A genome-wide association study for clinical mastitis in Italian Holstein

Clinical mastitis (CM) has a huge detrimental impact on animal welfare, farms' net profit and antimicrobial resistance. Nowadays, on-farm CM diagnoses are available in Italy from the Livestock Environment Opendata (LEO) project of the Italian Breeders Association (AIA). The aim of this study was to identify the SNPs associated to CM resistance and investigate its genetic background performing a genome-wide association study (GWAS). CM was considered a binary trait. Data came from 4 North-Italian regions (Lombardia, Emilia-Romagna, Veneto and Piemonte), recorded from 2014 to 2020: only first records per lactation, from 1 to 305 days in milk, were included. The maximum parity considered was 5. Lower and upper bounds of incidence per herd per year were set to 0.15 and 0.75 respectively. Herd-year-season of calving groups with less than 10 animals were discarded. The edited dataset had 113,289 records; the prevalence was 0.32. The 4 generations pedigree was composed of 140,385 animals. Heritability was previously calculated with a single-trait repeatability threshold animal model: (co)variances were converted to the observed scale in order to fit the trait as linear. Heritability on the observed scale was 0.04. GWAS analysis was performed and, in the intersection of the highest thousand SNPs for explained variance and the thousand most significant SPs, we identifed 32 SNPs. There were 47 genes in their vicinity considering windows of 200 kb, mostly located on chromosomes 5, 7, 25 and 27. Among others, PLXNC1, associated with mastitis resistance in sheep, SEMA7A, associated with immune response in humans and CEP83, associated with paratuberculosis pathological outcomes in Holstein catte. Results confirmed the complexity of the trait and its highly polygenic nature and provide a better understanding of CM resistance in Italian Holstein.