Identification of QTL localized in the runs of homozygosity in sheep breeds raised in Russia
https://doi.org/10.32634/0869-8155-2025-399-10-102-109
Abstract
Relevance. Quantitative trait loci (QTL) are genomic regions that influence economically significant traits of sheep. Addressing the QTL distribution in the genomes of sheep breeds raised in Russia, overlapping with selection signatures, is relevant for deepening the understanding of the genetic mechanisms underlying their phenotypic variability.
Methods. The materials for the study were genome-wide SNP profiles of ten sheep breeds that included 42,230 SNPs and were generated using the OvineSNP50 BeadChip and Ovine Infinium HD BeadChip Arrays (Illumina, USA). Genotyping quality control and filtering were performed using PLINK v1.90. Overlapping homozygous segments (ROH) with a minimum length of 0.3 MB, common to more than 50% of the samples within the breed, were selected as indicators of islands of homozygosity (ROH) in the sheep genome. Matching analysis of the genomic coordinates of the runs of homozygosity islands with QTL was performed using the Sheep QTLdb database.
Results. We found that 58 unique QTL were localized within the runs of homozygosity islands in ten sheep breeds. The most frequent traits body weight (10.34%), fat weight in carcass (8.62%), hot carcass weight (6.9%), and milk yield (6.9%). QTL #127011 associated with fat deposition in tail was identified in the ROH islands in Buubei and Karachay breeds. A large group of QTLS located in ROH islands were identified in experiments on QTL mapping associated with milk and meat productivity in resource populations.
Keywords
genotyping,
the runs of homozygosity islands,
DNA chips,
local sheep breeds,
QTL,
economically significant traits
Supporting agencies: The study was funded by the Ministry of Science and Higher Education of the Russian Federation (FGGN-2024-0015).
About the Author
T. E. Deniskova
L.K. Ernst Federal Research Center for Animal Husbandry
Russian Federation
Russian Federation
Tatiana Evgenievna Deniskova - Candidate of Biological Sciences, Leading Researcher,
60 Dubrovitsy, Podolsk Municipal District, Moscow Region, 142132
References
1. Jahuey-Martínez F.J., Martínez-Quintana J.A., Rodríguez-Almeida F.A., Parra-Bracamonte G.M. Exploration and Enrichment Analysis of the QTLome for Important Traits in Livestock Species. Genes. 2024; 15(12): 1513. https://doi.org/10.3390/genes15121513
2. Hu Z.-L., Park C.A., Reecy J.M. Bringing the Animal QTLdb and CorrDB into the future: meeting new challenges and providing updated services. Nucleic Acids Research. 2022; 50(D1): D956–D961. https://doi.org/10.1093/nar/gkab1116
3. Gou Y. et al. AnimalGWASAtlas: Annotation and prioritization of GWAS loci and quantitative trait loci for animal complex traits. Journal of Biological Chemistry. 2025; 301(3): 108267. https://doi.org/10.1016/j.jbc.2025.108267
4. Macé T. et al. Genome-wide analyses reveal a strong association between LEPR gene variants and body fat reserves in ewes. BMC Genomics. 2022; 23: 412. https://doi.org/10.1186/s12864-022-08636-z
5. Zhang W., Lu Z., Guo T., Yuan C., Liu J. Construction of a highdensity genetic map and QTL localization of body weight and wool production related traits in Alpine Merino sheep based on WGR. BMC Genomics. 2024; 25: 641. https://doi.org/10.1186/s12864-024-10535-4
6. Yuan C. et al. A global analysis of CNVs in Chinese indigenous finewool sheep populations using whole-genome resequencing. BMC Genomics. 2021; 22: 78. https://doi.org/10.1186/s12864-021-07387-7
7. Koncagül S., Kiraz S., Koyun H. Detection of putative loci affecting milk yield in Turkish Awassi sheep using microsatellite markers. Tropical Animal Health and Production. 2024; 56(8): 322. https://doi.org/10.1007/s11250-024-04165-x
8. Matika O. et al. Characterization of OAR1 and OAR18 QTL associated with muscle depth in British commercial terminal sire sheep. Animal Genetics. 2011; 42(2): 172–180. https://doi.org/10.1111/j.1365-2052.2010.02121.x
9. Al-Mamun H.A., Kwan P., Clark S.A., Ferdosi M.H., Tellam R., Gondro C. Genome-wide association study of body weight in Australian Merino sheep reveals an orthologous region on OAR6 to human and bovine genomic regions affecting height and weight. Genetics Selection Evolution. 2015; 47: 66. https://doi.org/10.1186/s12711-015-0142-4
