Identification of genomic regions affecting nitrogen excretion intensity in Brown Swiss dairy cows

Dairy cows with a lower nitrogen excretion intensity (N_exi) excrete less nitrogen, ammonia (NH₃) and nitrous oxide (N₂O), a highly potent greenhouse gas (GHG), per kg of milk produced and therefore represent a lower environmental impact while maintaining food security. To date, the genomics background of N_exi is unknown. Here we performed a genetic association study, overlap analysis and functional enrichment analysis for N_exi in 875 genotyped dairy cows with 2,147 lactations from 200 herds. We identified 1456 single nucleotide polymorphisms (SNPs) that significantly affect N_exi. We found 140 SNPs overlapping with 148 protein-coding genes. The MAN1A1 gene is a strong candidate gene for N_exi. Genotype CC of rs42786248, the most significantly associated SNP located in the MAN1A1 gene, had higher N_exi than genotypes AA (p < 0.001) and AC (p < 0.001). We identified 33 genes involved in biological processes related to nitrogen metabolism. Our results form the basis for further research on the genomics background of N_exi. The identified SNPs serve as potential targets for selective breeding programs, aimed at reducing N_exi and associated NH₃ and N₂O emissions in cattle production, thus contributing to more environmentally sustainable milk production.