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Worku D, Verma A. Genetic variation in bovine LAP3 and SIRT1 genes associated with fertility traits in dairy cattle. BMC Genom Data 2024; 25:32. [PMID: 38500063 PMCID: PMC10949778 DOI: 10.1186/s12863-024-01209-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 02/15/2024] [Indexed: 03/20/2024] Open
Abstract
BACKGROUND The genetic progress of fertility and reproduction traits in dairy cattle has been constrained by the low heritability of these traits. Identifying candidate genes and variants associated with fertility and reproduction could enhance the accuracy of genetic selection and expedite breeding process of dairy cattle with low-heritability traits. While the bovine LAP3 and SIRT1 genes exhibit well-documented associations with milk production traits in dairy cattle, their effect on cow fertility have not yet been explored. Eleven single nucleotide polymorphisms (SNPs), comprising five in the promoter (rs717156555: C > G, rs720373055: T > C, rs516876447: A > G, rs461857269: C > T and rs720349928: G > A), two in 5'UTR (rs722359733: C > T and rs462932574: T > G), two in intron 12 (rs110932626: A > G and rs43702363: C > T), and one in 3'UTR of exon 13 (rs41255599: C > T) in LAP3 and one in SIRT1 (rs718329990:T > C) genes, have previously been reported to be associated with various traits of milk production and clinical mastitis in Sahiwal and Karan Fries dairy cattle. In this study, the analysis primarily aimed to assess the impact of SNPs within LAP3 and SIRT1 genes on fertility traits in Sahiwal and Karan Fries cattle. Association studies were conducted using mixed linear models, involving 125 Sahiwal and 138 Karan Fries animals in each breed. The analysis utilized a designated PCR-RFLP panel. RESULTS In the promoter region of the LAP3 gene, all variants demonstrated significant (P < 0.05) associations with AFC, except for rs722359733: C > T. However, specific variants with the LAP3 gene's promoter region, namely rs722359733: C > T, rs110932626: A > G, rs43702363: C > T, and rs41255599: C > T, showed significant associations with CI and DO in Sahiwal and Karan Fries cows, respectively. The SNP rs718329990: T > C in the promoter region of SIRT1 gene exhibited a significant association with CI and DO in Sahiwal cattle. Haplotype-based association analysis revealed significant associations between haplotype combinations and AFC, CI and DO in the studied dairy cattle population. Animals with H2H3 and H2H4 haplotype combination exhibited higher AFC, CI and DO than other combinations. CONCLUSIONS These results affirm the involvement of the LAP3 and SIRT1 genes in female fertility traits, indicating that polymorphisms within these genes are linked to the studied traits. Overall, the significant SNPs and haplotypes identified in this study could have the potential to enhance herd profitability and ensure long-term sustainability on dairy farms by enabling the selection of animals with early age first calving and enhance reproductive performance in the dairy cattle breeding program.
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Affiliation(s)
- Destaw Worku
- Department of Animal Science, College of Agriculture, Food and Climate Science, Injibara University, Injibara, Ethiopia.
| | - Archana Verma
- Animal Genetics and Breeding Division, ICAR -National Dairy Research Institute, Karnal, India
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Origins, timing and introgression of domestic geese revealed by whole genome data. J Anim Sci Biotechnol 2023; 14:26. [PMID: 36782272 PMCID: PMC9926862 DOI: 10.1186/s40104-022-00826-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 12/14/2022] [Indexed: 02/15/2023] Open
Abstract
BACKGROUND Geese are among the most important poultry species in the world. The current generally accepted hypothesis is that the European domestic geese originated from greylag geese (Anser anser), and Chinese domestic geese have two origins, most of which originated from swan geese (Anser cygnoides), and the Yili goose originated from greylag geese. To explain the origin and demographic history of geese, we selected 14 goose breeds from Europe and China and wild populations of swan and greylag geese, and whole genome sequencing data were obtained for 74 samples. RESULTS Population structure analysis and phylogenetic trees showed that the wild ancestor of Chinese domestic geese, except for Yili, is the swan geese, and the wild ancestor of Chinese Yili and European domestic geese is greylag geese. Analysis of the demographic history suggests that the domestication of Chinese geese occurred ~ 3499 years ago and that of the European geese occurred ~ 7552 years ago. Furthermore, gene flow was observed between domestic geese and their wild ancestors. Analysis of introgression showed that Yili geese had been introgressed by Chinese domestic geese, and the body size of Yili geese may be influenced by introgression events of some growth-related genes, including IGF-1. CONCLUSIONS Our study provides evidence for the origin of geese at the genome-wide level and advances the understanding of the history of goose domestication and the traits affected by introgression events.
