. The monoclonal cells were then passaged through more than 50 generations after puromycin selection. The GMEC line was evaluated by reverse transcriptase polymerase chain reaction, the cell cycle, karyotype analysis, detection of apoptosis, Western blotting, and β-casein (CSN2) inducible assays. The GMEC line had a strong proliferation capacity relative to the primary GMECs. GMECs had the same karyotype as the primary cells. The GMEC lines maintained basic biological properties and had estrogen, prolactin, and progesterone receptors as same the primary cells. Additionally, the cells and the cell line could synthesize and secrete β-casein proteins. Finally, the rate of apoptosis of the transfected cells suggested that the cell line could provide a useful tool for signal research and mammary gland bioreactors.
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Affiliation(s)
- Hongyan Zhang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai'an, China
| | - Tianzhen Liu
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai'an, China
| | - Boyu Li
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai'an, China
| | - Kang Zhang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai'an, China
| | - Dong Wang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai'an, China
| | - Ying Liu
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai'an, China
| | - Lijiang Ge
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai'an, China
| | - Yunliang Jiang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai'an, China
| | - Feng Su
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai'an, China
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Bakhtiarizadeh MR, Alamouti AA. RNA-Seq based genetic variant discovery provides new insights into controlling fat deposition in the tail of sheep. Sci Rep 2020; 10:13525. [PMID: 32782325 PMCID: PMC7419499 DOI: 10.1038/s41598-020-70527-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 07/27/2020] [Indexed: 01/09/2023] Open
Abstract
Genetic basis of fat deposition in sheep tail have not been completely elucidated yet. Understanding the genetic mechanisms controlling fat-tail size can improve breeding strategies to modulate fat deposition. RNA sequencing has made it possible to discover genetic variants that may underlie various phenotypic differences. Hence, to identify genetic variants that are important for describing different fat-tail phenotypes in sheep, RNA sequencing was used for single nucleotide polymorphism (SNP) calling in two Iranian sheep breeds (Lori-Bakhtiari, fat-tailed; n = 4, vs Zel, thin-tailed; n = 4). Using a stringent pipeline, a total of 112,344 known SNPs were genotyped, of which 30,550 and 42,906 SNPs were shared by at least two Lori-Bakhtiari and Zel, respectively. Comparing these SNPs showed 2,774 (including 209 missense and 25 deleterious SNPs) and 10,470 (including 1,054 missense and 116 deleterious SNPs) breed-specific SNPs in Lori-Bakhtiari and Zel sheep, respectively. Potential breed-specific SNPs were detected by considering those located in QTL regions associated with fatness or reported as important candidates in previous similar studies. Of the breed-specific SNPs, 724 and 2,905 were located in the QTL regions. Functional enrichment analysis of the affected genes revealed several enriched gene ontologies and KEGG pathways related to fat metabolism. Based on the results, several affected genes were proposed to be strongly linked with fat deposition such as DGAT2, ACSL1, ACACA, ADIPOQ, ACLY, FASN, CPT2, SCD, ADCY6, PER3, CSF1R, SLC22A4, GFPT1, CDS2, BMP6, ACSS2, ELOVL6, HOXA10 and FABP4. Moreover, several SNPs were found in the candidate genes related to fatty acid oxidation introducing them as promising candidates responsible for lower fat content in tail of Zel. Our findings provided new insights into the genetic mechanisms of fat deposition in sheep, which can serve to designing appropriate breeding programs.
