Prioritization of genes associated with the pathogenesis of leukosis in cattle
Selection by means of genetic markers is a promising approach to the eradication of infectious diseases in farm animals, especially in the absence of effective methods of treatment and prevention. Bovine leukemia virus (BLV) is spread throughout the world and represents one of the biggest problems fo...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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Siberian Branch of the Russian Academy of Sciences, Federal Research Center Institute of Cytology and Genetics, The Vavilov Society of Geneticists and Breeders
2019-01-01
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| Series: | Вавиловский журнал генетики и селекции |
| Subjects: | |
| Online Access: | https://vavilov.elpub.ru/jour/article/view/1810 |
| _version_ | 1797214056157806592 |
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| author | N. S. Yudin N. L. Podkolodnyy T. A. Agarkova E. V. Ignatieva |
| author_facet | N. S. Yudin N. L. Podkolodnyy T. A. Agarkova E. V. Ignatieva |
| author_sort | N. S. Yudin |
| collection | DOAJ |
| description | Selection by means of genetic markers is a promising approach to the eradication of infectious diseases in farm animals, especially in the absence of effective methods of treatment and prevention. Bovine leukemia virus (BLV) is spread throughout the world and represents one of the biggest problems for the livestock production and food security in Russia. However, recent genome-wide association studies have shown that sensitivity/resistance to BLV is polygenic. The aim of this study was to create a catalog of cattle genes and genes of other mammalian species involved in the pathogenesis of BLV-induced infection and to perform gene prioritization using bioinformatics methods. Based on manually collected information from a range of open sources, a total of 446 genes were included in the catalog of cattle genes and genes of other mammals involved in the pathogenesis of BLV-induced infection. The following criteria were used to prioritize 446 genes from the catalog: (1) the gene is associated with leukemia according to a genome-wide association study; (2) the gene is associated with leukemia according to a case-control study; (3) the role of the gene in leukemia development has been studied using knockout mice; (4) protein-protein interactions exist between the gene-encoded protein and either viral particles or individual viral proteins; (5) the gene is annotated with Gene Ontology terms that are overrepresented for a given list of genes; (6) the gene participates in biological pathways from the KEGG or REACTOME databases, which are over-represented for a given list of genes; (7) the protein encoded by the gene has a high number of protein-protein interactions with proteins encoded by other genes from the catalog. Based on each criterion, a rank was assigned to each gene. Then the ranks were summarized and an overall rank was determined. Prioritization of 446 candidate genes allowed us to identify 5 genes of interest (TNF, LTB, BOLA-DQA1, BOLA-DRB3, ATF2), which can affect the sensitivity/resistance of cattle to leukemia. |
| first_indexed | 2024-03-07T16:05:43Z |
| format | Article |
| id | doaj.art-10fe579b71734029b83583ea10a374ac |
| institution | Directory Open Access Journal |
| issn | 2500-3259 |
| language | English |
| last_indexed | 2024-04-24T11:08:06Z |
| publishDate | 2019-01-01 |
| publisher | Siberian Branch of the Russian Academy of Sciences, Federal Research Center Institute of Cytology and Genetics, The Vavilov Society of Geneticists and Breeders |
| record_format | Article |
| series | Вавиловский журнал генетики и селекции |
| spelling | doaj.art-10fe579b71734029b83583ea10a374ac2024-04-11T15:31:00ZengSiberian Branch of the Russian Academy of Sciences, Federal Research Center Institute of Cytology and Genetics, The Vavilov Society of Geneticists and BreedersВавиловский журнал генетики и селекции2500-32592019-01-012281063106910.18699/VJ18.451858Prioritization of genes associated with the pathogenesis of leukosis in cattleN. S. Yudin0N. L. Podkolodnyy1T. A. Agarkova2E. V. Ignatieva3Institute of Cytology and Genetics, SB RAS; Novosibirsk State UniversityInstitute of Cytology and Genetics, SB RAS; Institute of Computational Mathematics and Mathematical Geophysics, SB RASSiberian Federal Research Center of Agro-BioTechnologies, RASInstitute of Cytology and Genetics, SB RAS; Novosibirsk State UniversitySelection by means of genetic markers is a promising approach to the eradication of infectious diseases in farm animals, especially in the absence of effective methods of treatment and prevention. Bovine leukemia virus (BLV) is spread throughout the world and represents one of the biggest problems for the livestock production and food security in Russia. However, recent genome-wide association studies have shown that sensitivity/resistance to BLV is polygenic. The aim of this study was to create a catalog of cattle genes and genes of other mammalian species involved in the pathogenesis of BLV-induced infection and to perform gene prioritization using bioinformatics methods. Based on manually collected information from a range of open sources, a total of 446 genes were included in the catalog of cattle genes and genes of other mammals involved in the pathogenesis of BLV-induced infection. The following criteria were used to prioritize 446 genes from the catalog: (1) the gene is associated with leukemia according to a genome-wide association study; (2) the gene is associated with leukemia according to a case-control study; (3) the role of the gene in leukemia development has been studied using knockout mice; (4) protein-protein interactions exist between the gene-encoded protein and either viral particles or individual viral proteins; (5) the gene is annotated with Gene Ontology terms that are overrepresented for a given list of genes; (6) the gene participates in biological pathways from the KEGG or REACTOME databases, which are over-represented for a given list of genes; (7) the protein encoded by the gene has a high number of protein-protein interactions with proteins encoded by other genes from the catalog. Based on each criterion, a rank was assigned to each gene. Then the ranks were summarized and an overall rank was determined. Prioritization of 446 candidate genes allowed us to identify 5 genes of interest (TNF, LTB, BOLA-DQA1, BOLA-DRB3, ATF2), which can affect the sensitivity/resistance of cattle to leukemia.https://vavilov.elpub.ru/jour/article/view/1810bovine leukemia virusgenome-wide association studygenesingle-nucleotide polymorphismassociationprioritizationgo analysisprotein-protein interactions |
| spellingShingle | N. S. Yudin N. L. Podkolodnyy T. A. Agarkova E. V. Ignatieva Prioritization of genes associated with the pathogenesis of leukosis in cattle Вавиловский журнал генетики и селекции bovine leukemia virus genome-wide association study gene single-nucleotide polymorphism association prioritization go analysis protein-protein interactions |
| title | Prioritization of genes associated with the pathogenesis of leukosis in cattle |
| title_full | Prioritization of genes associated with the pathogenesis of leukosis in cattle |
| title_fullStr | Prioritization of genes associated with the pathogenesis of leukosis in cattle |
| title_full_unstemmed | Prioritization of genes associated with the pathogenesis of leukosis in cattle |
| title_short | Prioritization of genes associated with the pathogenesis of leukosis in cattle |
| title_sort | prioritization of genes associated with the pathogenesis of leukosis in cattle |
| topic | bovine leukemia virus genome-wide association study gene single-nucleotide polymorphism association prioritization go analysis protein-protein interactions |
| url | https://vavilov.elpub.ru/jour/article/view/1810 |
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