Genome-wide patterns of copy number variation in case-control mastitis study of Polish HF cows using high-density Illumina BovineSNP50 v3 BeadChip array

Abstract

Background: The mastitis is one of the most important diseases affecting losses of milk yield and functional longevity resulting in economic losses in dairy farms. The cow's inflammation of the mammary gland is a consequence of complex processes in the innate immune system, activation of several cells and accompanying factors that lead to the elimination of microorganism invaders. The study aimed to investigate genetic background by the genome-wide association study (GWAS) for identified copy number variations (CNVs) in one of the most important economically disorders – the mastitis in dairy cattle.

Methods: We investigated 682 Polish-HF cows previously genotyped and analyzed using the following steps: i) identification of CNVs across all the cows based on ARS-UCD1.2 genome map, ii) to perform the GWAS with the utilization of logistic regression models, iii) functional analysis for identified CNVs to indicate putative candidate genes. The cow's genotypes were deposited in the Polish cattle SNP genotypes database (cSNP-db). The phenotype database information covered the veterinary history of mastitis was collected from four experimental farms belonging to the National Institute of Animal Production, Balice, Poland.

Results: Study identified 326 CNVs of which only 28 CNVs were significant with p-value <0.05. The most significant CNVs were identified for BTA17, BTA22, and BTA25, respectively. However, the most interesting from the functional point of view of previously reported CNVs overlapped with genes associated with mastitis were loaded on BTA03 (MSH4), BTA18 (FOXC2, FOXL1, MTHFSD) and BTA27 (TLR3), respectively.

Conclusions: The study clearly concluded that the identification of candidate genes associated with mastitis using of CNVs is feasible. Therefore, one can apply this GWAS approach between the common CNVs and mastitis as a case-control experiment. Our study identified few genes like MSH4, MTHFSD, FOXC2, FOXL1, and TLR3 which were overlapped with tree CNVs to functionally assess and might be considered as the candidate genes for mastitis in Polish HF cattle population. Moreover, obtained results supported by the different genome and transcriptome analysis could lead to a better understood of the genetic background of mastitis.