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Affiliation(s)
| | - Ali A Alamouti
- Department of Animal and Poultry Science, College of Aburaihan, University of Tehran, Tehran, Iran
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Xiao Y, Zheng X, Li G, Zhou C, Wu C, Xu Z, Hu G, Guo X, Li L, Cao H, Latigo V, Liu P. Investigation of the effects of dichlorvos poisoning on AMPK signaling pathway in chicken brain tissues. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 261:114109. [PMID: 32109818 DOI: 10.1016/j.envpol.2020.114109] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 01/09/2020] [Accepted: 01/29/2020] [Indexed: 06/10/2023]
Abstract
Dichlorvos is a common crop insecticide widely used by people which causes extensive and serious environmental pollution. However, it has been shown that organophosphorus poisoning causes energy metabolism and neural disorders. The overall purpose of this study was to investigate the damage to brain tissue and the changes in AMPK signaling pathway-related gene expression after dichlorvos poisoning in chickens. White-feathered broiler chickens, as the research subjects of this experiment, were divided into three groups: control group, low-dose group (77.5% dichlorvos at 1.13 mg/kg dose) and high-dose group (77.5% dichlorvos at 10.2 mg/kg dose). Clinical symptoms were observed after modeling, and an integrative analysis was conducted using HE staining microscopy, immune-histochemical microscopy, electron microscopy and PCR arrays. The results showed that the high-dose group had more obvious dyspnea, salivation, convulsion and other neurological phenomena. Pathological sections showed that nuclear disintegration of neurons was most obvious in the low-dose group, and apoptosis of brain cells was most obvious in the high-dose group, and the mitochondrial structure was destroyed in the two poisoned group, i.e. low-dose group and high-dose group. PCR arrays showed that AMPK signaling pathway was inhibited and the expressions of genes involved in energy metabolism (ACACA and PRKAA1) were significantly changed. Furthermore, genes associated with protein synthesis (EIF4EBP1) were significantly upregulated. FASN and HMGCR expressions were significantly increased. There were significant changes in the expressions of cell cycle-related genes (STK11, TP53 and FOXO3). Organophosphate poisoning can cause a lot of nuclear disintegration of brain neurons, increases cell apoptosis, disrupts the energy metabolism of mitochondrial structure, and inhibits the AMPK signaling pathway. These results provide a certain idea and basis for studying the mechanism of AMPK signaling after organophosphorus poisoning and provide a research basis for the prevention and treatment of organophosphorus poisoning.
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Affiliation(s)
- Yanyu Xiao
- Jiangxi Provincial Key Laboratory for Animal Health, Institute of Animal Population Health, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, Jiangxi, China; Department of Animal Medicine, College of Animal Science and Technology, Guangxi University, Nanning, Guangxi, 530005, China
| | - Xibang Zheng
- Jiangxi Provincial Key Laboratory for Animal Health, Institute of Animal Population Health, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Guyue Li
- Jiangxi Provincial Key Laboratory for Animal Health, Institute of Animal Population Health, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Changming Zhou
- Jiangxi Provincial Key Laboratory for Animal Health, Institute of Animal Population Health, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Cong Wu
- Jiangxi Provincial Key Laboratory for Animal Health, Institute of Animal Population Health, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Zheng Xu
- Department of Mathematics and Statistic, Wright State University Dayton, OH, 45435, USA
| | - Guoliang Hu
- Jiangxi Provincial Key Laboratory for Animal Health, Institute of Animal Population Health, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Xiaoquan Guo
- Jiangxi Provincial Key Laboratory for Animal Health, Institute of Animal Population Health, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Lin Li
- Jiangxi Provincial Key Laboratory for Animal Health, Institute of Animal Population Health, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Huabin Cao
- Jiangxi Provincial Key Laboratory for Animal Health, Institute of Animal Population Health, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Vincent Latigo
- Jiangxi Provincial Key Laboratory for Animal Health, Institute of Animal Population Health, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Ping Liu
- Jiangxi Provincial Key Laboratory for Animal Health, Institute of Animal Population Health, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, Jiangxi, China.
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Fan H, Hou Y, Sahana G, Gao H, Zhu C, Du L, Zhao F, Wang L. A Transcriptomic Study of the Tail Fat Deposition in Two Types of Hulun Buir Sheep According to Tail Size and Sex. Animals (Basel) 2019; 9:ani9090655. [PMID: 31491862 PMCID: PMC6770480 DOI: 10.3390/ani9090655] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 08/28/2019] [Accepted: 08/30/2019] [Indexed: 01/19/2023] Open
Abstract
Simple Summary Based on tail types, Hulun Buir sheep were divided into two lines including small and big fat-tailed, but these two lines have similar genetic background. In this study, we investigated the morphology and transcription level differences of tail fat between these two lines. The RNA-seq analyses indicated several differentially expressed genes when compared between sexes or two tail sizes. Interestingly, we also found an obvious sex difference in the fat metabolism in Hulun Buir sheep. Two different co-expression networks were only shown either in male or in female sheep. Our findings will provide theoretical background in understanding the genetic mechanism of fat deposition in sheep. Abstract Hulun Buir sheep of similar genetic background were divided into two lines based on tail types: Small- and big fat-tailed. To explore the molecular mechanism of fat deposition in sheep tails, we firstly evaluated the morphology and transcription level differences of tail fat between these two lines. RNA-Seq technology was used to identify differentially expressed genes (DEGs) in phenotypic extremes of tail sizes. Five comparisons were performed taking into account two factors, sex and tail type. We screened out 373 DEGs between big-tailed and small-tailed Hulun Buir sheep, and 775 and 578 DEGs between two types of tails in male and female sheep, respectively. The results showed an obvious sex difference in the fat metabolism in sheep based on gene ontology (GO), pathway, and network analyses. Intriguingly, there were two different co-expression networks only respectively shown in male and female sheep, which were insulin-related network acting on upstream pathways and PPARG-related network effect in downstream pathways. Furthermore, these two networks were linked by a classic pathway of regulating adipogenesis. This is the first study to investigate the sex differences of fat metabolism in domestic animals, and it demonstrates a new experimental way to study fat metabolism. Our findings will provide theoretical background in understanding the tail-size phenotype in sheep and can be exploited in breeding small-tailed sheep.
