Genomic Loci Affecting Milk Production in German Black Pied Cattle (DSN)

Abstract

German Black Pied cattle (DSN) is an endangered population of about 2,550 dual-purpose cattle in Germany. Having a milk yield of about 2,500 kg less than the predominant dairy breed Holstein, the preservation of DSN is supported by the German government and the EU. The identification of the genomic loci affecting milk production in DSN can provide a basis for selection decisions for genetic improvement of DSN in order to increase market chances through the improvement of milk yield. A genome-wide association analysis of 30 milk traits was conducted in different lactation periods and numbers. Association using multiple linear regression models in R was performed on 1,490 DSN cattle genotyped with BovineSNP50 SNP-chip. 41 significant and 20 suggestive SNPs affecting milk production traits in DSN were identified, as well as 15 additional SNPs for protein content which are less reliable due to high inflation. The most significant effects on milk yield in DSN were detected on chromosomes 1, 6, and 20. The region on chromosome 6 was located nearby the casein gene cluster and the corresponding haplotype overlapped the CSN3 gene (casein kappa). Associations for fat and protein yield and content were also detected. High correlation between traits of the same lactation period or number led to some SNPs being significant for multiple investigated traits. Half of all identified SNPs have been reported in other studies, previously. 15 SNPs were associated with the same traits in other breeds. The other associated SNPs have been reported previously for traits such as exterior, health, meat and carcass, production, and reproduction traits. No association could be detected between DGAT1 and other known milk genes with milk production traits despite the close relationship between DSN and Holstein. The results of this study confirmed that many SNPs identified in other breeds as associated with milk traits also affect milk traits in dual-purpose DSN cattle and can be used for further genetic analysis to identify genes and causal variants that affect milk production in DSN cattle.

Genome-Wide Association Study Using Whole-Genome Sequence Data for Fertility, Health Indicator, and Endoparasite Infection Traits in German Black Pied Cattle

“…For FPR, we detected a cluster of ten closely related genes on BTA 13. This finding is in contrast to the GWAS by Korkuć et al [24], where no SNP reached the significance threshold on BTA 13 for milk fat and protein traits in a population of 1816 50K genotyped DSN. However, similar to our findings, the authors detected SVs on BTA 9, 11, 12, and 27 associated with milk fat content or milk fat yield in DSN.…”

“…Hence, our detected genes influencing fertility in DSN may have similar functions for fertility in other cattle breeds. This observation is in accordance with Korkuć et al [24], who found a high overlap of genomic regions in DSN and HF for milk production traits, although they identified no common genes for DSN and HF. Although we identified genes for CTFS and NR56 in DSN which were previously described in other breeds, the same gene can be differentially expressed in different breeds, which might phenotypically explain improved fertility in DSN.…”

“…Furthermore, Jaeger [10] identified DGAT1 for fat content in a multi-breed GWAS including a quite large number of DSN cows. However, although genomic relatedness between DSN and HF is high, we detected no associations in the DGAT1 gene for FPR in DSN, which coincides with the observation by Korkuć et al [24] for other milk production traits in DSN. We identified the glycerol-3-phosphatase acyltranserase 4 (GPAT4) gene on BTA 27 as a potential candidate gene for FPR.…”

“…We focused on fertility, udder health, metabolic health and stability indicator traits, and endoparasite infection traits since these are highly relevant for the conservation of the breed [10,24]. For CTFS, we identified SVs on BTA 12, 13, 15, and 28 with the largest number of associations on BTA 13.…”

“…Further GWAS in DSN were based on commercial 50 K SNP chip panels with focus on milk production [24] and udder health traits [25]. These studies revealed candidate genes previously described in HF and other cattle breeds, raising the interest in identifying species-specific variants for functional traits in DSN with WGS data.…”