vavilovВавиловский журнал генетики и селекцииVavilov Journal of Genetics and Breeding2500-3259Institute of Cytology and Genetics of Siberian Branch of the RAS10.18699/VJ18.418vavilov-1661Research ArticleГЕНЕТИКА ЖИВОТНЫХANIMAL GENETICSОценка современного состояния генофонда холмогорской и чернопестрой пород крупного рогатого скота на основе полногеномного SNP-анализаEvaluation of current gene pool of Kholmogor and Black-and-white cattle breeds based on whole genome SNP analysishttps://orcid.org/0000-0003-3418-2511ДоцевА. В.DotsevA. V.

Московская область, Подольск.

Moscow Region, Podolsk.

asnd@mail.ruhttps://orcid.org/0000-0002-1799-6014СермягинА. А.SermyaginA. A.

Московская область, Подольск.

Moscow Region, Podolsk.

https://orcid.org/0000-0003-4959-878XШахинА. В.ShakhinA. V.

Московская область, Подольск.

Moscow Region, Podolsk.

ПаронянИ. А. ParonyanI. A.

Санкт-Петербург, Пушкин.

St. Petersburg, Pushkin.

https://orcid.org/0000-0002-5952-0436ПлемяшовК. В.PlemyashovK. V.

Санкт-Петербург, Пушкин.

St. Petersburg, Pushkin.

https://orcid.org/0000-0001-6470-0434РейерХ.ReyerH.

Думмерсторф.

Dummerstorf.

https://orcid.org/0000-0002-9523-6790ВиммерсК.WimmersK.

Думмерсторф.

Dummerstorf.

https://orcid.org/0000-0002-7522-0708БремГ.BremG.

Подольск ; Вена.

Moscow Region, Podolsk; Vienna.

https://orcid.org/0000-0003-4017-6863ЗиновьеваН. А.ZinovievaN. A.

Подольск .

Moscow Region, Podolsk.

n_zinovieva@mail.ruФедеральный научный центр животноводства – ВИЖ им. академика Л.К. Эрнста.РоссияL.K. Ernst Federal Science Center for Animal Husbandry.Russian FederationВсероссийский научно-исследовательский институт генетики и разведения сельскохозяйственных животных – филиал Федерального научного центра животноводства – ВИЖ им. академика Л.К. Эрнста.РоссияRussian Research Institute of Farm Animal Genetics and Breeding – Subsidiary of L.K. Ernst Federal Science Center for Animal Husbandry.Russian FederationИнститут геномной биологии Института биологии домашних животных Лейбница.ГерманияInstitute of Genome Biology, Leibniz Institute for Farm Animal Biology.GermanyФедеральный научный центр животноводства – ВИЖ им. академика Л.К. Эрнста, Московская область; Институт животноводства и генетики ветеринарно-медицинского университета.РоссияL.K. Ernst Federal Science Center for Animal Husbandry; Institute of Animal Breeding and Genetics, University of Veterinary Medicine.Russian FederationФедеральный научный центр животноводства – ВИЖ им. академика Л.К. Эрнста, Московская область.РоссияL.K. Ernst Federal Science Center for Animal Husbandry.Russian Federation201826092018226742747Copyright © Доцев А.В., Сермягин А.А., Шахин А.В., Паронян И.А., Племяшов К.В., Рейер Х., Виммерс К., Брем Г., Зиновьева Н.А., 20182018Доцев А.В., Сермягин А.А., Шахин А.В., Паронян И.А., Племяшов К.В., Рейер Х., Виммерс К., Брем Г., Зиновьева Н.А.Dotsev A.V., Sermyagin A.A., Shakhin A.V.,  Paronyan I.A., Plemyashov K.V., Reyer H., Wimmers K., Brem G., Zinovieva N.A.This work is licensed under a Creative Commons Attribution 4.0 License.https://vavilov.elpub.ru/jour/article/view/1661

