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Ribeiro G, Baldi F, Cesar ASM, Alexandre PA, Peripolli E, Ferraz JBS, Fukumasu H. Detection of potential functional variants based on systems-biology: the case of feed efficiency in beef cattle. BMC Genomics 2022; 23:774. [PMID: 36434498 PMCID: PMC9700932 DOI: 10.1186/s12864-022-08958-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 10/20/2022] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND Potential functional variants (PFVs) can be defined as genetic variants responsible for a given phenotype. Ultimately, these are the best DNA markers for animal breeding and selection, especially for polygenic and complex phenotypes. Herein, we described the identification of PFVs for complex phenotypes (in this case, Feed Efficiency in beef cattle) using a systems-biology driven approach based on RNA-seq data from physiologically relevant organs. RESULTS The systems-biology coupled with deep molecular phenotyping by RNA-seq of liver, muscle, hypothalamus, pituitary, and adrenal glands of animals with high and low feed efficiency (FE) measured by residual feed intake (RFI) identified 2,000,936 uniquely variants. Among them, 9986 variants were significantly associated with FE and only 78 had a high impact on protein expression and were considered as PFVs. A set of 169 significant uniquely variants were expressed in all five organs, however, only 27 variants had a moderate impact and none of them a had high impact on protein expression. These results provide evidence of tissue-specific effects of high-impact PFVs. The PFVs were enriched (FDR < 0.05) for processing and presentation of MHC Class I and II mediated antigens, which are an important part of the adaptive immune response. The experimental validation of these PFVs was demonstrated by the increased prediction accuracy for RFI using the weighted G matrix (ssGBLUP+wG; Acc = 0.10 and b = 0.48) obtained in the ssGWAS in comparison to the unweighted G matrix (ssGBLUP; Acc = 0.29 and b = 1.10). CONCLUSION Here we identified PFVs for FE in beef cattle using a strategy based on systems-biology and deep molecular phenotyping. This approach has great potential to be used in genetic prediction programs, especially for polygenic phenotypes.
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Affiliation(s)
- Gabriela Ribeiro
- grid.11899.380000 0004 1937 0722Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of Sao Paulo, Pirassununga, Sao Paulo, 13635-900 Brazil
| | - Fernando Baldi
- grid.410543.70000 0001 2188 478XDepartment of Animal Science, São Paulo State University (UNESP), Jaboticabal, São Paulo, Brazil
| | - Aline S. M. Cesar
- grid.11899.380000 0004 1937 0722Escola Superior de Agricultura “Luiz de Queiroz”, University of Sao Paulo, Piracicaba, São Paulo, Brazil
| | - Pâmela A. Alexandre
- grid.11899.380000 0004 1937 0722Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of Sao Paulo, Pirassununga, Sao Paulo, 13635-900 Brazil ,CSIRO Agriculture & Food, 306 Carmody Rd., St. Lucia, Brisbane, QLD 4067 Australia
| | - Elisa Peripolli
- grid.11899.380000 0004 1937 0722Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of Sao Paulo, Pirassununga, Sao Paulo, 13635-900 Brazil ,grid.410543.70000 0001 2188 478XDepartment of Animal Science, São Paulo State University (UNESP), Jaboticabal, São Paulo, Brazil
| | - José B. S. Ferraz
- grid.11899.380000 0004 1937 0722Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of Sao Paulo, Pirassununga, Sao Paulo, 13635-900 Brazil
| | - Heidge Fukumasu
- grid.11899.380000 0004 1937 0722Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of Sao Paulo, Pirassununga, Sao Paulo, 13635-900 Brazil
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Batool K, Wajid A, Ain Q, Shahid S, Namat T, Batool A, Hussain T, Babar ME. Sequence-Based Structural and Evolution of Polymorphisms in Bovine Toll-Like Receptor2 Gene in Dhanni and Jersey Cattle Breeds. Genetic polymorphisms in bovine TLR2. RUSS J GENET+ 2021. [DOI: 10.1134/s1022795420120030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Kalashnikov AE, Kalashnikova L, Novák K. Analyzing the exome heterogeneity of cattle immunity genes with the method of flow-cell sequencing. BIO WEB OF CONFERENCES 2020. [DOI: 10.1051/bioconf/20201700247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Toll-like receptors belong to the pattern-recognition receptors (PRRs), which have evolved to recognize conserved features of bacterial and viral molecules. We used the approach developed earlier to screen for the polymorphism in TLR genes in a representative set of historical and modern cattle breeds from Russia. The method pipeline included the steps of obtaining the overlapping amplification products from the coding regions of all ten bovine TLR genes, their subsequent purification and normalization. While the anti-bacterial group included TLR1, -2, -4, -5 and -6, the anti-viral group compressed TLR3, -7, -8, -9 and -10 (in spite of its unclear specificity). Animals from the about seven breeds, both bulls and cows, was used for analysis. The samples from the pooled genomic DNA were sequenced on the PacBio platform. After identification of variations, Bayesian analysis was carried out, followed by filtration on quality of sequencing. The 5–36 structural variants of TLRs were annotated according to their biological significance. Both new and already identified sites of variability, already annotated and documented in dbSNP, have been found. The data are needed for further breeding of local breeds in Russia with respect to their natural resistance to various diseases.
