Estimating Linkage Disequilibrium and Effective Population Size Across Generations in Holstein Cattle

Background Understanding the structure of linkage disequilibrium (LD) and accurately estimating the effective population size (Ne) are crucial for maintaining genetic diversity and ensuring population survival. These metrics are vital for decision‐making in conservation genetics and breeding programs. Objectives This study aimed to analyse the LD structure and estimate Ne in global Holstein cattle populations to assess genetic diversity and population dynamics. Methods Genomic data from 2127 cows across eight countries (Poland, Sweden, Ireland, Iran, France, China, Canada and the Netherlands) were analysed. Data quality control was performed using PLINK 1.9. Adjusted R ‐squared ( r 2 ) values for SNP markers up to 38 Mbp and Ne values from ancestral generations to the present were calculated using SNeP 1.1. Results LD values decreased nonlinearly with increasing physical distance, ranging from 0.102–0.320 at <25 kbp to 0.007–0.059 at 38 Mbp. Ne values have declined significantly since 2000 generations ago, with a sharp reduction from 70 to 10 generations ago. However, the decline slowed in the last 10 generations, with slight increases in some populations. Current Ne values range from 74 (French Holstein) to 171 (Polish Holstein). The rapid decline in Ne is attributed to the intensive use of limited superior bulls, reducing genetic diversity. Conclusions The recent slowdown in Ne decline and slight increases in some populations may reflect improved breeding strategies, including genetic material importation. These findings highlight the importance of managing genetic diversity and mitigating inbreeding effects in Holstein cattle populations. Effective breeding programs are essential to sustain genetic health, productivity and long‐term adaptability in commercial dairy cattle.