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Worku D, Gowane GR, Mukherjee A, Alex R, Joshi P, Verma A. Associations between polymorphisms of LAP3 and SIRT1 genes with clinical mastitis and milk production traits in Sahiwal and Karan Fries dairy cattle. Vet Med Sci 2022; 8:2593-2604. [DOI: 10.1002/vms3.924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Affiliation(s)
- Destaw Worku
- Molecular Genetics Lab, Animal Genetics and Breeding Division ICAR‐National Dairy Research Institute Karnal Haryana India
- Department of Animal Science Salale University Fitche Ethiopia
| | - G. R. Gowane
- Molecular Genetics Lab, Animal Genetics and Breeding Division ICAR‐National Dairy Research Institute Karnal Haryana India
| | - Anupama Mukherjee
- Molecular Genetics Lab, Animal Genetics and Breeding Division ICAR‐National Dairy Research Institute Karnal Haryana India
| | - Rani Alex
- Molecular Genetics Lab, Animal Genetics and Breeding Division ICAR‐National Dairy Research Institute Karnal Haryana India
| | - Pooja Joshi
- Molecular Genetics Lab, Animal Genetics and Breeding Division ICAR‐National Dairy Research Institute Karnal Haryana India
| | - Archana Verma
- Molecular Genetics Lab, Animal Genetics and Breeding Division ICAR‐National Dairy Research Institute Karnal Haryana India
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Worku D, Gowane G, Alex R, Joshi P, Verma A. Inputs for optimizing selection platform for milk production traits of dairy Sahiwal cattle. PLoS One 2022; 17:e0267800. [PMID: 35604915 PMCID: PMC9126386 DOI: 10.1371/journal.pone.0267800] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 04/14/2022] [Indexed: 12/17/2022] Open
Abstract
The premises for the potential success of molecular breeding is the ability to identify major genes associated with important dairy related traits. The present study was taken up with the objectives to identify single nucleotide polymorphism (SNP) of bovine MASP2 and SIRT1 genes and its effect on estimated breeding values (EBVs) and to estimate genetic parameters for lactation milk yield (LMY), 305-day milk yield (305dMY), 305-day fat yield (305dFY), 305-day solid not fat yield (305dSNFY) and lactation length (LL) in Sahiwal dairy cattle to devise a promising improvement strategy. Genetic parameters and breeding values of milk production traits were estimated from 935 Sahiwal cattle population (1979–2019) reared at National Dairy Research Institute at Karnal, India. A total of 7 SNPs, where one SNP (g.499C>T) in exon 2 and four SNPs (g.576G>A, g.609T>C, g.684G>T and g.845A>G) in exon 3 region of MASP2 gene and 2 SNPs (g.-306T>C and g.-274G>C) in the promoter region of SIRT1 gene were identified in Sahiwal cattle population. Five of these identified SNPs were chosen for further genotyping by PCR-RFLP and association analysis. Association analysis was performed using estimated breeding values (n = 150) to test the effect of SNPs on LMY, 305dMY, 305dFY, 305dSNFY and LL. Association analysis revealed that, three SNP markers (g.499C>T, g.609T>C and g.-306T>C) were significantly associated with all milk yield traits. The estimates for heritability using repeatability model for LMY, 305dMY, 305dFY, 305dSNFY and LL were low, however the corresponding estimates from first parity were 0.20±0.08, 0.17±0.08, 0.13±0.09, 0.13±0.09 and 0.24, respectively. The repeatability estimates were moderate to high indicating consistency of performance over the parities and hence reliability of first lactation traits. Genetic correlations among the traits of first parity were high (0.55 to 0.99). From the results we could conclude that optimum strategy to improve the Sahiwal cattle further would be selecting the animals based on their first lactation 305dMY. Option top include the significant SNP in selection criteria can be explored. Taken together, a 2-stage selection approach, select Sahiwal animals early for the SNP and then on the basis of first lactation 305dMY will help to save resources.
