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Abdelmanova A.S., Deniskova T.E., Shakhin A.V., Nikolaev A.A., Abramov G.O., Boronetskaya O.I., Bagirov V.A., Truchachev V.I., Zinovieva N.A. Search for selection signatures in genomes of northern and steppe modern cattle in Russia as compared to samples of XIX-XX centuries. Sel'skokhozyaistvennaya Biologiya [Agricultural Biology], 2025, Vol. 60, № 6, p. 986-1004.
(how to cite this article)

doi: 10.15389/agrobiology.2025.6.986eng

UDC: 636.2:636.082.2:577.2

Acknowledgements:
Supported financially from the Russian Science Foundation, project No. 19-76-20012.

 

SEARCH FOR SELECTION SIGNATURES IN GENOMES OF NORTHERN AND STEPPE MODERN CATTLE IN RUSSIA AS COMPARED TO SAMPLES OF XIX-XX CENTURIES

A.S. Abdelmanova ✉, T.E. Deniskova, A.V. Shakhin, A.A. Nikolaev,
G.O. Abramov, O.I. Boronetskaya, V.A. Bagirov, V.I. Truchachev,
N.A. Zinovieva

Ernst Federal Research Center for Animal Husbandry, 60, pos. Dubrovitsy, Podolsk District, Moscow Province, 142132 Russia, e-mail abdelmanova@vij.ru (✉ corresponding author) horarka@yandex.ru, alexshakhin@vij.ru,
alexandralces@yandex.ru, g0work@mail.ru, liskun@rgau-msha.ru, vugarbagirov@mail.ru, rector@rgau-msha.ru,
n_zinovieva@mail.ru

ORCID:
Abdelmanova A.S. orcid.org/0000-0003-4752-0727
Boronetskaya O.I. orcid.org/0000-0001-8389-5572
Deniskova T.E. orcid.org/0000-0002-5809-1262
Bagirov V.A. orcid.org/0000-0001-5398-8815
Shakhin A.V. orcid.org/0000-0003-4959-878X
Truchachev V.I. orcid.org/0000-0003-4676-5407
Nikolaev A.A. orcid.org/0000-0001-9355-3285
Zinovieva N.A. orcid.org/0000-0003-4017-6863
Abramov G.O. orcid.org/0009-0000-7239-3227

Final revision received May 29, 2025
Accepted July 22, 2025

The development of whole genome sequencing (WGS) technology opens new opportunities in studying the genomic variability of farm animals under the influence of natural and artificial selection. Analysis of WGS data allows us to identify key genes and genomic regions responsible for the formation of adaptive properties to specific natural and climatic breeding conditions. Selection and genetic drift are key sources of genetic differentiation between representatives of original and modern breeds. Studying the dynamics of changes in the gene pool of local breeds is relevant, since local breeds are carriers of rare and valuable genetic variants that may become a priority in the event of changing market demands and climate change. This paper describes for the first time the results of identifying genomic regions fixed as a result of selection in contrasting groups of cattle adapted to significantly different environmental conditions, and provides a structural and functional annotation of the genes localized in them. Genes common to modern and ancestral cattle populations of the studied groups were identified. The aim of the study was to compare the genomes of historical and modern cattle of different breeds based on WGS data to identifygenomic regions affected by natural and artificial selection. The study material included museum cattle skull specimens from the E.F. Liskun Livestock Museum (Timiryazev Russian State Agrarian University - Moscow Agricultural Academy, Moscow), dating from the late 19th to early 20th centuries, as well as samples from breeding animals stored in the biological collection of the National Center for Farm Animal Genetic Resources of the L.K. Ernst Federal Research Center for Animal Husbandry. The northern cattle group was represented by samples of the Kholmogor and Yaroslavl breeds, and the steppe cattle group was represented by samples of Kalmyk cattle. The sample of historical specimens (n = 20)included 15 samples of northern cattle (Kholmogor cattle, n = 8; Yaroslavl cattle, n = 7) and 5 samples of steppe (Kalmyk) cattle. The sample of modern specimens included 17, 11 and12 samples of the above-mentioned breeds, respectively. The final data set included the genotypes for 1,615,259 SNPs. DNA extraction from museum specimens was performed using the previously described method, and from modern specimens, using the DNA-Extran 2 kit (Sintol JSC, Moscow). Libraries for whole-genome sequencing using NGS technology were prepared using the TruSeq DNA Nano Library Prep kit (Illumina, Inc., USA) and the Accel-NGS® 2S Plus DNA Library Kit (IDT). Sequencing was performed on a NovaSeq 6000 sequencer (2.5150 bp). Three methods were used to identify genomic regions under selection pressure: pairwise comparison of populations based on FST genetic distances usinga sliding window, analysis of cross-population extended haplotype homozygosity (XP-EHH), and identification of regions of excess homozygosity (ROH islands). The absence of overlapping genomic regions under selection pressure in the genome of the historical and modern populations of studied cattle breeds based on the results of a comparative analysis of FST and XP-EHH for pairs (Kholmogor + Yaroslavl) – Kalmyk indicates significant differences in the breeding goals in different periods of breed formation. Seven ROH islands have been identified, overlapping in museum and modern samples of Kholmogor and Yaroslavl cattle, localized in the known QTL for milk yield, milk composition, growth, body size andfertility, which indicates the long-term use of the above-mentioned indices as target parameters at breeding these breeds. The genes common to modern and historical cattlepopulations of the studied groups have been identified. The identified genomic regions, which are under selection pressure in the historical populations of the studied breeds andoverlap with the signature of selection in the genome of modern representatives of the same breeds, can be used in the selection of animals for inclusion in genetic resourceconservation programs in order to preserve authentic genomic components.

Keywords: cattle, Kholmogor breed, Yaroslavl breed, Kalmyk breed, museum specimens, whole genome sequencing, selection pressure, candidate genes.

 

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