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Rahman JU, Kumar D, Singh SP, Shahi BN, Ghosh AK, Verma MK, Pathak A, Dar AH, Kumar A, Sharma RK. Genome-wide identification and annotation of SNPs and their mapping in candidate genes related to milk production and fertility traits in Badri cattle. Trop Anim Health Prod 2023; 55:117. [PMID: 36928332 DOI: 10.1007/s11250-023-03535-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 03/06/2023] [Indexed: 03/18/2023]
Abstract
This study was conducted in Badri cattle using a double digest restriction-site associated DNA sequencing approach. The study aimed to identify and annotate high confidence single nucleotide polymorphisms (SNPs) and their mapping in candidate genes related to production and fertility in dairy cattle. A total of 7,168,552 genome-wide SNPs were initially identified in Badri cattle by alignment with the Bos indicus reference genome. After filtration of SNPs, 65,483 high confidence SNPs were retained and further used for downstream analysis. Annotation of high confidence SNPs revealed 99.197% SNPs had modifier impact, 0.326% SNPs were low impact, 0.036% were high impact, and 0.441% were moderate impact SNPs. Most SNPs in Badri cattle were found in intergenic, transcript and intronic regions. The candidate genes for milk production PRKCE, ABCG2, GHR, EPS8, CAST and NRXN1 were found to harbour maximum high confidence variants. Among candidate genes for fertility in cattle, ATP2B1, SOX5, WDR27, ARHGAP12, CACNA1D, ANKRD6, GRIA3, ZNF521 and CAST822 have maximum high confidence variants mapped in them. The SNPs found mapped in the candidate genes will be important genetic tools in the search for phenotype-modifying nucleotide changes and will aid in formulating relevant genetic improvement programmes for dairy cattle.
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Affiliation(s)
- Javid Ur Rahman
- Dapartment of Animal Genetics and Breeding, College of Veterinary & Animal Sciences, Govind Ballabh Pant University of Agriculture and Technology, Pantnagar, Uttarakhand, 263145, India.
| | - Devendra Kumar
- Dapartment of Animal Genetics and Breeding, College of Veterinary & Animal Sciences, Govind Ballabh Pant University of Agriculture and Technology, Pantnagar, Uttarakhand, 263145, India
| | - Satya Pal Singh
- Department of Veterinary Pharmacology and Toxicology, College of Veterinary & Animal Sciences, Govind Ballabh Pant University of Agriculture and Technology, Pantnagar, Uttarakhand, 263145, India
| | - Bijendra Narayan Shahi
- Dapartment of Animal Genetics and Breeding, College of Veterinary & Animal Sciences, Govind Ballabh Pant University of Agriculture and Technology, Pantnagar, Uttarakhand, 263145, India
| | - Ashis Kumar Ghosh
- Dapartment of Animal Genetics and Breeding, College of Veterinary & Animal Sciences, Govind Ballabh Pant University of Agriculture and Technology, Pantnagar, Uttarakhand, 263145, India
| | - Manish Kumar Verma
- Department of Veterinary Pharmacology and Toxicology, College of Veterinary & Animal Sciences, Govind Ballabh Pant University of Agriculture and Technology, Pantnagar, Uttarakhand, 263145, India
| | - Abhishek Pathak
- Department of Veterinary Pharmacology and Toxicology, College of Veterinary & Animal Sciences, Govind Ballabh Pant University of Agriculture and Technology, Pantnagar, Uttarakhand, 263145, India
| | - Aashaq Hussain Dar
- Department of Livestock Production and Management, College of Veterinary & Animal Sciences, Govind Ballabh Pant University of Agriculture and Technology, Pantnagar, Uttarakhand, 263145, India
| | - Anil Kumar
- Department of Livestock Production and Management, College of Veterinary & Animal Sciences, Govind Ballabh Pant University of Agriculture and Technology, Pantnagar, Uttarakhand, 263145, India
| | - Rabendra Kumar Sharma
- Department of Livestock Production and Management, College of Veterinary & Animal Sciences, Govind Ballabh Pant University of Agriculture and Technology, Pantnagar, Uttarakhand, 263145, India
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Vineeth MR, Surya T, Sivalingam J, Kumar A, Niranjan SK, Dixit SP, Singh K, Tantia MS, Gupta ID. Genome-wide discovery of SNPs in candidate genes related to production and fertility traits in Sahiwal cattle. Trop Anim Health Prod 2019; 52:1707-1715. [DOI: 10.1007/s11250-019-02180-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Accepted: 12/05/2019] [Indexed: 12/16/2022]
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Nemova NN, Kyaivyaryainen EI, Krupnova MY. Dynamics of activity of intracellular cysteine-dependent proteases and some peptidases in embryogenesis of Atlantic salmon Salmo salar L. Russ J Dev Biol 2017. [DOI: 10.1134/s1062360417040075] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Cochran SD, Cole JB, Null DJ, Hansen PJ. Discovery of single nucleotide polymorphisms in candidate genes associated with fertility and production traits in Holstein cattle. BMC Genet 2013; 14:49. [PMID: 23759029 PMCID: PMC3686577 DOI: 10.1186/1471-2156-14-49] [Citation(s) in RCA: 101] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2013] [Accepted: 05/23/2013] [Indexed: 11/22/2022] Open
