Genome-Wide Association Analysis of Milk Fat, Protein, and Fertility Traits in a New Zealand Holstein-Friesian Dairy Herd

Abstract

This case study presents a genome-wide association analysis of Australian Breeding Values (ABVs) for milk-fat yield (FAT), milk-protein yield (PROT), daughter fertility (FER), and mastitis resistance (MAS) in New Zealand Holstein-Friesian heifers. In total, 1330 heifers were genotyped, of which 1002 had available ABVs and were included in the association analyses. Population-structure analysis of the 1330 genotyped heifers identified three clusters associated with sire-line composition and breeding history, highlighting the need to account for family structure and genetic stratification in the association analyses. A chromosome 16 association signal was detected for both FAT and PROT, spanning the genomic region from 35.1 to 38.6 Mb for FAT and from 35.1 to 35.9 Mb for PROT. AX-106760165, located at 35,401,543 bp within the RGS7 gene, was the most strongly associated marker for both traits and showed opposite estimated allele effects on FAT and PROT. RGS7 encodes a regulator of G-protein signaling and has previously been implicated in milk-production traits, suggesting a potential role in endocrine signaling, cellular responses, or nutrient partitioning relevant to milk-component yield. However, the functional consequence of AX-106760165 is unknown, and the association may reflect linkage disequilibrium with another functional variant within or near RGS7. No SNP reached genome-wide significance for FER or MAS. Differences in the detected associations among traits likely reflect variation in effect-size distributions, ABV accuracy, and statistical power. The chromosome 16 association and the potential involvement of RGS7 require independent validation and functional investigation before use in selection or mating decisions.