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Verma S, Thakur A, Katoch S, Shekhar C, Wani AH, Kumar S, Dohroo S, Singh G, Sharma M. Differences in innate and adaptive immune response traits of Pahari (Indian non-descript indigenous breed) and Jersey crossbred cattle. Vet Immunol Immunopathol 2017; 192:20-27. [PMID: 29042011 DOI: 10.1016/j.vetimm.2017.09.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Revised: 09/11/2017] [Accepted: 09/15/2017] [Indexed: 01/24/2023]
Abstract
Cattle are an integral part of the largely agrarian economy of India. Indigenous breeds of cattle comprise about 80% of total cattle population of the country and contribute significantly to the overall milk production. There are 40 recognized indigenous breeds of cattle and a number of uncharacterized non-descript cattle. Pahari cattle of Himachal Pradesh in Northern India are one such non-descript indigenous breed. Here we describe a comprehensive evaluation of haematobiochemical parameters and innate and adaptive immune response traits of Pahari cattle and a comparison with Jersey crossbred cattle. The study shows demonstrable differences in the two breeds with respect to some innate and adaptive immunological traits. This is a first attempt to characterize immune response traits of Pahari cattle and the results of the study provide an understanding of breed differences in immune status of cattle which could be useful for their breeding and conservations programs.
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Affiliation(s)
- Subhash Verma
- Department of Veterinary Microbiology, Dr. G. C. Negi College of Veterinary and Animal Sciences, CSK HPKV, Palampur,176062, Himachal Pradesh, India.
| | - Aneesh Thakur
- Department of Veterinary Microbiology, Dr. G. C. Negi College of Veterinary and Animal Sciences, CSK HPKV, Palampur,176062, Himachal Pradesh, India
| | - Shailja Katoch
- Department of Veterinary Microbiology, Dr. G. C. Negi College of Veterinary and Animal Sciences, CSK HPKV, Palampur,176062, Himachal Pradesh, India
| | - Chander Shekhar
- Department of Veterinary Microbiology, Dr. G. C. Negi College of Veterinary and Animal Sciences, CSK HPKV, Palampur,176062, Himachal Pradesh, India
| | - Aasim Habib Wani
- Department of Veterinary Microbiology, Dr. G. C. Negi College of Veterinary and Animal Sciences, CSK HPKV, Palampur,176062, Himachal Pradesh, India
| | - Sandeep Kumar
- Department of Veterinary Microbiology, Dr. G. C. Negi College of Veterinary and Animal Sciences, CSK HPKV, Palampur,176062, Himachal Pradesh, India
| | - Shweta Dohroo
- Department of Veterinary Microbiology, Dr. G. C. Negi College of Veterinary and Animal Sciences, CSK HPKV, Palampur,176062, Himachal Pradesh, India
| | - Geetanjali Singh
- Department of Veterinary Physiology and Biochemistry, Dr. G. C. Negi College of Veterinary and Animal Sciences, CSK HPKV, Palampur,176062, Himachal Pradesh, India
| | - Mandeep Sharma
- Department of Veterinary Microbiology, Dr. G. C. Negi College of Veterinary and Animal Sciences, CSK HPKV, Palampur,176062, Himachal Pradesh, India
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Gurao A, Kashyap SK, Singh R. β-defensins: An innate defense for bovine mastitis. Vet World 2017; 10:990-998. [PMID: 28919695 PMCID: PMC5591491 DOI: 10.14202/vetworld.2017.990-998] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Accepted: 07/29/2017] [Indexed: 11/16/2022] Open
Abstract
Immune challenges are inevitable for livestock that are exposed to a varied range of adverse conditions ranging from environmental to pathogenic stresses. The β-defensins are antimicrobial peptides, belonging to “defensin” family and therefore acts as the first line of defense against the major infections occurring in dairy cattle including intramammary infections. The better resistance to mastitis displayed by Bos indicus is implicit in the fact that they have better adapted and also has more sequence variation with rare allele conserved due to lesser artificial selection pressure than that of Bos taurus. Among the 58 in silico predicted β-defensins, only a few have been studied in the aspect of intramammary infections. The data on polymorphisms occurring in various β-defensin genes is limited in B. indicus, indicating toward higher possibilities for exploring marker for mastitis resistance. The following review shall focus on concisely summarizing the up-to-date research on β-defensins in B. taurus and discuss the possible scope for research in B. indicus.
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Affiliation(s)
- Ankita Gurao
- Department of Veterinary Microbiology and Biotechnology, College of Veterinary and Animal Sciences, Rajasthan University for Veterinary and Animal Sciences, Bikaner - 334 001, Rajasthan, India
| | - Sudhir Kumar Kashyap
- Department of Veterinary Microbiology and Biotechnology, College of Veterinary and Animal Sciences, Rajasthan University for Veterinary and Animal Sciences, Bikaner - 334 001, Rajasthan, India
| | - Ravinder Singh
- Department of Biotechnology, Sri Guru Granth Sahib World University, Fatehgarh Sahib - 140 407, Punjab, India
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