Сохранение генофонда отечественных пород крупного рогатого скота является важной задачей для обеспечения продовольственной безопасности населения. В последние годы в Российской Федерации местные популяции скота либо замещаются высокопродуктивными импортными породами, либо происходит их метизация, в результате которой от исходной породы остается лишь незначительная часть генов. Целью нашей рабо ты было выявление генетических различий между популяциями холмогорского и черно-пестрого скота с разной степенью кровности по голштинской породе. Нами выполнен анализ полногеномных SNP-профилей (SNP – однонуклеотидный полиморфизм) животных вышеуказанных пород. Холмогорская была подразделена на три группы: чистопородные (KHLM, n = 3), голштинизированные (KHLM-HLST, n = 4) и представители старого типа (KHLM-INTA, n = 15); черно-пестрая – на четыре группы: чистопородные (BLWT, n = 9), с долей кров ности голштинского скота от 6 до 25 % (BLWT-75, n = 8), от 80 до 99 % (BLWT-HLST, n = 10) и представленные архивными об разцами 1970–1980-х гг. (BLWT-OLD, n = 15). В качестве группы сравнения были использованы животные голштинской породы (HLST, n = 27). Обработку данных и расчеты проводили в программах PLINK 1.07, Admixture 1.3, SplitsTree 4.14.6 и R пакет StAMMP. После проведения контроля качества для анализа были отобраны 29 688 SNP. Многомерное шкалирование (MDS), кластерный анализ и дендрограмма, построенная по методу «сеть соседей» (Neighbor-Net), выявили наличие трех кластеров, относящихся к холмогорской, черно-пестрой и голштинской породам. В первый попали KHLM и KHLM-INTA, во второй – BLWT и BLWT-OLD, в третий – HLST, KHLM-HLST и BLWT-HLST. Образцы, относящиеся к группе BLWT-75, заняли промежуточное положение между HLST и BLWT. Таким образом, наши результаты показали, что в настоящее время сохранились популяции с уникальными генотипами отечественных пород, которые необходимо сохранять. Популяции животных, голштинизированные на 80 % и более, нельзя рассматривать в качестве холмогорской и черно-пестрой пород, правильнее их относить к голштинской породе отечественной селекции. 

Conservation of local cattle genetic resources is an important strategy for achieving Russia’s food security. During last decades, in the Russian Federation, local livestock populations were either crossbred or replaced by highly productive imported breeds, which led to a loss of the major part of original breeds identities. The objective of our study was to identify genetic differences between the populations of Kholmogor and Black-and-white cattle with varying degrees of admixture with the Holstein breed. The aforementioned breeds were studied using their whole-genome single nucleotide polymorphism (SNP) genotypes. The Kholmogor breed was subdivided into three groups: purebred (KHLM, n = 3), admixed with Holsteins (KHLM-HLST, n = 4) and representatives of old-type breed (KHLM-INTA, n = 15). Blackand-white was subdivided into four groups: purebred (BLWT, n = 9), with a low (BLWT-75, n = 8) and a high (BLWT-HLST, n = 10) level of admixture with Holstein, and represented by archival samples from the 1970s and 1980s (BLWT-OLD, n = 15). The Holsteins genetic profiles (HLST, n = 27) were taken as a comparison group. PLINK 1.07, Admixture 1.3, SplitsTree 4.14.6 and R package StAMPP were used to infer genetic relationship between the studied groups. After quality control, 29 688 SNPs were selected for analysis. Multidimensional scaling (MDS), Admixture analysis and a dendrogram constructed using the Neighbor-Net method, revealed the presence of three clusters belonging to the Kholmogor, Black-and-white and Holstein breeds. The first one included KHLM and KHLM-INTA, the second – BLWT and BLWT-OLD, and the third – HLST, KHLM-HLST and BLWT-HLST. The BLWT-75 samples were placed between HLST and BLWT. Thus, our results showed that currently the populations of native cattle breeds with valuable genotypes still exist. The populations with a high level of admixture with Holsteins could be considered neither as the Kholmogor nor as Blackand-white breeds, and would rather be referred as the Holstein breed of local breeding.

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