Johne’s disease (JD) is a major worldwide economic burden caused by an infectious gastrointestinal sickness. The purpose of this research was to use current data to analyze the genetic features and phenotypic alterations of JD in Holstein cattle in the United States. The data set includes 365,980 Holstein cows from 1,048 herds that participated in a voluntary JD control program. Two protocol kits, Idexx Paratuberculosis Screening Ab Test (IDX) and Parachek® 2 (PCK), were used to test milk samples by ELISA. The overall prevalence of JD in US Holstein cattle was 4.72%. 25,000 animals were genotyped using 78,964 SNP markers. The posterior heritability estimates for JD susceptibility ranged from low to high. The average reliability of anticipated breeding values of JD susceptibility using single-step analysis was 0.18 (THR) to 0.22 (ssTHR) for IDX and 0.14 (THR to 0.18) for PCK. The projected genetic trends for JD susceptibility were negative and very significant (P-value < 0.01). There were little relationships between bulls’ estimated transmitting ability and economically significant traits such as milk yield, milk protein, milk fat, somatic cell score, and mastitis, indicating a non-overlapping genetic selection process with features in current genetic evaluations. The results indicate that including JD into national genetic evaluation programs might possibly lower the incidence rate.
