The GWAS-MAP|ovis platform for aggregation and analysis of genome-wide association study results in sheep
In recent years, the number of genome-wide association studies (GWAS) carried out for various economically important animal traits has been increasing. GWAS discoveries provide summary statistics that can be used both for targeted marker-oriented selection and for studying the genetic control of eco...
| Main Authors: | , , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Siberian Branch of the Russian Academy of Sciences, Federal Research Center Institute of Cytology and Genetics, The Vavilov Society of Geneticists and Breeders
2022-07-01
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| Series: | Вавиловский журнал генетики и селекции |
| Subjects: | |
| Online Access: | https://vavilov.elpub.ru/jour/article/view/3388 |
| _version_ | 1797213928662499328 |
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| author | A. V. Kirichenko A. S. Zlobin T. I. Shashkova N. A. Volkova B. S. Iolchiev V. A. Bagirov P. M. Borodin L. С. Karssen Y. A. Tsepilov Y. S. Aulchenko |
| author_facet | A. V. Kirichenko A. S. Zlobin T. I. Shashkova N. A. Volkova B. S. Iolchiev V. A. Bagirov P. M. Borodin L. С. Karssen Y. A. Tsepilov Y. S. Aulchenko |
| author_sort | A. V. Kirichenko |
| collection | DOAJ |
| description | In recent years, the number of genome-wide association studies (GWAS) carried out for various economically important animal traits has been increasing. GWAS discoveries provide summary statistics that can be used both for targeted marker-oriented selection and for studying the genetic control of economically important traits of farm animals. In contrast to research in human genetics, GWAS on farm animals often does not meet generally accepted standards (availability of information about effect and reference alleles, the size and direction of the effect, etc.). This greatly complicates the use of GWAS results for breeding needs. Within the framework of human genetics, there are several technological solutions for researching the harmonized results of GWAS, including one of the largest, the GWAS-MAP platform. For other types of living organisms, including economically important agricultural animals, there are no similar solutions. To our knowledge, no similar solution has been proposed to date for any of the species of economically important animals. As part of this work, we focused on creating a platform similar to GWAS-MAP for working with the results of GWAS of sheep, since sheep breeding is one of the most important branches of agriculture. By analogy with the GWAS-MAP platform for storing, unifying and analyzing human GWAS, we have created the GWAS-MAP|ovis platform. The platform currently contains information on more than 34 million associations between genomic sequence variants and traits of meat production in sheep. The platform can also be used to conduct colocalization analysis, a method that allows one to determine whether the association of a particular locus with two different traits is the result of pleiotropy or whether these traits are associated with different variants that are in linkage disequilibrium. This platform will be useful for breeders to select promising markers for breeding, as well as to obtain information for the introduction of genomic breeding and for scientists to replicate the results obtained. |
| first_indexed | 2024-03-07T16:04:50Z |
| format | Article |
| id | doaj.art-27c004fc02154e65a863fd8cc4bfa23f |
| institution | Directory Open Access Journal |
| issn | 2500-3259 |
| language | English |
| last_indexed | 2024-04-24T11:06:04Z |
| publishDate | 2022-07-01 |
| 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-27c004fc02154e65a863fd8cc4bfa23f2024-04-11T15:31:05ZengSiberian 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 селекции2500-32592022-07-0126437838410.18699/VJGB-22-461271The GWAS-MAP|ovis platform for aggregation and analysis of genome-wide association study results in sheepA. V. Kirichenko0A. S. Zlobin1T. I. Shashkova2N. A. Volkova3B. S. Iolchiev4V. A. Bagirov5P. M. Borodin6L. С. Karssen7Y. A. Tsepilov8Y. S. Aulchenko9Kurchatov Genomic Center of ICG SB RASKurchatov Genomic Center of ICG SB RASInstitute of Cytology and Genetics of the Siberian Branch of the Russian Academy of SciencesFederal Research Center for Animal Husbandry named after Academy Member L.K. ErnstFederal Research Center for Animal Husbandry named after Academy Member L.K. ErnstFederal Research Center for Animal Husbandry named after Academy Member L.K. ErnstInstitute of Cytology and Genetics of the Siberian Branch of the Russian Academy of SciencesPolyKnomics BVKurchatov Genomic Center of ICG SB RAS; Novosibirsk State UniversityKurchatov Genomic Center of ICG SB RASIn recent years, the number of genome-wide association studies (GWAS) carried out for various economically important animal traits has been increasing. GWAS discoveries provide summary statistics that can be used both for targeted marker-oriented selection and for studying the genetic control of economically important traits of farm animals. In contrast to research in human genetics, GWAS on farm animals often does not meet generally accepted standards (availability of information about effect and reference alleles, the size and direction of the effect, etc.). This greatly complicates the use of GWAS results for breeding needs. Within the framework of human genetics, there are several technological solutions for researching the harmonized results of GWAS, including one of the largest, the GWAS-MAP platform. For other types of living organisms, including economically important agricultural animals, there are no similar solutions. To our knowledge, no similar solution has been proposed to date for any of the species of economically important animals. As part of this work, we focused on creating a platform similar to GWAS-MAP for working with the results of GWAS of sheep, since sheep breeding is one of the most important branches of agriculture. By analogy with the GWAS-MAP platform for storing, unifying and analyzing human GWAS, we have created the GWAS-MAP|ovis platform. The platform currently contains information on more than 34 million associations between genomic sequence variants and traits of meat production in sheep. The platform can also be used to conduct colocalization analysis, a method that allows one to determine whether the association of a particular locus with two different traits is the result of pleiotropy or whether these traits are associated with different variants that are in linkage disequilibrium. This platform will be useful for breeders to select promising markers for breeding, as well as to obtain information for the introduction of genomic breeding and for scientists to replicate the results obtained.https://vavilov.elpub.ru/jour/article/view/3388genome-wide association studymarker-based breedingsheepdatabaseweb interface |
| spellingShingle | A. V. Kirichenko A. S. Zlobin T. I. Shashkova N. A. Volkova B. S. Iolchiev V. A. Bagirov P. M. Borodin L. С. Karssen Y. A. Tsepilov Y. S. Aulchenko The GWAS-MAP|ovis platform for aggregation and analysis of genome-wide association study results in sheep Вавиловский журнал генетики и селекции genome-wide association study marker-based breeding sheep database web interface |
| title | The GWAS-MAP|ovis platform for aggregation and analysis of genome-wide association study results in sheep |
| title_full | The GWAS-MAP|ovis platform for aggregation and analysis of genome-wide association study results in sheep |
| title_fullStr | The GWAS-MAP|ovis platform for aggregation and analysis of genome-wide association study results in sheep |
| title_full_unstemmed | The GWAS-MAP|ovis platform for aggregation and analysis of genome-wide association study results in sheep |
| title_short | The GWAS-MAP|ovis platform for aggregation and analysis of genome-wide association study results in sheep |
| title_sort | gwas map ovis platform for aggregation and analysis of genome wide association study results in sheep |
| topic | genome-wide association study marker-based breeding sheep database web interface |
| url | https://vavilov.elpub.ru/jour/article/view/3388 |
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