References

vavilov

Вавиловский журнал генетики и селекции

Vavilov Journal of Genetics and Breeding

2500-3259

Institute of Cytology and Genetics of Siberian Branch of the RAS

10.18699/VJGB-23-57

vavilov-3858

Research Article

ГЕНЕТИКА ЖИВОТНЫХ

ANIMAL GENETICS

Идентификация гомозиготно обогащенных участков в геноме голштинов

Identification of homozygosity-rich regions in the Holstein genome

https://orcid.org/0000-0002-5087-6444

Смарагдов

М. Г.

Smaragdov

M. G.

Санкт-Петербург, Пушкин

St. Petersburg, Pushkin

mik7252@yandex.ru

Всероссийский научно-исследовательский институт генетики и разведения сельскохозяйственных животных – филиал Федерального исследовательского центра животноводства – ВИЖ им. академика Л.К. Эрнста (ВНИИГРЖ)РоссияRussian Research Institute of Farm Animal Genetics and Breeding – Branch of the L.K. Ernst Federal Science Center for Animal HusbandryRussian Federation

2023

08092023

275471479

2023

Смарагдов М.Г.

Smaragdov M.G.

This work is licensed under a Creative Commons Attribution 4.0 License.

https://vavilov.elpub.ru/jour/article/view/3858

В настоящем исследовании 371 корова голштинской породы из шести стад и 26 быков голштинской породы, которые использовались в этих стадах, были генотипированы с помощью чипа llumina BovineSNP50. Для идентификации гомозиготных последовательностей (ROH) выполнялись последовательные и скользящие сканирования с помощью программ detectRUNS и Plink. Пропущенные SNP генотипы не оказали существенного влияния на данные ROH. Среднее количество RОН, выявленное у коров при последовательных сканированиях, составило 95.4 ± 2.7, при скользящих сканированиях – 86.0 ± 2.6, тогда как у быков голштинской породы оно было меньше – 58.9 ± 1.9. Длина сегментов ROH варьировала от 1 до 16 Мб и более, при этом основное количество ROH имело длину 1–2 Мб. Из 29 хромосом наиболее насыщены ROH оказались ВТА 14, ВТА 16 и ВТА 7. Средний коэффициент инбридинга по стадам составил 0.111 ± 0.003 и 0.104 ± 0.004 на основе последовательных и скользящих сканирований соответственно, а для быков на основе последовательных сканирований – 0.078 ± 0.005. Эти значения не превышали показатели для голштинского скота в Северной Америке. Результаты исследования подтвердили более точную идентификацию ROH последовательными сканированиями, а также то, что количество разрешенных гетерозиготных SNP в ROH может оказывать существенное влияние на данные ROH.

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.

ROHSNPинбридингкрупный рогатый скот

ROHSNPinbreedingcattle

This work was supported by the Ministry of Science and Higher Education of the Russian Federation (State Assignment Program No. 121052600352-3).

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The authors declare that there are no conflicts of interest present.