Simultaneous Effects of Single-Nucleotide Polymorphisms on the Estimated Breeding Value of Milk, Fat, and Protein Yield of Holstein Friesian Cows in Hungary

Abstract

This study aimed to find SNPs that have an effect on the estimated breeding values (EBVs) of milk (MY), fat (FY), and protein yield (PY) of Holstein Friesian cows in Hungary. Holstein Friesian cows (n = 2963) were genotyped on a Eurogenomics (EuroG_MDv4) chip. The EBVs for MY, FY, and PY were obtained from the Association of Hungarian Holstein Breeders (AHHB). The loci associated with the EBVs were identified via three approaches: the calculation of genetic distance of the SNPs (Fst_marker), linear regression, and haplotype association tests. Nine SNPs were significantly associated with MY, FY, and PY located on BTA 2, 5, 28, and X. Among the nine SNPs identified, BTB-00219372 on BTA 5 had a positive β coefficient for MY and a negative β coefficient for FY and PY. In addition, BovineHD3000027615 on BTA X had a positive β coefficient for both MY and PY, as well as a negative β coefficient for FY. The identified SNPs were located near several genes that remain unstudied in cattle, which are potential targets for closer scrutiny in relation to milk properties. The markers associated with two or three EBVs could be used in selection with high efficiency to accelerate genetic development and help AHHB experts achieve their breeding. Most marker effects point in the same direction on EBVs; however, we found that BTB-00219372 and BovineHD3000027615 could be used with caution to increase one EBV while decreasing the other EBV or EBVs.

Keywords

• Holstein
• genome-wide association
• single-nucleotide polymorphism
• estimated breeding value