10. Matika O. et al. Genome-wide association reveals QTL for growth, bone and in vivo carcass traits as assessed by computed tomography in Scottish Blackface lambs. Genetics Selection Evolution. 2016; 48: 11. https://doi.org/10.1186/s12711-016-0191-3
11. Karamichou E., Richardson R.I., Nute G.R., Gibson K.P., Bishop S.C. Genetic analyses and quantitative trait loci detection, using a partial genome scan, for intramuscular fatty acid composition in Scottish Blackface sheep. Journal of Animal Science. 2006; 84(12): 3228–3238. https://doi.org/10.2527/jas.2006-204
12. Beraldi D., McRae A.F., Gratten J., Slate J., Visscher P.M., Pemberton J.M. Mapping quantitative trait loci underlying fitnessrelated traits in a free-living sheep population. Evolution. 2007; 61(6): 1403–1416. https://doi.org/10.1111/j.1558-5646.2007.00106.x
13. Johnson P.L., McEwan J.C., Dodds K.G., Purchas R.W., Blair H.T. Meat quality traits were unaffected by a quantitative trait locus affecting leg composition traits in Texel sheep. Journal of Animal Science. 2005; 83(12): 2729–2735. https://doi.org/10.2527/2005.83122729x
14. Ponz R. et al. Assessment of genetic variation explained by markers for wool traits in sheep via a segment mapping approach. Mammalian Genome. 2001; 12(7): 569–572. https://doi.org/10.1007/s003350030007
15. Yuan Z. et al. Selection signature analysis reveals genes associated with tail type in Chinese indigenous sheep. Animal Genetics. 2017; 48(1): 55–66. https://doi.org/10.1111/age.12477
16. Di Gerlando R. et al. Genome-wide association study between CNVs and milk production traits in Valle del Belice sheep. PloS ONE. 2019; 14(4): e0215204. https://doi.org/10.1371/journal.pone.0215204
17. Gutiérrez-Gil B. et al. Quantitative trait loci underlying milk production traits in sheep. Animal Genetics. 2009; 40(4): 423–434. https://doi.org/10.1111/j.1365-2052.2009.01856.x
18. Garcia-Gámez E., Gutiérrez-Gil B., Suarez-Vega A., de la Fuente L.F., Arranz J.J. Identification of quantitative trait loci underlying milk traits in Spanish dairy sheep using linkage plus combined linkage disequilibrium and linkage analysis approaches. Journal of Dairy Science. 2013; 96(9): 6059–6069. https://doi.org/10.3168/jds.2013-6824
19. Mateescu R.G., Thonney M.L. Genetic mapping of quantitative trait loci for milk production in sheep. Animal Genetics. 2010; 41(5): 460–466. https://doi.org/10.1111/j.1365-2052.2010.02045.x
20. Raadsma H.W. et al. Mapping quantitative trait loci (QTL) in sheep. I. A new male framework linkage map and QTL for growth rate and body weight. Genetics Selection Evolution. 2009; 41: 34. https://doi.org/10.1186/1297-9686-41-34
21. Cavanagh C.R., Jonas E., Hobbs M., Thomson P.C., Tammen I., Raadsma H.W. Mapping Quantitative Trait Loci (QTL) in sheep. III. QTL for carcass composition traits derived from CT scans and aligned with a meta-assembly for sheep and cattle carcass QTL. Genetics Selection Evolution. 2010; 42: 36. https://doi.org/10.1186/1297-9686-42-36
22. Raadsma H.W., Jonas E., McGill D., Hobbs M., Lam M.K, Thomson P.C. Mapping quantitative trait loci (QTL) in sheep. II. Meta-assembly and identification of novel QTL for milk production traits in sheep. Genetics Selection Evolution. 2009; 41: 45. https://doi.org/10.1186/1297-9686-41-45
23. Meuwissen T., van den Berg I., Goddard M. On the use of wholegenome sequence data for across-breed genomic prediction and finescale mapping of QTL. Genetics Selection Evolution. 2021; 53: 19. https://doi.org/10.1186/s12711-021-00607-4
24. Deniskova T.E., Koshkina O.A., Petrov S.N., Sermyagin A.A., Zinovieva N.A. Identification of candidate genes associated with growth and development of sheep from a crossbred population using genome-wide association studies. Agricultural Science Euro-NorthEast. 2024; 25(2): 236–250 (in Russian). https://doi.org/10.30766/2072-9081.2024.25.2.236-250
25. Koshkina O.A., Deniskova T.E., Zinovieva N.A. Development and validation of a test system for determining the polymorphism in the DGKH and PPP1R1C genes associated with body weight of sheep. Agrarian science. 2023; (12): 80–84 (in Russian). https://doi.org/10.32634/0869-8155-2023-377-12-80-84
Review
For citations:
Deniskova T.E. Identification of QTL localized in the runs of homozygosity in sheep breeds raised in Russia. Agrarian science. 2025;(10):102-109. (In Russ.) https://doi.org/10.32634/0869-8155-2025-399-10-102-109
Views:
10
Email this article 