Identification of homozygosity-rich regions in the Holstein genome
In this study, 371 Holstein cows from six herds and 26 Holstein bulls, which were used in these herds, were genotyped by the Illumina BovineSNP50 array. For runs of homozygosity (ROH) identification, consecutive and sliding runs were performed by the detectRUNS and Plink software. The missing calls...
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| 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
2023-09-01
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| Series: | Вавиловский журнал генетики и селекции |
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| Online Access: | https://vavilov.elpub.ru/jour/article/view/3858 |
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| author | M. G. Smaragdov |
| author_facet | M. G. Smaragdov |
| author_sort | M. G. Smaragdov |
| collection | DOAJ |
| description | In this study, 371 Holstein cows from six herds and 26 Holstein bulls, which were used in these herds, were genotyped by the Illumina BovineSNP50 array. For runs of homozygosity (ROH) identification, consecutive and sliding runs were performed by the detectRUNS and Plink software. The missing calls did not significantly affect the ROH data. The mean number of ROH identified by consecutive runs was 95.4 ± 2.7, and that by sliding runs was 86.0 ± 2.6 in cows, while this number for Holstein bulls was lower 58.9 ± 1.9. The length of the ROH segments varied from 1 Mb to over 16 Mb, with the largest number of ROH having a length of 1–2 Mb. Of the 29 chromosomes, BTA 14, BTA 16, and BTA 7 were the most covered by ROH. The mean coefficient of inbreeding across the herds was 0.111 ± 0.003 and 0.104 ± 0.004 based on consecutive and sliding runs, respectively, and 0.078 ± 0.005 for bulls based on consecutive runs. These values do not exceed those for Holstein cattle in North America. The results of this study confirmed the more accurate identification of ROH by consecutive runs, and also that the number of allowed heterozygous SNPs may have a significant effect on ROH data. |
| format | Article |
| id | doaj-art-bae72cdd06894db2b5519d7c1212fe11 |
| institution | Kabale University |
| issn | 2500-3259 |
| language | English |
| publishDate | 2023-09-01 |
| 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-bae72cdd06894db2b5519d7c1212fe112025-02-01T09:58:12ZengSiberian 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 селекции2500-32592023-09-0127547147910.18699/VJGB-23-571371Identification of homozygosity-rich regions in the Holstein genomeM. G. Smaragdov0Russian Research Institute of Farm Animal Genetics and Breeding – Branch of the L.K. Ernst Federal Science Center for Animal HusbandryIn this study, 371 Holstein cows from six herds and 26 Holstein bulls, which were used in these herds, were genotyped by the Illumina BovineSNP50 array. For runs of homozygosity (ROH) identification, consecutive and sliding runs were performed by the detectRUNS and Plink software. The missing calls did not significantly affect the ROH data. The mean number of ROH identified by consecutive runs was 95.4 ± 2.7, and that by sliding runs was 86.0 ± 2.6 in cows, while this number for Holstein bulls was lower 58.9 ± 1.9. The length of the ROH segments varied from 1 Mb to over 16 Mb, with the largest number of ROH having a length of 1–2 Mb. Of the 29 chromosomes, BTA 14, BTA 16, and BTA 7 were the most covered by ROH. The mean coefficient of inbreeding across the herds was 0.111 ± 0.003 and 0.104 ± 0.004 based on consecutive and sliding runs, respectively, and 0.078 ± 0.005 for bulls based on consecutive runs. These values do not exceed those for Holstein cattle in North America. The results of this study confirmed the more accurate identification of ROH by consecutive runs, and also that the number of allowed heterozygous SNPs may have a significant effect on ROH data.https://vavilov.elpub.ru/jour/article/view/3858rohsnpinbreedingcattle |
| spellingShingle | M. G. Smaragdov Identification of homozygosity-rich regions in the Holstein genome Вавиловский журнал генетики и селекции roh snp inbreeding cattle |
| title | Identification of homozygosity-rich regions in the Holstein genome |
| title_full | Identification of homozygosity-rich regions in the Holstein genome |
| title_fullStr | Identification of homozygosity-rich regions in the Holstein genome |
| title_full_unstemmed | Identification of homozygosity-rich regions in the Holstein genome |
| title_short | Identification of homozygosity-rich regions in the Holstein genome |
| title_sort | identification of homozygosity rich regions in the holstein genome |
| topic | roh snp inbreeding cattle |
| url | https://vavilov.elpub.ru/jour/article/view/3858 |
| work_keys_str_mv | AT mgsmaragdov identificationofhomozygosityrichregionsintheholsteingenome |