Candidate genes for productivity identified by genome-wide association study with indicators of class in the Russian meat merino sheep breed
Genome-wide association studies allow identification of loci and polymorphisms associated with the formation of relevant phenotypes. When conducting a full genome analysis of sheep, particularly promising is the study of individuals with outstanding productivity indicators – exhibition animals, repr...
| 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
2020-12-01
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| Series: | Вавиловский журнал генетики и селекции |
| Subjects: | |
| Online Access: | https://vavilov.elpub.ru/jour/article/view/2843 |
| _version_ | 1797214025007759360 |
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| author | A. Y. Krivoruchko O. A. Yatsyk E. Y. Safaryan |
| author_facet | A. Y. Krivoruchko O. A. Yatsyk E. Y. Safaryan |
| author_sort | A. Y. Krivoruchko |
| collection | DOAJ |
| description | Genome-wide association studies allow identification of loci and polymorphisms associated with the formation of relevant phenotypes. When conducting a full genome analysis of sheep, particularly promising is the study of individuals with outstanding productivity indicators – exhibition animals, representatives of the super-elite class. The aim of this study was to identify new candidate genes for economically valuable traits based on the search for single nucleotide polymorphisms (SNPs) associated with belonging to different evaluation classes in rams of the Russian meat merino breed. Animal genotyping was performed using Ovine Infinium HD BeadChip 600K DNA, association search was performed using PLINK v. 1.07 software. Highly reliable associations were found between animals belonging to different evaluation classes and the frequency of occurrence of individual SNPs on chromosomes 2, 6, 10, 13, and 20. Most of the substitutions with high association reliability are concentrated on chromosome 10 in the region 10: 30859297–31873769. To search for candidate genes, 15 polymorphisms with the highest association reliability were selected (–log10(р) > 9). Determining the location of the analyzed SNPs relative to the latest annotation Oar_rambouillet_v1.0 allowed to identify 11 candidate genes presumably associated with the formation of a complex of phenotypic traits of animals in the exhibition group: RXFP2, ALOX5AP, MEDAG, OPN5, PRDM5, PTPRT, TRNAS-GGA, EEF1A1, FRY, ZBTB21-like, and B3GLCT-like. The listed genes encode proteins involved in the control of the cell cycle and DNA replication, regulation of cell proliferation and apoptosis, lipid and carbohydrate metabolism, the development of the inflammatory process and the work of circadian rhythms. Thus, the candidate genes under consideration can influence the formation of exterior features and productive qualities of sheep. However, further research is needed to confirm the influence of genes and determine the exact mechanisms for implementing this influence on the phenotype. |
| first_indexed | 2024-03-07T16:05:19Z |
| format | Article |
| id | doaj.art-a8fb0d18ade84844adb9c54d5d72b930 |
| institution | Directory Open Access Journal |
| issn | 2500-3259 |
| language | English |
| last_indexed | 2024-04-24T11:07:36Z |
| publishDate | 2020-12-01 |
| 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-a8fb0d18ade84844adb9c54d5d72b9302024-04-11T15:31:03ZengSiberian 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 селекции2500-32592020-12-0124883684310.18699/VJ20.6811113Candidate genes for productivity identified by genome-wide association study with indicators of class in the Russian meat merino sheep breedA. Y. Krivoruchko0O. A. Yatsyk1E. Y. Safaryan2All-Russian Research Institute of Sheep and Goat Breeding – Branch of the North Caucasus Federal Agricultural Research CenterAll-Russian Research Institute of Sheep and Goat Breeding – Branch of the North Caucasus Federal Agricultural Research CenterAll-Russian Research Institute of Sheep and Goat Breeding – Branch of the North Caucasus Federal Agricultural Research CenterGenome-wide association studies allow identification of loci and polymorphisms associated with the formation of relevant phenotypes. When conducting a full genome analysis of sheep, particularly promising is the study of individuals with outstanding productivity indicators – exhibition animals, representatives of the super-elite class. The aim of this study was to identify new candidate genes for economically valuable traits based on the search for single nucleotide polymorphisms (SNPs) associated with belonging to different evaluation classes in rams of the Russian meat merino breed. Animal genotyping was performed using Ovine Infinium HD BeadChip 600K DNA, association search was performed using PLINK v. 1.07 software. Highly reliable associations were found between animals belonging to different evaluation classes and the frequency of occurrence of individual SNPs on chromosomes 2, 6, 10, 13, and 20. Most of the substitutions with high association reliability are concentrated on chromosome 10 in the region 10: 30859297–31873769. To search for candidate genes, 15 polymorphisms with the highest association reliability were selected (–log10(р) > 9). Determining the location of the analyzed SNPs relative to the latest annotation Oar_rambouillet_v1.0 allowed to identify 11 candidate genes presumably associated with the formation of a complex of phenotypic traits of animals in the exhibition group: RXFP2, ALOX5AP, MEDAG, OPN5, PRDM5, PTPRT, TRNAS-GGA, EEF1A1, FRY, ZBTB21-like, and B3GLCT-like. The listed genes encode proteins involved in the control of the cell cycle and DNA replication, regulation of cell proliferation and apoptosis, lipid and carbohydrate metabolism, the development of the inflammatory process and the work of circadian rhythms. Thus, the candidate genes under consideration can influence the formation of exterior features and productive qualities of sheep. However, further research is needed to confirm the influence of genes and determine the exact mechanisms for implementing this influence on the phenotype.https://vavilov.elpub.ru/jour/article/view/2843sheepsnpgenome-wide association studygwascandidate generussian meat merino |
| spellingShingle | A. Y. Krivoruchko O. A. Yatsyk E. Y. Safaryan Candidate genes for productivity identified by genome-wide association study with indicators of class in the Russian meat merino sheep breed Вавиловский журнал генетики и селекции sheep snp genome-wide association study gwas candidate gene russian meat merino |
| title | Candidate genes for productivity identified by genome-wide association study with indicators of class in the Russian meat merino sheep breed |
| title_full | Candidate genes for productivity identified by genome-wide association study with indicators of class in the Russian meat merino sheep breed |
| title_fullStr | Candidate genes for productivity identified by genome-wide association study with indicators of class in the Russian meat merino sheep breed |
| title_full_unstemmed | Candidate genes for productivity identified by genome-wide association study with indicators of class in the Russian meat merino sheep breed |
| title_short | Candidate genes for productivity identified by genome-wide association study with indicators of class in the Russian meat merino sheep breed |
| title_sort | candidate genes for productivity identified by genome wide association study with indicators of class in the russian meat merino sheep breed |
| topic | sheep snp genome-wide association study gwas candidate gene russian meat merino |
| url | https://vavilov.elpub.ru/jour/article/view/2843 |
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