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Vaishnav S, Chauhan A, Ajay A, Saini BL, Kumar S, Kumar A, Bhushan B, Gaur GK. Allelic to genome wide perspectives of swine genetic variation to litter size and its component traits. Mol Biol Rep 2023; 50:3705-3721. [PMID: 36642776 DOI: 10.1007/s11033-022-08168-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 12/01/2022] [Indexed: 01/17/2023]
Abstract
Litter size is a complex and sex limited trait that depends on various biological, managemental and environmental factors. Owing to its low heritability it is inefficaciously selected by traditional methods. However, due to higher heritability of ovulation rate and embryo survival, selection based on component traits of litter size is advocated. QTL analysis and candidate gene approach are among the various supplementary/alternate strategies for selection of litter size. QTL analysis is aimed at identifying genomic regions affecting trait of interest significantly. Candidate gene approach necessitates identification of genes potentially affecting the trait. There are various genes that significantly affect litter size and its component traits viz. ESR, LEP, BF, IGFBP, RBP4, PRLR, CTNNAL1, WNT10B, TCF12, DAZ, and RNF4. These genes affect litter size in a complex interacting manner. Lately, genome wide association study (GWAS) have been utilized to unveil the genetic and biological background of litter traits, and elucidate the genes governing litter size. Favorable SNPs in these genes have been identified and offers a scope for inclusion in selection programs thereby increasing breeding efficiency and profit in pigs. The review provides a comprehensive coverage of investigations carried out globally to unravel the genetic variation in litter size and its component traits in pigs, both at allelic and genome wide level. It offers a current perspective on different strategies including the profiling of candidate genes, QTLs, and genome wide association studies as an aid to efficient selection for litter size and its component traits.
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Affiliation(s)
| | - Anuj Chauhan
- Indian Veterinary Research Institute, Bareilly, India.
| | - Argana Ajay
- Indian Veterinary Research Institute, Bareilly, India
| | | | - Subodh Kumar
- Indian Veterinary Research Institute, Bareilly, India
| | - Amit Kumar
- Indian Veterinary Research Institute, Bareilly, India
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Mehrotra A, Bhushan B, Kumar A, Panigrahi M, Chauhan A, Kumari S, Saini BL, Dutt T, Mishra BP. Characterisation and comparison of immune response mechanisms in an indigenous and a commercial pig breed after classical swine fever vaccination. Anim Genet 2021; 53:68-79. [PMID: 34729794 DOI: 10.1111/age.13152] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 08/29/2021] [Accepted: 10/14/2021] [Indexed: 01/27/2023]
Abstract
The live attenuated classical swine fever (CSF) vaccine has been successfully used to prevent and control CSF outbreaks for 6 decades. However, the immune response mechanisms against the vaccine remain poorly understood. Moreover, very few reports exist regarding the breed differences in the response to CSF vaccine. In this study, we generated the peripheral blood mononuclear cell transcriptomes of indigenous Ghurrah and commercial Landrace pig breeds, before and 7 days after CSF vaccination. Subsequently, between and within-breed differential gene expression analyses were carried out. Results revealed large differences in pre-vaccination peripheral blood mononuclear cell transcriptome profiles of the two breeds, which were homogenised 7 days after vaccination. Before vaccination, gene set enrichment analysis showed that pathways related to antigen sensing and innate immune response were enriched in Ghurrah, while pathways related to adaptive immunity were enriched in Landrace. Ghurrah exhibited greater immunomodulation compared to Landrace following the vaccination. In Ghurrah, cell-cycle processes and T-cell response pathways were upregulated after vaccination. However, no pathways were upregulated in Landrace after vaccination. Pathways related to inflammation were downregulated in both the breeds after vaccination. Key regulators of inflammation such as IL1A, IL1B, NFKBIA and TNF genes were strongly downregulated in both the breeds after vaccination. Overall, our results have elucidated the mechanisms of host immune response against CSF vaccination in two distinct breeds and revealed common key genes instrumental in the global immune response to the vaccine.
