Associations between Bovine β-Defensin 4 Genotypes and Production Traits of Polish Holstein-Friesian Dairy Cattle

SIMPLE SUMMARY: Mastitis negatively affects dairy cattle, causing inferior milk quality and premature animal culling, which leads to economic losses. Therefore, selection based on genetic markers (i.g., marker-assisted selection) should also include functional traits with low heritability, such as resistance to udder inflammation. Single nucleotide polymorphisms (SNPs) identified in genes involved in the immune system, such as defensins with antibacterial properties, could be valuable markers. We chose two SNPs within the bovine neutrophil beta-defensin 4 (BNBD4) gene analyzed in a previous study related to milk production and udder health. Since these SNPs are located very close to each other in the gene intron, it is useful to analyze their association with production traits as a combined genotype. The results showed that these genotypes are indeed associated with productivity, as well as functional traits (milk, fat, and protein yields, fat, protein, lactose, and dry matter contents, and somatic cell count). The differences between the results based on the phenotypic data and the breeding values of studied traits may confirm the results of simulation studies that indicate a high rate of false-positives in genome-wide association study (GWAS) based on classically calculated estimated breeding values (EBVs) using best linear unbiased prediction (BLUP) methodology. ABSTRACT: This study analyzed the associations between two single-nucleotide polymorphisms (C2239T and A1674C), used together as a genotype located in BNBD4, and milk traits and breeding values of productivity traits of Polish Holstein-Friesian dairy cows. The research was carried out on 322 cows, with 7070 milk parameter and somatic cell count records in daily milking, as well as 897 records covering data on whole lactations, and 2209 breeding value records for productivity traits. The DMU statistical package with a one-trait repeatability test-day animal model was used to estimate the associations. The differences between the genotype effects were analyzed using Duncan’s post-hoc tests. The CC/AA and CT/AC genotypes had the highest frequencies (0.62 and 0.23, respectively). For use in marker-assisted selection, the CC/AC genotype is the most promising as an indicator of high-yielding cows potentially resistant to mastitis, because it was associated with the lowest somatic cell count (SCC), highest milk, fat, and protein yields in daily milking, as well as with milk yield in the whole lactation. The studied genotypes were also related to the breeding values of all the investigated production traits. However, some simulation studies have indicated a high rate of false-positives in GWAS based on classically calculated EBVs.