Genomic regions associated with blood metabolites and subclinical ketosis in early-lactation Holstein cows

Modern dairy cattle populations have been intensively selected for high milk production; therefore, cows experience significant metabolic stress after calving and during the transition period. Breeding strategies aimed at making cows more robust and resistant to diseases without compromising milk productivity exist and have been implemented in some countries. Whereas genomic investigations have been conducted on both clinical and subclinical forms of ketosis, few studies have focused on measurable features reflecting metabolic processes, such as the blood concentrations of BHB and nonesterified fatty acids (NEFA) and urea, an indicator of nitrogen metabolism. A better understanding of the coding genes and polygenic nature of blood metabolites is advisable for genomic selection and evaluation. Therefore, this study aimed to identify genomic regions associated with major hematic biomarkers of ketosis predicted from mid-infrared milk spectra in the Italian Holstein population. A single-step GWAS was performed using predicted blood phenotypes collected from 6,190 clinically healthy Holstein cows from 5 to 35 DIM, reared in 374 herds, and genotyped with arrays of different SNP density. The analyzed traits included: BHB (log-transformed), NEFA (log-transformed), urea concentration (mmol/L), and subclinical ketosis (SCK), which was identified when BHB was >= 1.20 mmol/L. Specifically, 5.51% of cows were identified as being at risk of SCK. After imputation and conventional quality control, 64,202 markers located in the autosomes were used for the association study. The genomic h2 was generally low (<0.11) for all the traits investigated. Signals of BHB were scattered across several locations (BTA2, 4, 6, 7, 18, 21, 22, 25, and 28) in regions related to metabolic processes and immune system function and response. In contrast, the significant SNP for SCK were mainly concentrated in BTA1, 5, 11, and 15, confirming the combined action of multiple genes on health-related phenotypes and suggesting that the genetic control of SCK is more restricted to specific chromosomal regions than that of blood biomarker concentration. For traits such as NEFA and urea, the number of significant signals was lower, and they were mainly related to lipid metabolism. Although the results should be interpreted with caution and validated in future research, our findings provide novel insights into the genetic and molecular mechanisms underlying negative energy balance and SCK in Holstein cows, offering potential targets for future functional studies and genetic improvement strategies.