Distribution of Homozygosity Regions in the Genome of Kazakh Cattle Breeds
Runs of homozygosity (ROH) are contiguous stretches of homozygous genotypes that are passed from parents to their offspring. ROHs are suitable for determining population history, inbreeding rates, and the genetic relationships between individuals in the populations, as well as to detect candidate ge...
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MDPI AG
2022-04-01
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| author | Indira Beishova Kairat Dossybayev Alzhan Shamshidin Alena Belaya Anuarbek Bissembayev Kadyrzhan Khamzin Alexandr Kovalchuk Askar Nametov |
| author_facet | Indira Beishova Kairat Dossybayev Alzhan Shamshidin Alena Belaya Anuarbek Bissembayev Kadyrzhan Khamzin Alexandr Kovalchuk Askar Nametov |
| author_sort | Indira Beishova |
| collection | DOAJ |
| description | Runs of homozygosity (ROH) are contiguous stretches of homozygous genotypes that are passed from parents to their offspring. ROHs are suitable for determining population history, inbreeding rates, and the genetic relationships between individuals in the populations, as well as to detect candidate genes responsible for economic traits in farm animals. In this study, we observed that the Kazakh white-headed (KWh) cattle breed (ROH <i>n</i> = 55,976) had a higher number of ROH compared to the Auliekol (AK) breed (ROH <i>n</i> = 13,137). When calculating the mean length of ROH, there were considerable differences between Kazakh white-headed (211.59 ± 92.98 Mb) and Auliekol (99.62 ± 46.48 Mb) populations. The maximum length of ROH was higher in Auliekol cattle (510.25 Mb) than in Kazakh white-headed cattle (498.91 Mb). The average inbreeding coefficient rate was equal to 0.084 ± 0.037 in Kazakh white-headed cattle and 0.039 ± 0.018 in Auliekol cattle. The high frequency of genomic regions showed that the strongest patterns were observed on chromosomes 2, 6, and 26 for KWh and 1, 5, and 14 for AK. The estimation of ROH numbers per animal showed that the number of ROH decreased with increasing ROH length in both populations. The genomic inbreeding coefficient of both cattle breeds was calculated based on the ROH, and ancient inbreeding was observed. The harbored genes within ROH islands were associated with meat growth and milk production. |
| first_indexed | 2024-03-09T10:56:29Z |
| format | Article |
| id | doaj.art-9ffb95b11c9641b294065e96343e49ca |
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| language | English |
| last_indexed | 2024-03-09T10:56:29Z |
| publishDate | 2022-04-01 |
| publisher | MDPI AG |
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| series | Diversity |
| spelling | doaj.art-9ffb95b11c9641b294065e96343e49ca2023-12-01T01:37:14ZengMDPI AGDiversity1424-28182022-04-0114427910.3390/d14040279Distribution of Homozygosity Regions in the Genome of Kazakh Cattle BreedsIndira Beishova0Kairat Dossybayev1Alzhan Shamshidin2Alena Belaya3Anuarbek Bissembayev4Kadyrzhan Khamzin5Alexandr Kovalchuk6Askar Nametov7Zhengir Khan West Kazakhstan Agrarian Technical University, Zhangir Khan Street, 51, Uralsk 090009, KazakhstanFaculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Al-Farabi Ave., 71, Almaty 050040, KazakhstanZhengir Khan West Kazakhstan Agrarian Technical University, Zhangir Khan Street, 51, Uralsk 090009, KazakhstanDepartment of Morphology and Physiology of Humans and Animals, Faculty of Natural Sciences “Belarusian State Pedagogical University Named after Maxim Tank”, Sovetskaya St., 18, 220050 Minsk, BelarusScientific and Production Center of Animal Husbandry and Veterinary Medicine, Baykonyr District, Yevgeny Brusilovsky St., 2, Apartment 85, Nur-Sultan 010000, KazakhstanLTD “Republican Chamber of Meat Sheep”, Micro District Zerdeli, 39, Almaty 050000, KazakhstanZhengir Khan West Kazakhstan Agrarian Technical University, Zhangir Khan Street, 51, Uralsk 090009, KazakhstanZhengir Khan West Kazakhstan Agrarian Technical University, Zhangir Khan Street, 51, Uralsk 090009, KazakhstanRuns of homozygosity (ROH) are contiguous stretches of homozygous genotypes that are passed from parents to their offspring. ROHs are suitable for determining population history, inbreeding rates, and the genetic relationships between individuals in the populations, as well as to detect candidate genes responsible for economic traits in farm animals. In this study, we observed that the Kazakh white-headed (KWh) cattle breed (ROH <i>n</i> = 55,976) had a higher number of ROH compared to the Auliekol (AK) breed (ROH <i>n</i> = 13,137). When calculating the mean length of ROH, there were considerable differences between Kazakh white-headed (211.59 ± 92.98 Mb) and Auliekol (99.62 ± 46.48 Mb) populations. The maximum length of ROH was higher in Auliekol cattle (510.25 Mb) than in Kazakh white-headed cattle (498.91 Mb). The average inbreeding coefficient rate was equal to 0.084 ± 0.037 in Kazakh white-headed cattle and 0.039 ± 0.018 in Auliekol cattle. The high frequency of genomic regions showed that the strongest patterns were observed on chromosomes 2, 6, and 26 for KWh and 1, 5, and 14 for AK. The estimation of ROH numbers per animal showed that the number of ROH decreased with increasing ROH length in both populations. The genomic inbreeding coefficient of both cattle breeds was calculated based on the ROH, and ancient inbreeding was observed. The harbored genes within ROH islands were associated with meat growth and milk production.https://www.mdpi.com/1424-2818/14/4/279Auliekol cattleKazakh white-headed cattleruns of homozygosityGeneSeek GGP Bovine 150 KSNPDNA |
| spellingShingle | Indira Beishova Kairat Dossybayev Alzhan Shamshidin Alena Belaya Anuarbek Bissembayev Kadyrzhan Khamzin Alexandr Kovalchuk Askar Nametov Distribution of Homozygosity Regions in the Genome of Kazakh Cattle Breeds Diversity Auliekol cattle Kazakh white-headed cattle runs of homozygosity GeneSeek GGP Bovine 150 K SNP DNA |
| title | Distribution of Homozygosity Regions in the Genome of Kazakh Cattle Breeds |
| title_full | Distribution of Homozygosity Regions in the Genome of Kazakh Cattle Breeds |
| title_fullStr | Distribution of Homozygosity Regions in the Genome of Kazakh Cattle Breeds |
| title_full_unstemmed | Distribution of Homozygosity Regions in the Genome of Kazakh Cattle Breeds |
| title_short | Distribution of Homozygosity Regions in the Genome of Kazakh Cattle Breeds |
| title_sort | distribution of homozygosity regions in the genome of kazakh cattle breeds |
| topic | Auliekol cattle Kazakh white-headed cattle runs of homozygosity GeneSeek GGP Bovine 150 K SNP DNA |
| url | https://www.mdpi.com/1424-2818/14/4/279 |
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