Abstract
Background Identification of single nucleotide polymorphisms (SNPs) for specific genes involved in reproduction might improve reliability of genomic estimates for these low-heritability traits. Semen from 550 Holstein bulls of high (≥ 1.7; n = 288) or low (≤ −2; n = 262) daughter pregnancy rate (DPR) was genotyped for 434 candidate SNPs using the Sequenom MassARRAY® system. Three types of SNPs were evaluated: SNPs previously reported to be associated with reproductive traits or physically close to genetic markers for reproduction, SNPs in genes that are well known to be involved in reproductive processes, and SNPs in genes that are differentially expressed between physiological conditions in a variety of tissues associated in reproductive function. Eleven reproduction and production traits were analyzed. Results A total of 40 SNPs were associated (P < 0.05) with DPR. Among these were genes involved in the endocrine system, cell signaling, immune function and inhibition of apoptosis. A total of 10 genes were regulated by estradiol. In addition, 22 SNPs were associated with heifer conception rate, 33 with cow conception rate, 36 with productive life, 34 with net merit, 23 with milk yield, 19 with fat yield, 13 with fat percent, 19 with protein yield, 22 with protein percent, and 13 with somatic cell score. The allele substitution effect for SNPs associated with heifer conception rate, cow conception rate, productive life and net merit were in the same direction as for DPR. Allele substitution effects for several SNPs associated with production traits were in the opposite direction as DPR. Nonetheless, there were 29 SNPs associated with DPR that were not negatively associated with production traits. Conclusion SNPs in a total of 40 genes associated with DPR were identified as well as SNPs for other traits. It might be feasible to include these SNPs into genomic tests of reproduction and other traits. The genes associated with DPR are likely to be important for understanding the physiology of reproduction. Given the large number of SNPs associated with DPR that were not negatively associated with production traits, it should be possible to select for DPR without compromising production.
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Affiliation(s)
- Sarah D Cochran
- Department of Animal Sciences, D.H. Barron Reproductive and Perinatal Biology Research Program, and Genetics Institute, University of Florida, Gainesville, FL 32611-0910, USA
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An XP, Hou JX, Li G, Peng JY, Liu XQ, Liu HY, Xiao WP, Wang JG, Song YX, Cao BY. Analysis of Differentially Expressed Genes in Ovaries of Polytocous versus Monotocous Dairy Goats Using Suppressive Subtractive Hybridization. Reprod Domest Anim 2011; 47:498-503. [DOI: 10.1111/j.1439-0531.2011.01910.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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Dutt P, Croall DE, Arthur JSC, Veyra TD, Williams K, Elce JS, Greer PA. m-Calpain is required for preimplantation embryonic development in mice. BMC DEVELOPMENTAL BIOLOGY 2006; 6:3. [PMID: 16433929 PMCID: PMC1382200 DOI: 10.1186/1471-213x-6-3] [Citation(s) in RCA: 116] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2005] [Accepted: 01/24/2006] [Indexed: 12/13/2022]
Abstract
Background μ-calpain and m-calpain are ubiquitously expressed proteases implicated in cellular migration, cell cycle progression, degenerative processes and cell death. These heterodimeric enzymes are composed of distinct catalytic subunits, encoded by Capn1 (μ-calpain) or Capn2 (m-calpain), and a common regulatory subunit encoded by Capn4. Disruption of the mouse Capn4 gene abolished both μ-calpain and m-calpain activity, and resulted in embryonic lethality, thereby suggesting essential roles for one or both of these enzymes during mammalian embryogenesis. Disruption of the Capn1 gene produced viable, fertile mice implying that either m-calpain could compensate for the loss of μ-calpain, or that the loss of m-calpain was responsible for death of Capn4-/- mice. Results To distinguish between the alternatives described above, we deleted an essential coding region in the mouse Capn2 gene in embryonic stems cells and transmitted this mutant allele through the mouse germline. Breeding of heterozygous animals failed to produce homozygous mutant live offspring or implanted embryos. A nested PCR genotyping protocol was established, and homozygous preimplantation mutant embryos were detected at the morula but not at the blastocyts stage. Conclusion We conclude that homozygous disruption of the Capn2 gene results in pre-implantation embryonic lethality between the morula and blastocyst stage. This establishes that μ-calpain and m-calpain have distinct functions, and that m-calpain is vital for development of the preimplantation murine embryo.