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Affiliation(s)
- Destaw Worku
- Animal Genetics and Breeding Division, National Dairy Research Institute, Karnal, Haryana, India
- * E-mail:
| | - Gopal Gowane
- Animal Genetics and Breeding Division, National Dairy Research Institute, Karnal, Haryana, India
| | - Rani Alex
- Animal Genetics and Breeding Division, National Dairy Research Institute, Karnal, Haryana, India
| | - Pooja Joshi
- Animal Genetics and Breeding Division, National Dairy Research Institute, Karnal, Haryana, India
| | - Archana Verma
- Animal Genetics and Breeding Division, National Dairy Research Institute, Karnal, Haryana, India
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Ouyang X, Becker E, Bone NB, Johnson MS, Craver J, Zong WX, Darley-Usmar VM, Zmijewski JW, Zhang J. ZKSCAN3 in severe bacterial lung infection and sepsis-induced immunosuppression. J Transl Med 2021; 101:1467-1474. [PMID: 34504306 PMCID: PMC8868012 DOI: 10.1038/s41374-021-00660-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 08/10/2021] [Accepted: 08/11/2021] [Indexed: 11/22/2022] Open
Abstract
The mortality rates among patients who initially survive sepsis are, in part, associated with a high risk of secondary lung infections and respiratory failure. Given that phagolysosomes are important for intracellular killing of pathogenic microbes, we investigated how severe lung infections associated with post-sepsis immunosuppression affect phagolysosome biogenesis. In mice with P. aeruginosa-induced pneumonia, we found a depletion of both phagosomes and lysosomes, as evidenced by decreased amounts of microtubule associated protein light chain 3-II (LC3-II) and lysosomal-associated membrane protein (LAMP1). We also found a loss of transcription factor E3 (TFE3) and transcription factor EB (TFEB), which are important activators for transcription of genes encoding autophagy and lysosomal proteins. These events were associated with increased expression of ZKSCAN3, a repressor for transcription of genes encoding autophagy and lysosomal proteins. Zkscan3-/- mice had increased expression of genes involved in the autophagy-lysosomal pathway along with enhanced killing of P. aeruginosa in the lungs, as compared to wild-type mice. These findings highlight the involvement of ZKSCAN3 in response to severe lung infection, including susceptibility to secondary bacterial infections due to immunosuppression.
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Affiliation(s)
- Xiaosen Ouyang
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, USA
- Center for Free Radical Biology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Eugene Becker
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Nathaniel B Bone
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Michelle S Johnson
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, USA
- Center for Free Radical Biology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Jason Craver
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, USA
- Center for Free Radical Biology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Wei-Xing Zong
- Department of Chemical Biology, Rutgers University, Piscataway, NJ, USA
| | - Victor M Darley-Usmar
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, USA
- Center for Free Radical Biology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Jaroslaw W Zmijewski
- Center for Free Radical Biology, University of Alabama at Birmingham, Birmingham, AL, USA.
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA.
| | - Jianhua Zhang
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, USA.
- Center for Free Radical Biology, University of Alabama at Birmingham, Birmingham, AL, USA.