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Affiliation(s)
- Hongying Fan
- Key Laborary of Animal Genetics, Breeding and Reproduction (Poultry) of Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- Key Laboratory of Mariculture, Ocean University of China, Qingdao 266000, China
| | - Yali Hou
- Beijing Institute of Genomics, Chinese Academy of Sciences and University of Chinese Academy of Sciences, Beijing 100101, China
| | - Goutam Sahana
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, 8830 Tjele, Denmark
| | - Hongding Gao
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, 8830 Tjele, Denmark
| | - Caiye Zhu
- Key Laborary of Animal Genetics, Breeding and Reproduction (Poultry) of Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Lixin Du
- Key Laborary of Animal Genetics, Breeding and Reproduction (Poultry) of Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Fuping Zhao
- Key Laborary of Animal Genetics, Breeding and Reproduction (Poultry) of Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Lixian Wang
- Key Laborary of Animal Genetics, Breeding and Reproduction (Poultry) of Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
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Identification and Expression Analysis of Long Noncoding RNAs in Fat-Tail of Sheep Breeds. G3-GENES GENOMES GENETICS 2019; 9:1263-1276. [PMID: 30787031 PMCID: PMC6469412 DOI: 10.1534/g3.118.201014] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Emerging evidence suggests that long non-coding RNAs (lncRNAs) participate in the regulation of a diverse range of biological processes. However, most studies have been focused on a few established model organisms and little is known about lncRNAs in fat-tail development in sheep. Here, the first profile of lncRNA in sheep fat-tail along with their possible roles in fat deposition were investigated, based on a comparative transcriptome analysis between fat-tailed (Lori-Bakhtiari) and thin-tailed (Zel) Iranian sheep breeds. Among all identified lncRNAs candidates, 358 and 66 transcripts were considered novel intergenic (lincRNAs) and novel intronic (ilncRNAs) corresponding to 302 and 58 gene loci, respectively. Our results indicated that a low percentage of the novel lncRNAs were conserved. Also, synteny analysis identified 168 novel lincRNAs with the same syntenic region in human, bovine and chicken. Only seven lncRNAs were identified as differentially expressed genes between fat and thin tailed breeds. Q-RT-PCR results were consistent with the RNA-Seq data and validated the findings. Target prediction analysis revealed that the novel lncRNAs may act in cis or trans and regulate the expression of genes that are involved in the lipid metabolism. A gene regulatory network including lncRNA-mRNA interactions were constructed and three significant modules were found, with genes relevant to lipid metabolism, insulin and calcium signaling pathway. Moreover, integrated analysis with AnimalQTLdb database further suggested six lincRNAs and one ilncRNAs as candidates of sheep fat-tail development. Our results highlighted the putative contributions of lncRNAs in regulating expression of genes associated with fat-tail development in sheep.
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Zhang HM, Xia HL, Jiang HR, Mao YJ, Qu KX, Huang BZ, Gong YC, Yang ZP. Longissimus dorsi muscle transcriptomic analysis of Yunling and Chinese simmental cattle differing in intramuscular fat content and fatty acid composition. Genome 2018; 61:549-558. [PMID: 29883552 DOI: 10.1139/gen-2017-0164] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Intramuscular fat (IMF) content and fatty acid (FA) composition vary significantly across beef cattle breeds, which play an important role in taste and nutritional value. However, the molecular mechanisms underlying these phenotypic differences remain unknown. The present study compared meat quality traits between Yunling cattle and Chinese Simmental cattle. Yunling cattle showed a lower IMF content and proportion of monounsaturated fatty acids (MUFA), as well as higher proportions of saturated fatty acids (SFA), polyunsaturated fatty acids (PUFA), and short-chain fatty acids (sc-FA) in the longissimus dorsi (LD) muscle than Chinese Simmental cattle. To further identify the candidate genes and pathways responsible for these phenotypic differences, the transcriptome of LD muscle from the two breeds were measured using RNA-seq. A total of 1347 differentially expressed genes were identified. The major metabolic pathways that were differentially modulated were lipolysis and glycometabolism. Yunling cattle showed a higher expression of lipolysis genes (ALDH9A1, ACSL5, ACADM, ACAT2, ACOT2) and a lower expression of genes related to glycometabolism (PGM1, GALM, PGM1, GPI, LDHA). This research identified candidate genes and pathways for IMF content and FA composition in the LD muscle of beef cattle, which may facilitate the design of new selection strategies to improve meat quality.
