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Estimating Linkage Disequilibrium and Effective Population Size Across Generations in Holstein Cattle
Ronak Salehi1, Arash Javanmard1, Mahdi Mokhber2
1Department of Animal Science, Faculty of Agricultural, University of Tabriz, Tabriz, Iran.
Veterinary Medicine and Science
|November 14, 2025
Summary
Global Holstein cattle show declining genetic diversity due to intensive breeding. Recent trends suggest a slowdown in this decline, potentially due to improved breeding strategies, highlighting the need for careful management of genetic diversity.
Area of Science:
- Animal Genetics
- Conservation Genetics
- Population Genetics
Background:
- Effective population size (Ne) and linkage disequilibrium (LD) are critical for genetic diversity and survival.
- These metrics inform conservation genetics and breeding programs for livestock.
Purpose of the Study:
- Analyze LD structure and estimate Ne in global Holstein cattle.
- Assess genetic diversity and population dynamics in Holstein populations worldwide.
Main Methods:
- Genomic data from 2127 Holstein cows across eight countries were analyzed.
- Linkage disequilibrium (LD) and effective population size (Ne) were calculated using PLINK 1.9 and SNeP 1.1.
Main Results:
- LD decreased with increasing physical distance between SNP markers.
- Effective population size (Ne) has significantly declined over generations, with a recent slowdown and slight increases in some populations.
- Current Ne ranges from 74 (French Holstein) to 171 (Polish Holstein), with declines attributed to intensive use of superior sires.
Conclusions:
- A slowdown in Ne decline may indicate improved breeding strategies and genetic material importation.
- Managing genetic diversity and mitigating inbreeding are crucial for Holstein cattle.
- Effective breeding programs are essential for sustaining genetic health, productivity, and adaptability in dairy cattle.
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