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Shabalina T, Yin T, König S. Survival analyses in Holstein cows considering direct disease diagnoses and specific SNP marker effects. J Dairy Sci 2020; 103:8257-8273. [DOI: 10.3168/jds.2020-18174] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 05/07/2020] [Indexed: 12/11/2022]
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Selvaggi M, Carbonara C, Ciotola F, Albarella S, Aiudi G, Tufarelli V, Dario C. Determination of a possible relationship between a single nucleotide polymorphism (SNP) in the promoter region of the SIRT1 gene and production and reproduction traits in the Agerolese cattle breed. Arch Anim Breed 2019; 62:107-112. [PMID: 31807620 PMCID: PMC6852848 DOI: 10.5194/aab-62-107-2019] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 03/14/2019] [Indexed: 12/25/2022] Open
Abstract
Sirtuins (sir2-like proteins) belong to the family of class III
NAD+-dependent histone deacetylases. Among them, SIRT1 is the most
studied sirtuin. It plays a key role in many biological processes in the
liver, adipose tissue, muscle, pancreas, testis, ovary and mammary gland. It
has an important function in endocrine signaling, with a specific role in
glucose and fat metabolism. To date, in bovine species, only few SIRT1 single
nucleotide polymorphisms (SNPs) have been reported in the literature. Thus,
the aims of the present study were to estimate the allele and genotype
frequencies at the g.-274C > G locus in the promoter region of the SIRT1
gene and to investigate, for the first time, the relationship among
different genotypes and milk production and some reproduction traits in a
sample of cows belonging to the Agerolese breed. All the animals were
genotyped at the abovementioned locus using the PCR-RFLP technique. The investigated population was found to be polymorphic
at the investigated locus. Concerning milk production performances,
significant differences between genotypes were found in daily milk yield
(DMY), fat percentage (FC), lactation length (LL), peak daily milk yield (PY)
and 305-day milk yield (305MY). Moreover, the effect of the g.-274C > G
genotype on age at first calving and calving period was significant. In
conclusion, our findings are promising and should encourage scientists to
further investigate the effect of genetic polymorphism of sirtuins on milk
performance and reproductive traits.
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Affiliation(s)
- Maria Selvaggi
- Department of Agricultural and Environmental Science, University of Bari Aldo Moro, Bari, Italy
| | - Claudia Carbonara
- Department of Agricultural and Environmental Science, University of Bari Aldo Moro, Bari, Italy
| | - Francesca Ciotola
- Department of Veterinary Medicine and Animal Production, University Federico II, Naples, Italy
| | - Sara Albarella
- Department of Veterinary Medicine and Animal Production, University Federico II, Naples, Italy
| | - Giulio Aiudi
- Department of Veterinary Medicine, University of Bari Aldo Moro, Bari, Italy
| | - Vincenzo Tufarelli
- Department of DETO, Section of Veterinary Science and Animal Production, University of Bari Aldo Moro, Bari, Italy
| | - Cataldo Dario
- Department of Agricultural and Environmental Science, University of Bari Aldo Moro, Bari, Italy
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8
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Zhang Q, Jin Y, Jiang F, Cheng H, Wang Y, Lan X, Song E. Relationship between an indel mutation within the SIRT4 gene and growth traits in Chinese cattle. Anim Biotechnol 2019; 30:352-357. [DOI: 10.1080/10495398.2018.1520716] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Qingfeng Zhang
- Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, Shandong, China
- Shandong Key Laboratory of Animal Disease control and Breeding, Jinan, Shandong, China
| | - Yunyun Jin
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Fugui Jiang
- Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, Shandong, China
- Shandong Key Laboratory of Animal Disease control and Breeding, Jinan, Shandong, China
| | - Haijian Cheng
- Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, Shandong, China
- Shandong Key Laboratory of Animal Disease control and Breeding, Jinan, Shandong, China
| | - Yafang Wang
- Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, Shandong, China
- College of Life Sciences, Shandong Normal University, Jinan, Shandong, China
| | - Xianyong Lan
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Enliang Song
- Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, Shandong, China