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Affiliation(s)
- H M Zhang
- a Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu 225009, China.,b Joint International Research Laboratory of Agriculture & Agri-Product Safety, Ministry of Education, Yangzhou University, Yangzhou 225009, China
| | - H L Xia
- a Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu 225009, China.,b Joint International Research Laboratory of Agriculture & Agri-Product Safety, Ministry of Education, Yangzhou University, Yangzhou 225009, China
| | - H R Jiang
- a Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu 225009, China.,b Joint International Research Laboratory of Agriculture & Agri-Product Safety, Ministry of Education, Yangzhou University, Yangzhou 225009, China
| | - Y J Mao
- a Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu 225009, China.,b Joint International Research Laboratory of Agriculture & Agri-Product Safety, Ministry of Education, Yangzhou University, Yangzhou 225009, China
| | - K X Qu
- c Yunnan Academy of Grassland and Animal Science, Kunming, Yunnan 650212, China
| | - B Z Huang
- c Yunnan Academy of Grassland and Animal Science, Kunming, Yunnan 650212, China
| | - Y C Gong
- d The Centre for the Analysis of Genome Evolution and Function (CAGEF), University of Toronto, Toronto, ON M5S 2J7, Canada
| | - Z P Yang
- a Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu 225009, China.,b Joint International Research Laboratory of Agriculture & Agri-Product Safety, Ministry of Education, Yangzhou University, Yangzhou 225009, China
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Full-length sequencing and identification of novel polymorphisms in the ACACA gene of Valle del Belice sheep breed. J Genet 2018; 96:591-597. [PMID: 28947707 DOI: 10.1007/s12041-017-0807-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The essential role of the acetyl-CoA carboxylase (ACACA) enzyme in milk fatty acid (FA) synthesis suggests that it may be responsible for the phenotypic variability observed inmilk.Before attempting association analyses between this gene and/or enzyme and phenotypic traits, a study on the genetic variability within this locus is required. The aim of this work was to sequence the entire coding region of ACACA gene in Valle del Belice sheep breed to identify polymorphic sites. A total of 51 coding exons of ACACA gene were sequenced in 32 individuals of Valle del Belice sheep breed. Sequencing analysis and alignment of obtained sequences showed the presence of 23 polymorphic sites. The most polymorphic was exon 53 which showed presence of 12 single-nucleotide polymorphisms (SNPs), ofwhich eightweremissensemutations, caused amino acid changes and therefore may affect protein function or stability causing variation in phenotype. The identified polymorphisms showed high variability of the ACACA gene. Sequences analysis allowed to find six new SNPs in exon 53 (6832C>T; 6835C>A; 6840G>A; 6847G>T; 6852C>T and 6860G>C). A total of 31 haplotypes were inferred. Although this study could not provide association study with production traits, it shows finding of novel SNPs that might be important in future studies and laid the basis for further association analyses needed to evaluate the potential use of these SNPs as genetic markers for fat content and FAs composition in milk of Valle del Belice sheep breed.
