Single nucleotide polymorphism and haplotype effects associated with somatic cell score in German Holstein cattle

Abstract

BackgroundTo better understand the genetic determination of udder health, we performed a genome-wide association study (GWAS) on a population of 2354 German Holstein bulls for which daughter yield deviations (DYD) for somatic cell score (SCS) were available. For this study, we used genetic information of 44 576 informative single nucleotide polymorphisms (SNPs) and 11 725 inferred haplotype blocks.ResultsWhen accounting for the sub-structure of the analyzed population, 16 SNPs and 10 haplotypes in six genomic regions were significant at the Bonferroni threshold of P ≤ 1.14 × 10-6. The size of the identified regions ranged from 0.05 to 5.62 Mb. Genomic regions on chromosomes 5, 6, 18 and 19 coincided with known QTL affecting SCS, while additional genomic regions were found on chromosomes 13 and X. Of particular interest is the region on chromosome 6 between 85 and 88 Mb, where QTL for mastitis traits and significant SNPs for SCS in different Holstein populations coincide with our results. In all identified regions, except for the region on chromosome X, significant SNPs were present in significant haplotypes. The minor alleles of identified SNPs on chromosomes 18 and 19, and the major alleles of SNPs on chromosomes 6 and X were favorable for a lower SCS. Differences in somatic cell count (SCC) between alternative SNP alleles reached 14 000 cells/mL.ConclusionsThe results support the polygenic nature of the genetic determination of SCS, confirm the importance of previously reported QTL, and provide evidence for the segregation of additional QTL for SCS in Holstein cattle. The small size of the regions identified here will facilitate the search for causal genetic variations that affect gene functions.

Validating genome‐wide associated signals for clinical mastitis in German Holstein cattle

“…This study revealed six genomic regions affecting DYDs for SCS (Abdel‐Shafy et al . ). The identified loci have been further validated in different datasets of subsequent generations using SCS (Abdel‐Shafy et al .…”

“…) for 10 single nucleotide polymorphisms (SNPs) that had previously been significantly associated with DYDs for SCS (Abdel‐Shafy et al . ). Primers of genotyped SNPs are described in Table .…”

“…In addition, this study confirms an effect on CM on BTA13, which has been identified as a novel locus affecting DYDs for SCS in German Holstein cattle (Abdel‐Shafy et al . ). This locus has not been reported before, either in other Holstein or other breeds ( http://www.animalgenome.org; Release 30).…”

“…This was at the same magnitude as previously found for DYDs of SCS in the bull population and SCS in the cow population: 1.9% and 1.7% respectively (Abdel‐Shafy et al . ,b). Even though the effects were small, they seem to be consistent for these three traits in both populations and deserve more attention as factors contributing to CM variation.…”

“…; Abdel‐Shafy et al . ) have revealed a large number of associated genomic loci. These loci are located on all chromosomes except 3, 21, 26, 27 and 28.…”