- Shandong Key Laboratory of Animal Disease control and Breeding, Jinan, Shandong, China
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The application of gene marker-assisted selection and proteomics for the best meat quality criteria and body measurements in Qinchuan cattle breed. Mol Biol Rep 2018; 45:1445-1456. [PMID: 30006771 DOI: 10.1007/s11033-018-4211-y] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2018] [Accepted: 06/09/2018] [Indexed: 12/25/2022]
Abstract
In the past few decades, enhancement of animal productivity has been gaining increasing attention among decisions-makers, politicians, mangers, and breeders, because of the increasing of world population and shortage of natural resources. The selection of high productivity animals is the main goal, through the application of genetic improvement programs. The use of molecular genetics has conferred significant breeding advantages over conventional breeding techniques. In this regard, many economic characteristics are controlled by a small number of multiple gene loci, each of which is responsible for trait diversity and hence they are referred to as quantitative trait loci (QTL). Single-nucleotide polymorphisms (SNPs), which have recently been discovered through DNA sequencing, are considered one of the most useful types of genetic marker. SNPs are found where different nucleotides occur at the same position in the DNA sequence. They are found in both coding and noncoding regions of the genome and are present at one SNP in every 1000 b. Strategies for the identification and application of markers are based on reference to examples of loci that can control various traits. Furthermore, markers for growth, body measurements, and meat quality traits are preferred, because they can be used to predict the performance of animals, via blood samples, in the first few days of animal life. Marker-assisted selection using SNPs, such asSIRT1, SIRT2, LPL, CRTC2, SIX4, UCPs, and ZBTB38as selection criteria of body measurements and meat traits in beef cattle, will be beneficial in selection and breeding programs. The proteomic is a novel marker and a new approache of biotechnology which increases the understanding of the biological processes, besides being a remarkable biomarker that interrelated to growth and meat quality traits. Proteomics is a vigorous tool as usage for deduces molecular processes between quality traits and muscle proteins, which are helpful in analyzing the mechanisms of biochemistry that influence quality. So they could be potential biomarker for some meat quality traits. Among them, Actin, Myosin, Heat shock proteins are used a novel approaches in the field of biotechnology to understand the proteomics changes. This review article highlights the novel findings on the potential use of MAS and proteomics as biomarker for the selection for meat quality and carcass traits in Qinchuan cattle breed.
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Jin Y, Yang Q, Gao J, Tang Q, Duan B, Yu T, Qi X, Liu J, Wang R, Dang R, Lei C, Chen H, Lan X. Detection of Insertions/Deletions Within SIRT1, SIRT2 and SIRT3 Genes and Their Associations with Body Measurement Traits in Cattle. Biochem Genet 2018; 56:663-676. [PMID: 29869077 DOI: 10.1007/s10528-018-9868-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 05/31/2018] [Indexed: 11/27/2022]
Abstract
Growth traits are complex quantitative traits controlled by numerous candidate genes, and they can be well-evaluated using body measurement traits. As the members of the nicotinamide adenine dinucleotide-dependent family of histone deacetylases, class I sirtuin genes (including SIRT1, SIRT2 and SIRT3) play crucial roles in regulating lipid metabolism, cellular growth and metabolism, suggesting that they are potential candidate genes affecting body measurement traits in animals. Hence, the objective of this work aimed to detect novel insertions/deletions (indels) of SIRT1, SIRT2 and SIRT3 genes in 955 cattle belonging to five breeds, as well as to evaluate their effects on body measurement traits. Herein, the novel 12-bp indel of SIRT1 gene, the 7-bp indel of SIRT2 gene and the 26-bp indel of SIRT3 gene were firstly reported, respectively. The association analysis indicated that the indels within SIRT1 and SIRT2 genes were significantly associated with body measurement traits such as body weight, chest circumference, height at hip cross, hip width, body height, etc. (P < 0.05 or P < 0.01). Therefore, based on these findings, the two novel indel variants within bovine SIRT1 and SIRT2 genes could be considered as potential molecular markers for growth traits in cattle selection practices and breeding.
