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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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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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Xu H, Zhang X, Zang R, Cai Y, Cao X, Yang J, Li J, Lan X, Wu J. Genetic variations in the sheep SIRT7 gene and their correlation with body size traits. Arch Anim Breed 2019; 62:189-197. [PMID: 31807629 PMCID: PMC6852881 DOI: 10.5194/aab-62-189-2019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 03/19/2019] [Indexed: 11/11/2022] Open
Abstract
As a nicotinamide adenine dinucleotide (NAD)-dependent histone deacetylase
and ADP ribosyl transferase, the silent information regulator 7 (Sirtuin 7,
SIRT7) plays a crucial role in regulating the differentiation of adipocytes
and myoblasts, lipid metabolism, glucose metabolism, and cellular growth in
mammals. It has been hypothesized that SIRT7 affects growth traits in animals;
therefore, in this study, the potential insertion/deletion (indel) of genetic variations within
the ovine SIRT7 gene and their correlation with sheep growth traits
were explored. A total of 709 individuals from five Chinese
and Mongolian sheep breeds were analyzed. Two novel indel loci of the sheep
SIRT7 gene were detected and were named 5′ promoter
region-insertion-7 bp (5′ promoter region-7 bp) and 3′
UTR-insertion-17 bp (3′ UTR-17 bp), respectively. In all of the sheep breeds,
frequencies of the 5′ promoter region-7 bp mutation were low, whereas
mutations of 3′ UTR-17 bp were high in Tong sheep and Lanzhou fat-tail
sheep (LFTS). Furthermore, both indel polymorphisms had significant
associations with different growth characteristics (P<0.05). Among
these associations, the 3′ UTR-17 bp was highly correlated with rump width
in small-tail Han sheep (STHS, rams; P<0.01), and
individuals with the ID genotype had better chest depth values than those
with the II genotype. In this paper, two novel indels within the sheep
SIRT7 gene were identified, and genetic diversity and its
effects on body size traits were explored. These findings will potentially provide
useful DNA markers for the improvement of economic traits in sheep genetic breeding.
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Affiliation(s)
- Hongwei Xu
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, China.,Science Experimental Center, Northwest Minzu University, Lanzhou, Gansu, China.,College of Life Science and Engineering, Northwest Minzu University, Lanzhou, Gansu, China
| | - Xiaoyu Zhang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Rongxin Zang
- Science Experimental Center, Northwest Minzu University, Lanzhou, Gansu, China.,College of Life Science and Engineering, Northwest Minzu University, Lanzhou, Gansu, China
| | - Yong Cai
- Science Experimental Center, Northwest Minzu University, Lanzhou, Gansu, China.,College of Life Science and Engineering, Northwest Minzu University, Lanzhou, Gansu, China
| | - Xin Cao
- Science Experimental Center, Northwest Minzu University, Lanzhou, Gansu, China.,College of Life Science and Engineering, Northwest Minzu University, Lanzhou, Gansu, China
| | - Jutian Yang
- Science Experimental Center, Northwest Minzu University, Lanzhou, Gansu, China.,College of Life Science and Engineering, Northwest Minzu University, Lanzhou, Gansu, China
| | - Jie Li
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Xianyong Lan
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Jianping Wu
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, China.,current address: College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, China
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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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