Genome-wide detection and analysis of copy number variations in Sal sheep using a high-density SNP array
https://doi.org/10.31043/2410-2733-2024-2-26-32
Abstract
Purpose: to identify CNV regions (CNVRs) and identify potentially specific CNVs in Sal sheep.
Materials and methods. The research was carried out on 48 Salsk breed sheep. Genotyping was performed using high-density microarrays Ovine SNP 600 K BeadChip array (Illumina, USA). DNA copy number variation (CNV) searches were performed using PennCNV software based on the Oar_v3.1 reference genome.
Results. We identified 4585 autosomal CNVs in 48 Sal breed sheep. The average CNV length was 92,3 Kb. 21,1 % of the total number of CNVs are less than 50 Kb in size. On average, from 65 to 138 CNVs were identified per animal. 527 autosomal CNVRs were obtained, representing 54,77 Mb of the entire sheep genome. The proportion of chromosomes covered by CNVR varies by chromosome, from 0,5 % on OAR25 to 9 % on OAR24. Analysis of CNVR in the ENCEMBL system revealed 42 genes in which CNVRs are localized; the remaining CNVRs are located in intergenic regions. Comparison of the identified CNVRs with sheep QTLs from the Animal QTL database showed that 39,24 % of the genes were responsible for reproductive traits, and 20,25 % were responsible for wool-related traits.
Conclusions. Functional annotation of CNVRs localized in genes and intergenic spaces was carried out and the total number of detected CNVRs in the QTL database was analyzed. The results showed that CNVs are localized in genes associated with selection-significant traits in sheep.
About the Author
N. F. Bakoev
L. K. Ernst Federal Research Center for Animal Husbandry
Russian Federation
Russian Federation
PhD (Agr. Sci.
Dubrovitsy, 60, Podolsk Municipal District, Moscow Region, 142132, Russia
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Review
For citations:
Bakoev N.F. Genome-wide detection and analysis of copy number variations in Sal sheep using a high-density SNP array. Genetics and breeding of animals. 2024;(2):26-32. (In Russ.) https://doi.org/10.31043/2410-2733-2024-2-26-32
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