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Affiliation(s)
- Yunyun Jin
- Shaanxi Key Laboratory of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Qing Yang
- Shaanxi Key Laboratory of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Jiayang Gao
- Shaanxi Key Laboratory of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Qi Tang
- Shaanxi Key Laboratory of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Bo Duan
- Shaanxi Key Laboratory of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Ting Yu
- Shaanxi Key Laboratory of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Xinglei Qi
- Xianan Cattle Technology Development Company, Biyang, 463700, Henan, People's Republic of China
- Bureau of Animal Husbandry, Biyang, 463700, Henan, People's Republic of China
| | - Jiming Liu
- Animal Husbandry Technology Promotion Station of Jiangxi, Nanchang, 330000, Jiangxi, People's Republic of China
| | - Rongmin Wang
- Animal Husbandry Technology Promotion Station of Jiangxi, Nanchang, 330000, Jiangxi, People's Republic of China
| | - Ruihua Dang
- Shaanxi Key Laboratory of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Chuzhao Lei
- Shaanxi Key Laboratory of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Hong Chen
- Shaanxi Key Laboratory of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Xianyong Lan
- Shaanxi Key Laboratory of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China.
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Jin Y, Yang Q, Zhang M, Zhang S, Cai H, Dang R, Lei C, Chen H, Lan X. Identification of a Novel Polymorphism in Bovine lncRNA ADNCR Gene and Its Association with Growth Traits. Anim Biotechnol 2018; 30:159-165. [DOI: 10.1080/10495398.2018.1456446] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Yunyun Jin
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi, P.R. China
| | - Qing Yang
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi, P.R. China
| | - Meng Zhang
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi, P.R. China
| | - Sihuan Zhang
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi, P.R. China
| | - Hanfang Cai
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi, P.R. China
| | - Ruihua Dang
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi, P.R. China
| | - Chuzhao Lei
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi, P.R. China
| | - Hong Chen
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi, P.R. China
| | - Xianyong Lan
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi, P.R. China
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Abstract
Objective Lung cancer, which is the leading cause of cancer death worldwide, is influenced by a wide variety of environmental and genetic risk factors. The silent information regulator 1 (SIRT1) gene is located on the long arm of chromosome 10 (10q21.3) and has been shown to play crucial roles in lung cancer development in previous studies. In this study, we determined whether variation in the SIRT1 gene is associated with lung cancer in Chinese population. Methods The case–control study comprised 246 controls and 257 non-small cell lung cancer patients, comprising 79 squamous cell carcinoma patients and 124 adenocarcinoma patients. All subjects were from Zhejiang, China. Four single-nucleotide polymorphisms of SIRT1 gene were analyzed: rs12778366 (C/T, lies in the 5′ upstream), rs3758391 (C/T, lies in the 5′ upstream), rs2273773 (C/T, lies in the coding) and rs4746720 (C/T, lies in the 3′ untranslated region). Results No significant difference of allele and genotype frequencies was observed between the different groups. Haplotype association analysis carried out on the four single-nucleotide polymorphisms within the case–control cohort also did not reveal a significant association with lung cancer (P>0.05). Conclusion The results suggest the tested SIRT1 gene polymorphisms may not contribute to lung cancer. Further studies are warranted to demonstrate the functional roles of the SIRT1 polymorphism in lung cancer.
