Pool-seq analysis of cheese making properties in Danish Holsteins

Rennet induced milk coagulation is an important trait for cheese production. Several genetic factors are known to affect milk coagulation, including variation in the major milk proteins, however, recent association studies indicate genetic effects from other genomic regions as well. The aim of this study was to detect genetic variation affecting milk coagulation properties, measured as curd firming rate (CFR) and raw milk pH. This was achieved by utilising a pool-seq strategy examining allele frequency differences between phenotypically extreme samples. CFR and raw milk pH were measured for 415 Danish Holstein cows and pools of whole genome sequence reads from samples with “extreme” values (high or low) were analysed for each phenotypic trait. Allele frequency differences were calculated between pools. Two SNPs located on chromosome 6 and one SNP located on chromosome 18 showed significant association explaining 1.2%, 0.8% and 2% of the phenotypic variance of CFR when genotyped in the entire sample set, respectively. The three interesting SNPs were located in close proximity to the candidate genes; SLC4A4, LIMCH1 and CCDC155, making them interesting targets for further analysis.