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Mastrangelo S, Tolone M, Sardina MT, Sottile G, Sutera AM, Di Gerlando R, Portolano B. Genome-wide scan for runs of homozygosity identifies potential candidate genes associated with local adaptation in Valle del Belice sheep. Genet Sel Evol 2017; 49:84. [PMID: 29137622 PMCID: PMC5684758 DOI: 10.1186/s12711-017-0360-z] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 11/07/2017] [Indexed: 11/23/2022] Open
Abstract
Background Because very large numbers of single nucleotide polymorphisms (SNPs) are now available throughout the genome, they are particularly suitable for the detection of genomic regions where a reduction in heterozygosity has occurred and they offer new opportunities to improve the accuracy of inbreeding (\documentclass[12pt]{minimal}
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\begin{document}$$F$$\end{document}F) estimates. Runs of homozygosity (ROH) are contiguous lengths of homozygous segments of the genome where the two haplotypes inherited from the parents are identical. Here, we investigated the occurrence and distribution of ROH using a medium-dense SNP panel to characterize autozygosity in 516 Valle del Belice sheep and to identify the genomic regions with high ROH frequencies. Results We identified 11,629 ROH and all individuals displayed at least one ROH longer than 1 Mb. The mean value of \documentclass[12pt]{minimal}
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\begin{document}$$F$$\end{document}F estimated from ROH longer than1 Mb was 0.084 ± 0.061. ROH that were shorter than 10 Mb predominated. The highest and lowest coverages of Ovis aries chromosomes (OAR) by ROH were on OAR24 and OAR1, respectively. The number of ROH per chromosome length displayed a specific pattern, with higher values for the first three chromosomes. Both number of ROH and length of the genome covered by ROH varied considerably between animals. Two hundred and thirty-nine SNPs were considered as candidate markers that may be under directional selection and we identified 107 potential candidate genes. Six genomic regions located on six chromosomes, corresponding to ROH islands, are presented as hotspots of autozygosity, which frequently coincided with regions of medium recombination rate. According to the KEGG database, most of these genes were involved in multiple signaling and signal transduction pathways in a wide variety of cellular and biochemical processes. A genome scan revealed the presence of ROH islands in genomic regions that harbor candidate genes for selection in response to environmental stress and which underlie local adaptation. Conclusions These results suggest that natural selection has, at least partially, a role in shaping the genome of Valle del Belice sheep and that ROH in the ovine genome may help to detect genomic regions involved in the determinism of traits under selection. Electronic supplementary material The online version of this article (10.1186/s12711-017-0360-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Salvatore Mastrangelo
- Dipartimento Scienze Agrarie, Alimentari e Forestali, Università degli Studi di Palermo, 90128, Palermo, Italy.
| | - Marco Tolone
- Dipartimento Scienze Agrarie, Alimentari e Forestali, Università degli Studi di Palermo, 90128, Palermo, Italy
| | - Maria T Sardina
- Dipartimento Scienze Agrarie, Alimentari e Forestali, Università degli Studi di Palermo, 90128, Palermo, Italy
| | - Gianluca Sottile
- Dipartimento di Scienze Economiche, Aziendali e Statistiche, Università degli Studi di Palermo, 90128, Palermo, Italy
| | - Anna M Sutera
- Dipartimento Scienze Agrarie, Alimentari e Forestali, Università degli Studi di Palermo, 90128, Palermo, Italy
| | - Rosalia Di Gerlando
- Dipartimento Scienze Agrarie, Alimentari e Forestali, Università degli Studi di Palermo, 90128, Palermo, Italy
| | - Baldassare Portolano
- Dipartimento Scienze Agrarie, Alimentari e Forestali, Università degli Studi di Palermo, 90128, Palermo, Italy
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A novel polymorphism in the oxytocin receptor encoding gene (OXTR) affects milk fatty acid composition in Italian Mediterranean river buffalo. J DAIRY RES 2017; 84:170-180. [DOI: 10.1017/s0022029917000127] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The oxytocin receptor, also known as OXTR, is a protein which functions as receptor for the hormone and neurotransmitter oxytocin and the complex oxytocin–oxytocin receptor plays an important role in the uterus during calving. A characterisation of the river buffalo OXTR gene, amino acid sequences and phylogenetic analysis is presented. The DNA regions of the OXTR gene spanning exons 1, 2 and 3 of ten Mediterranean river buffalo DNA samples were analysed and 7 single nucleotide polymorphisms were found. We focused on the g.129C > T SNP detected in exon 3 and responsible for the amino acid replacement CGCArg > TGCCys in position 353. The relative frequency of T allele was of 0·257. An association study between this detected polymorphism and milk fatty acids composition in Italian Mediterranean river buffalo was carried out. The fatty acid composition traits, fatty acid classes and fat percentage of 306 individual milk samples were determined. Associations between OXTR g.129C > T genotype and milk fatty acids composition were tested using a mixed linear model. The OXTR CC genotype was found significantly associated with higher contents of odd branched-chain fatty acids (OBCFA) (P < 0·0006), polyunsaturated FA (PUFA n 3 and n 6) (P < 0·0032 and P < 0·0006, respectively), stearic acid (C18) (P < 0·02) and lower level of palmitic acid (C16) (P < 0·02). The results of this study suggest that the OXTR CC animals might be useful in selection toward the improvement of milk fatty acid composition.
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