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Affiliation(s)
- A Mehrotra
- Division of Animal Genetics, ICAR - Indian Veterinary Research Institute, Izatnangar, Bareilly, UP, 243122, India
| | - B Bhushan
- Division of Animal Genetics, ICAR - Indian Veterinary Research Institute, Izatnangar, Bareilly, UP, 243122, India
| | - A Kumar
- Division of Animal Genetics, ICAR - Indian Veterinary Research Institute, Izatnangar, Bareilly, UP, 243122, India
| | - M Panigrahi
- Division of Animal Genetics, ICAR - Indian Veterinary Research Institute, Izatnangar, Bareilly, UP, 243122, India
| | - A Chauhan
- Division of Livestock Production and Management, ICAR - Indian Veterinary Research Institute, Izatnangar, Bareilly, UP, 243122, India
| | - S Kumari
- Division of Animal Genetics, ICAR - Indian Veterinary Research Institute, Izatnangar, Bareilly, UP, 243122, India
| | - B L Saini
- Division of Animal Genetics, ICAR - Indian Veterinary Research Institute, Izatnangar, Bareilly, UP, 243122, India
| | - T Dutt
- Division of Livestock Production and Management, ICAR - Indian Veterinary Research Institute, Izatnangar, Bareilly, UP, 243122, India
| | - B P Mishra
- Animal Biotechnology, ICAR - Indian Veterinary Research Institute, Izatnangar, Bareilly, UP, 243122, India
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Jaiswal RK, Mendiratta SK, Talukder S, Soni A, Chand S, Saini BL. Application of Lipase Based Enzymatic Time Temperature Indicator (TTI) as Quality Marker for Frozen Chicken Meat. FSTR 2020. [DOI: 10.3136/fstr.26.9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Rohit Kumar Jaiswal
- Division of Livestock Products Technology, ICAR-Indian Veterinary Research Institute
| | | | - Suman Talukder
- Division of Livestock Products Technology, ICAR-Indian Veterinary Research Institute
| | - Arvind Soni
- Division of Livestock Products Technology, ICAR-Indian Veterinary Research Institute
| | - Sagar Chand
- Division of Livestock Products Technology, ICAR-Indian Veterinary Research Institute
| | - Babu Lal Saini
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute
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Saini BL, Gaur GK, Sahoo NR, Mendiratta SK, Kumar A, Naha BC, Baranwal A, Yadav V, Jaiswal RK. Polymorphism distribution of RYR1, PRKAG3, HFABP, MYF-5 and MC4R genes in crossbred pigs. Mol Biol Rep 2018; 45:1575-1585. [PMID: 30288642 DOI: 10.1007/s11033-018-4263-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 07/13/2018] [Indexed: 01/04/2023]
Abstract
This study was designed to screen the crossbred pigs for SNPs in five candidate genes, associated with pork quality traits and to differentiate their genotypes by PCR-RFLP. The results indicated that genotypes of crossbred pigs were NN (90%) and Nn (10%) for RYR1; RR (83%) and QR (17%) for PRKAG3; HH (98%), Hh (1%) and hh (1%) for HFABP; DD (99%) and CD (1%) for MYF-5; and AG (57%), GG (26%) and AA (17%) for MC4R SNPs, respectively. Allelic frequencies for five SNPs {RYR1 (1843C>T), PRKAG3 (c.599G>A), HFABP (c.1322C>T), MYF-5 (c.1205A>C) and MC4R (c.1426A>G)} were 0.95 and 0.05 (N/n), 0.08 and 0.92 (Q/R), 0.99 and 0.01 (H/h), 0.00 and 1.00 (C/D) and 0.45 and 0.55 (A/G), respectively. The effect of RYR1 (1843C>T) SNP was significant on pH45 (P < 0.05), pH24 (P < 0.05) and protein % (P < 0.05). The PRKAG3 (c.599G>A) and MC4R (c.1426A>G) SNP had significant association with dressing percentages. The results revealed that RYR1, PRKAG3 and MC4R SNPs may be used in marker associated selection for pork quality traits in crossbred pigs.
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Affiliation(s)
- B L Saini
- Division of Animal Genetics, ICAR-IVRI, Izatnagar, 243122, India.
| | - G K Gaur
- Livestock Production and Management Section, ICAR-IVRI, Izatnagar, 243122, India
| | - N R Sahoo
- Division of Animal Genetics, ICAR-IVRI, Izatnagar, 243122, India
| | - S K Mendiratta
- Division of Livestock Products Technology, ICAR-IVRI, Izatnagar, 243122, India
| | - A Kumar
- Division of Animal Genetics, ICAR-IVRI, Izatnagar, 243122, India
| | - B C Naha
- Division of Animal Genetics, ICAR-IVRI, Izatnagar, 243122, India
| | - A Baranwal
- Division of Animal Genetics, ICAR-IVRI, Izatnagar, 243122, India
| | - V Yadav
- Dairy Cattle Breeding Division, ICAR-NDRI, Karnal, 132001, India
| | - R K Jaiswal
- Division of Livestock Products Technology, ICAR-IVRI, Izatnagar, 243122, India
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