TY - JOUR

T1 - Copy number variants in genomes of local sheep breeds from Russia

AU - Igoshin, A. V.

AU - Deniskova, T. E.

AU - Yurchenko, A. A.

AU - Yudin, N. S.

AU - Dotsev, A. V.

AU - Selionova, M. I.

AU - Zinovieva, N. A.

AU - Larkin, D. M.

N1 - Funding Information: The authors declare no conflict of interests. The work on CNV and CNVR detection in Russian sheep breeds was funded by the Russian Scientific Foundation (RSF) grant No. 19‐76‐20026. The genotyping of the Osetin breed has been carried out within the project No. 21‐66‐00007 supported by the Russian Scientific Foundation (RSF). Publisher Copyright: © 2021 Stichting International Foundation for Animal Genetics.

PY - 2022/2

Y1 - 2022/2

N2 - Copy number variants (CNVs) are genomic structural variations that contribute to many adaptive and economically important traits in livestock. In this study, we detected CNVs in 354 animals from 16 Russian indigenous sheep breeds and analysed their possible functional roles. Our analysis of the entire sample set resulted in 4527 CNVs forming 1450 CNV regions (CNVRs). When constructing CNVRs for individual breeds, a total of 2715 regions ranging from 88 in Groznensk to 337 in Osetin breeds were identified. To make interbreed CNVR frequency comparison possible, we also identified core CNVRs using CNVs with overlapping chromosomal locations found in different breeds. This resulted in 137 interbreed CNVRs with frequency >15% in at least one breed. Functional enrichment analysis of genes affected by CNVRs in individual breeds revealed 12 breeds with significant enrichments in olfactory perception, PRAME family proteins, and immune response. Function of genes affected by interbreed and breed-specific CNVRs revealed candidates related to domestication, adaptation to high altitudes and cold climates, reproduction, parasite resistance, milk and meat qualities, wool traits, fat storage, and fat metabolism. Our work is the first attempt to uncover and characterise the CNV makeup of Russian indigenous sheep breeds. Further experimental and functional validation of CNVRs would help in developing new and improving existing sheep breeds.

AB - Copy number variants (CNVs) are genomic structural variations that contribute to many adaptive and economically important traits in livestock. In this study, we detected CNVs in 354 animals from 16 Russian indigenous sheep breeds and analysed their possible functional roles. Our analysis of the entire sample set resulted in 4527 CNVs forming 1450 CNV regions (CNVRs). When constructing CNVRs for individual breeds, a total of 2715 regions ranging from 88 in Groznensk to 337 in Osetin breeds were identified. To make interbreed CNVR frequency comparison possible, we also identified core CNVRs using CNVs with overlapping chromosomal locations found in different breeds. This resulted in 137 interbreed CNVRs with frequency >15% in at least one breed. Functional enrichment analysis of genes affected by CNVRs in individual breeds revealed 12 breeds with significant enrichments in olfactory perception, PRAME family proteins, and immune response. Function of genes affected by interbreed and breed-specific CNVRs revealed candidates related to domestication, adaptation to high altitudes and cold climates, reproduction, parasite resistance, milk and meat qualities, wool traits, fat storage, and fat metabolism. Our work is the first attempt to uncover and characterise the CNV makeup of Russian indigenous sheep breeds. Further experimental and functional validation of CNVRs would help in developing new and improving existing sheep breeds.

KW - adaptation

KW - copy number variant regions

KW - copy number variants

KW - economically important trait

KW - local sheep breeds

KW - PennCNV

KW - Russian Federation

KW - DNA Copy Number Variations

KW - Russia

KW - Animals

KW - Sheep, Domestic/genetics

KW - Genome

KW - Wool

UR - http://www.scopus.com/inward/record.url?scp=85121111616&partnerID=8YFLogxK

U2 - 10.1111/age.13163

DO - 10.1111/age.13163

M3 - Article

C2 - 34904242

AN - SCOPUS:85121111616

VL - 53

SP - 119

EP - 132

JO - Animal Genetics

JF - Animal Genetics

SN - 0268-9146

IS - 1

ER -