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Volume 16
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Article

Examination of Runs of Homozygosity Distribution Patterns and Relevant Candidate Genes of Potential Economic Interest in Russian Goat Breeds Using Whole-Genome Sequencing

by
Tatiana E. Deniskova
1,
Arsen V. Dotsev
1,
Olga A. Koshkina
1,
Anastasia D. Solovieva
1,
Nadezhda A. Churbakova
1,
Sergey N. Petrov
1,
Alexey N. Frolov
2,
Stanislav A. Platonov
2,
Alexandra S. Abdelmanova
1,
Maxim A. Vladimirov
1,
Elena A. Gladyr
1,
Igor V. Gusev
1,
Svyatoslav V. Lebedev
2,
Darren K. Griffin
3,4,5,*,
Michael N. Romanov
1,3,4,* and
Natalia A. Zinovieva
1
1
L.K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk Municipal District, Podolsk 142132, Moscow Oblast, Russia
2
Federal Research Center for Biological Systems and Agrotechnologies of the Russian Academy of Sciences, 460000 Orenburg, Russia
3
School of Natural Sciences, University of Kent, Canterbury, Kent CT2 7NJ, UK
4
Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Chatuchak, Bangkok 10900, Thailand
5
Royal Veterinary College, University of London, London NW1 0TU, UK
*
Authors to whom correspondence should be addressed.
Genes 2025, 16(6), 631; https://doi.org/10.3390/genes16060631 (registering DOI)
Submission received: 26 April 2025 / Revised: 13 May 2025 / Accepted: 23 May 2025 / Published: 24 May 2025
(This article belongs to the Section Animal Genetics and Genomics)
Versions Notes

Abstract

Background/Objectives: Whole-genome sequencing (WGS) data provide valuable information about the genetic architecture of local livestock but have not yet been applied to Russian native goats, in particular, the Orenburg and Karachay breeds. A preliminary search for selection signatures based on single nucleotide polymorphism (SNP) genotype data in these breeds was not informative. Therefore, in this study, we aimed to address runs of homozygosity (ROHs) patterns and find the respective signatures of selection overlapping candidate genes in Orenburg and Karachay goats using the WGS approach. Methods: Paired-end libraries (150 bp reads) were constructed for each animal. Next-generation sequencing was performed using a NovaSeq 6000 sequencer (Illumina, Inc., San Diego, CA, USA), with ~20X genome coverage. ROHs were identified in sliding windows, and ROH segments shared by at least 50% of the samples were considered as ROH islands. Results: ROH islands were identified on chromosomes CHI3, CHI5, CHI7, CHI12, CHI13, and CHI15 in Karachay goats; and CHI3, CHI11, CHI12, CHI15, and CHI16 in Orenburg goats. Shared ROH islands were found on CHI12 (containing the PARP4 and MPHOSPH8 candidate genes) and on CHI15 (harboring STIM1 and RRM1). The Karachay breed had greater ROH length and higher ROH number compared to the Orenburg breed (134.13 Mb and 695 vs. 78.43 Mb and 438, respectively). The genomic inbreeding coefficient (FROH) varied from 0.032 in the Orenburg breed to 0.054 in the Karachay breed. Candidate genes associated with reproduction, milk production, immunity-related traits, embryogenesis, growth, and development were identified in ROH islands in the studied breeds. Conclusions: Here, we present the first attempt of elucidating the ROH landscape and signatures of selection in Russian local goat breeds using WGS analysis. Our findings will pave the way for further insights into the genetic mechanisms underlying adaption and economically important traits in native goats.
Keywords: goat (Capra hircus); Russian local breeds; whole-genome sequencing (WGS); runs of homozygosity (ROHs); signatures of selection; candidate genes goat (Capra hircus); Russian local breeds; whole-genome sequencing (WGS); runs of homozygosity (ROHs); signatures of selection; candidate genes

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MDPI and ACS Style

Deniskova, T.E.; Dotsev, A.V.; Koshkina, O.A.; Solovieva, A.D.; Churbakova, N.A.; Petrov, S.N.; Frolov, A.N.; Platonov, S.A.; Abdelmanova, A.S.; Vladimirov, M.A.; et al. Examination of Runs of Homozygosity Distribution Patterns and Relevant Candidate Genes of Potential Economic Interest in Russian Goat Breeds Using Whole-Genome Sequencing. Genes 2025, 16, 631. https://doi.org/10.3390/genes16060631

AMA Style

Deniskova TE, Dotsev AV, Koshkina OA, Solovieva AD, Churbakova NA, Petrov SN, Frolov AN, Platonov SA, Abdelmanova AS, Vladimirov MA, et al. Examination of Runs of Homozygosity Distribution Patterns and Relevant Candidate Genes of Potential Economic Interest in Russian Goat Breeds Using Whole-Genome Sequencing. Genes. 2025; 16(6):631. https://doi.org/10.3390/genes16060631

Chicago/Turabian Style

Deniskova, Tatiana E., Arsen V. Dotsev, Olga A. Koshkina, Anastasia D. Solovieva, Nadezhda A. Churbakova, Sergey N. Petrov, Alexey N. Frolov, Stanislav A. Platonov, Alexandra S. Abdelmanova, Maxim A. Vladimirov, and et al. 2025. "Examination of Runs of Homozygosity Distribution Patterns and Relevant Candidate Genes of Potential Economic Interest in Russian Goat Breeds Using Whole-Genome Sequencing" Genes 16, no. 6: 631. https://doi.org/10.3390/genes16060631

APA Style

Deniskova, T. E., Dotsev, A. V., Koshkina, O. A., Solovieva, A. D., Churbakova, N. A., Petrov, S. N., Frolov, A. N., Platonov, S. A., Abdelmanova, A. S., Vladimirov, M. A., Gladyr, E. A., Gusev, I. V., Lebedev, S. V., Griffin, D. K., Romanov, M. N., & Zinovieva, N. A. (2025). Examination of Runs of Homozygosity Distribution Patterns and Relevant Candidate Genes of Potential Economic Interest in Russian Goat Breeds Using Whole-Genome Sequencing. Genes, 16(6), 631. https://doi.org/10.3390/genes16060631

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