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Affiliation(s)
- Previn Dutt
- Division of Cancer Biology and Genetics, Queen's University Cancer Research Institute, Queen's University, Kingston, Ontario; K7L 3N6, Canada
- Department of Biochemistry, Queen's University, Kingston, Ontario; K7L 3N6, Canada
| | - Dorothy E Croall
- Department of Biochemistry, Microbiology and Molecular Biology, University of Maine, Orono, Maine, 04469-5735 USA
| | | | - Teresa De Veyra
- Division of Cancer Biology and Genetics, Queen's University Cancer Research Institute, Queen's University, Kingston, Ontario; K7L 3N6, Canada
| | - Karen Williams
- Division of Cancer Biology and Genetics, Queen's University Cancer Research Institute, Queen's University, Kingston, Ontario; K7L 3N6, Canada
| | - John S Elce
- Department of Biochemistry, Queen's University, Kingston, Ontario; K7L 3N6, Canada
| | - Peter A Greer
- Division of Cancer Biology and Genetics, Queen's University Cancer Research Institute, Queen's University, Kingston, Ontario; K7L 3N6, Canada
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, Ontario; K7L 3N6, Canada
- Department of Biochemistry, Queen's University, Kingston, Ontario; K7L 3N6, Canada
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Haim K, Ben-Aharon I, Shalgi R. Expression and immunolocalization of the calpain–calpastatin system during parthenogenetic activation and fertilization in the rat egg. Reproduction 2006; 131:35-43. [PMID: 16388007 DOI: 10.1530/rep.1.00697] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Calpastatin is an intrinsic intracellular inhibitor of calpain, a Ca2+-dependent thiol protease. The calpain–calpastatin system constitutes one functional proteolytic unit whose presence and function has already been investigated in various cell types, but not in the egg. We have previously shown that calpain is expressed in rat eggs and is activated upon egg activation. The present study was designed to investigate the calpain–calpastatin interplay throughout the process.Western blot analysis revealed two main calpastatin isoforms, the erythrocyte type (77 kDa) and the muscle tissue type (110 kDa). By immunohistochemistry and confocal laser scanning microscopy, we demonstrated that the 110 kDa calpastatin was localized at the membrane area and highly abundant at the meiotic spindle in eggs at the first and second meiotic divisions. The 77 kDa calpastatin isoform appeared to be localized as a cortical sphere of clusters. The 110kDa calpastatin and β-tubulin have both been localized to the spindle of metaphase II eggs, both being scattered all through the cytoplasm following spindle disruption by nocodazole treatment, implying a dynamic interaction between calpastatin and microtubule elements. Upon egg activation, membranous calpastatin translocated to the cortex whereas cortical millimolar (m)-calpain shifted towards the membrane. Spindle calpastatin and calpain remained static.We suggest that calpastatin serves as a regulator of m-calpain. The counter translocation of m-calpain and calpastatin could serve as a means of calpain escape from calpastatin inhibition and may reflect a step in the process of calpain activation, throughout egg activation, that is required for calpain to exert its proteolytic activity.
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Affiliation(s)
- K Haim
- Department of Cell and Developmental Biology, Sackler Faculty of Medicine, Tel Aviv University, Tel-Aviv, Israel
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