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. 2023 Nov 8;14(11):2054.
doi: 10.3390/genes14112054.

Finding Predictors of Leg Defects in Pigs Using CNV-GWAS

Lyubov Getmantseva  1   2 , Maria Kolosova  1 , Kseniia Fede  2 , Anna Korobeinikova  2 , Anatoly Kolosov  1 , Elena Romanets  1 , Faridun Bakoev  1 , Timofey Romanets  1 , Vladimir Yudin  2 , Anton Keskinov  2 , Siroj Bakoev  2
Affiliations

Finding Predictors of Leg Defects in Pigs Using CNV-GWAS

Lyubov Getmantseva et al. Genes (Basel). .

Abstract

One of the most important areas of modern genome research is the search for meaningful relationships between genetic variants and phenotypes. In the livestock field, there has been research demonstrating the influence of copy number variants (CNVs) on phenotypic variation. Despite the wide range in the number and size of detected CNVs, a significant proportion differ between breeds and their functional effects are underestimated in the pig industry. In this work, we focused on the problem of leg defects in pigs (lumps/growths in the area of the hock joint on the hind legs) and focused on searching for molecular genetic predictors associated with this trait for the selection of breeding stock. The study was conducted on Large White pigs using three CNV calling tools (PennCNV, QuantiSNP and R-GADA) and the CNVRanger association analysis tool (CNV-GWAS). As a result, the analysis identified three candidate CNVRs associated with the formation of limb defects. Subsequent functional analysis suggested that all identified CNVs may act as potential predictors of the hock joint phenotype of pigs. It should be noted that the results obtained indicate that all significant regions are localized in genes (CTH, SRSF11, MAN1A1 and LPIN1) responsible for the metabolism of amino acids, fatty acids, glycerolipids and glycerophospholipids, thereby related to the immune response, liver functions, content intramuscular fat and animal fatness. These results are consistent with previously published studies, according to which a predisposition to the formation of leg defects can be realized through genetic variants associated with the functions of the liver, kidneys and hematological characteristics.

Keywords: CNV; GWAS; SNP; leg defects; pig.

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Conflict of interest statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

Figure 1
Figure 1
Distribution of the amount of CNVs per sample.
Figure 2
Figure 2
Distribution of CNVs across chromosomes.
Figure 3
Figure 3
Genome-wide map of CNVR in Large White pigs.
Figure 4
Figure 4
Percentage of QTLs affected by CNVRs.
Figure 5
Figure 5
Manhattan plot for CNVR, red: odd chromosomes; blue: even chromosomes.
See this image and copyright information in PMC

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