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Affiliation(s)
- Yanbo Lv
- Department of Pathology, Zhejiang Hospital, Hangzhou City, Zhejiang, China
| | - Shuangyan Lin
- Department of Pathology, Zhejiang Hospital, Hangzhou City, Zhejiang, China
| | - Fang Peng
- Department of Pathology, Zhejiang Hospital, Hangzhou City, Zhejiang, China
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Liu G, Zhao H, Tan X, Cheng H, You W, Wan F, Liu Y, Song E, Liu X. <i>SIRT1</i> gene polymorphisms associated with carcass traits in Luxi cattle. Arch Anim Breed 2017. [DOI: 10.5194/aab-60-27-2017] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Abstract. SIRT1 is the gene that codes for Sirtuin 1, an NAD (nicotinamide adenine dinucleotide)-dependent class III histone deacetylase. This gene plays a key role in adipose tissue and muscle development in animals. Chinese Luxi cattle (n = 169) were selected to identify SIRT1 SNPs (single nucleotide polymorphisms) and investigate the relationship of these SNPs with carcass traits. Five SNPs (g.-382G > A, g.-274C > G, g.17324T > C, g.17379A > G, and g.17491G > A) were identified by direct sequencing. SNPs g.-382G > A and g.-274C > G were located within the promoter region of this gene. SNP g.-382G > A was significantly associated with dressing percentage, meat percentage, and striploin and ribeye weights, and the g.-274C > G polymorphism had a strong effect on carcass, tenderloin, and high rib weights in Luxi cattle. These findings will provide possible clues for the biological roles of SIRT1 underlying beef cattle carcass traits.
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Jin Y, Cai H, Liu J, Lin F, Qi X, Bai Y, Lei C, Chen H, Lan X. The 10 bp duplication insertion/deletion in the promoter region within paired box 7 gene is associated with growth traits in cattle. Arch Anim Breed 2016. [DOI: 10.5194/aab-59-469-2016] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Abstract. Paired box 7 (Pax7) gene, a member of the paired box gene family, plays a critical role in animal growth and muscle development, especially in cell proliferation and self-renewal. The aim of this study was to detect the 10 base pair (bp) duplication insertion/deletion (indel) in the promoter region within the bovine Pax7 gene as well as its association with growth traits. Herein, a total of 718 individuals from five Chinese cattle breeds were sampled and detected. The 10 bp duplication indel was found in these cattle breeds and there were three genotypes: II (insertion/insertion), ID (insertion/deletion), and DD (deletion/deletion). Moreover, this indel was significantly associated with the body weight in Xianan cattle (P = 0.006), the body height in Jinjiang cattle (P = 0.046), and the hip width in Pi'nan cattle (P = 0.020). Consistently, the individuals with II genotype showed better phenotypic traits than those with the other genotypes in these five breeds. These findings suggest that the 10 bp duplication indel within the bovine Pax7 gene could be considered as an effective DNA molecular marker that provides valuable theoretical basis for marker-assisted selection (MAS) in beef cattle in the future.
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Composite Selection Signals for Complex Traits Exemplified Through Bovine Stature Using Multibreed Cohorts of European and African Bos taurus. G3-GENES GENOMES GENETICS 2015; 5:1391-401. [PMID: 25931611 PMCID: PMC4502373 DOI: 10.1534/g3.115.017772] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Understanding the evolution and molecular architecture of complex traits is important in domestic animals. Due to phenotypic selection, genomic regions develop unique patterns of genetic diversity called signatures of selection, which are challenging to detect, especially for complex polygenic traits. In this study, we applied the composite selection signals (CSS) method to investigate evidence of positive selection in a complex polygenic trait by examining stature in phenotypically diverse cattle comprising 47 European and 8 African Bos taurus breeds, utilizing a panel of 38,033 SNPs genotyped on 1106 animals. CSS were computed for phenotypic contrasts between multibreed cohorts of cattle by classifying the breeds according to their documented wither height to detect the candidate regions under selection. Using the CSS method, clusters of signatures of selection were detected at 26 regions (9 in European and 17 in African cohorts) on 13 bovine autosomes. Using comparative mapping information on human height, 30 candidate genes mapped at 12 selection regions (on 8 autosomes) could be linked to bovine stature diversity. Of these 12 candidate gene regions, three contained known genes (i.e., NCAPG-LCORL, FBP2-PTCH1, and PLAG1-CHCHD7) related to bovine stature, and nine were not previously described in cattle (five in European and four in African cohorts). Overall, this study demonstrates the utility of CSS coupled with strategies of combining multibreed datasets in the identification and discovery of genomic regions underlying complex traits. Characterization of multiple signatures of selection and their underlying candidate genes will elucidate the polygenic nature of stature across cattle breeds.
