Development and Application of a Multiplex Fluorescent ARMS-PCR Assay for Screening 18 Monogenic Traits in Holstein Cattle

Genetic screening of monogenic traits is important for improving genetic health and increasing favorable milk protein in dairy cattle. This study developed and applied an amplification refractory mutation system PCR (ARMS-PCR) assay to simultaneously screen 21 causal variants underlying 18 monogenic traits in Holstein cattle, including 13 recessive genetic defects, 2 milk protein loci, and 3 morphological loci. The assay was designed as a unified multiplex PCR-capillary electrophoresis workflow, enabling clear detection of allele-specific products distinguished by fragment size and fluorescent color. Sanger sequencing validation of newly incorporated loci supported the accuracy of the assay. A total of 1656 cows from 12 commercial farms were genotyped using the multiplex ARMS-PCR panel, and amplicons were analyzed by capillary electrophoresis. Carriers were detected for all genetic defects except DUMPS, with carrier frequencies ranging from 0.12% to 6.64%. The highest frequencies were observed for HH5 (6.64%) and MWS (6.58%), whereas HH3, HH1, and HCD showed intermediate frequencies of 1.81% to 3.08%; all the remaining defects were below 1%. Overall, 22.10% of sampled cows carried at least 1 defect allele, including 20.47% carrying 1 defect, 1.51% carrying 2, and 0.12% carrying 3. For milk protein loci, the desirable β-casein A2A2 and κ-casein BB genotypes occurred at frequencies of 45.83% and 14.13%, respectively, and the favorable A2A2/BB combination was present in 6.22% of sampled cows. Dominant red, recessive red, and polled alleles were rare. These results indicate that multiplex fluorescent ARMS-PCR can serve as a practical targeted screening tool for the simultaneous management of known deleterious alleles and selection of favorable monogenic variants in dairy cattle breeding.