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Gui L, Hao R, Zhang Y, Zhao X, Zan L. Haplotype distribution in the class I sirtuin genes and their associations with ultrasound carcass traits in Qinchuan cattle (Bos taurus). Mol Cell Probes 2015; 29:167-71. [PMID: 25839883 DOI: 10.1016/j.mcp.2015.03.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Revised: 03/22/2015] [Accepted: 03/22/2015] [Indexed: 12/21/2022]
Abstract
Class I sirtuin genes including SIRT1, SIRT2 and SIRT3, are members of the nicotinamide adenine dinucleotide (NAD)-dependent family of histone deacetylases, and play essential roles in senescence, metabolism, and apoptosis. This study was conducted to detect potential polymorphisms of the bovine class I sirtuin genes and explore their relationships with ultrasound carcass traits in Qinchuan cattle. Four non-coding mutations in the 3'UTR (SIRT1: g.25751A > C, SIRT1: g.25846A > G, SIRT2: g.19676G > A and SIRT3: g. 25702C > T) and three mutations in exons (SIRT2: g.4062C > T; SIRT2: g.4406C > T and SIRT3: g.25557A > G) were identified in 468 individuals of Qinchuan cattle. Chi-square tests showed that g.25751A > C, g.19676G > A, and g.25702C > T were in Hardy-Weinberg disequilibrium (χ(2) < χ0.05(2)). The statistical analyses indicated that six SNPs were significantly associated with the ultrasound carcass traits (P < 0.05) except g.4062C > T (SIRT2) (P > 0.05). These results indicate that the variations in the class I sirtuin genes and their corresponding genotypes may be considered as molecular markers for economic traits in cattle breeding.
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Affiliation(s)
- Linsheng Gui
- College of Animal Science and Technology, Northwest A & F University, Yangling, Shaanxi 712100, PR China.
| | - Ruijie Hao
- College of Animal Science and Technology, Northwest A & F University, Yangling, Shaanxi 712100, PR China.
| | - Yaran Zhang
- College of Animal Science and Technology, Northwest A & F University, Yangling, Shaanxi 712100, PR China.
| | - Xianlin Zhao
- College of Animal Science and Technology, Northwest A & F University, Yangling, Shaanxi 712100, PR China.
| | - Linsen Zan
- College of Animal Science and Technology, Northwest A & F University, Yangling, Shaanxi 712100, PR China; National Beef Cattle Improvement Center of Northwest A & F University, Yangling, Shaanxi 712100, PR China.
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Gui L, Wang H, Wei S, Zhang Y, Zan L. Molecular characterization, expression profiles, and analysis of Qinchuan cattle SIRT1 gene association with meat quality and body measurement traits (Bos taurus). Mol Biol Rep 2014; 41:5237-46. [PMID: 24828021 DOI: 10.1007/s11033-014-3393-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2014] [Accepted: 05/02/2014] [Indexed: 10/25/2022]
Abstract
Silent information regulator (SIRT1), was closely associated with senescence, metabolism, and apoptosis. The objective of this study was to investigate whether SIRT1 gene could be used as a candidate gene in the breeding process of Qinchuan cattle. Via sequencing technology conducted in 453 individuals of Qinchuan cattle, single nucleotide polymorphisms (G25764A, A25846G, and T25868C) with 5 haplotypes and 6 combined genotypes in 3' untranslated region of SIRT1 gene were identified. In addition, three loci were significantly associated with some of the body measurements and meat quality traits in Qinchuan cattle (P < 0.05), and the H2H2 (GG-AA-CC) diplotypes had better performance than other combinations in Qinchuan cattle. These results suggest that the SIRT1 gene could be used in marker assisted selection to improve the production traits of Qinchuan cattle.
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Affiliation(s)
- Linsheng Gui
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
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