Epsilon Archive for Student Projects

Abstract

Inbreeding, genetic drift and selection are key forces that shape the genetic architecture of
domestic cattle populations. This study investigates the genomic consequences of these forces by
analysing runs of homozygosity (ROH) in both simulated and empirical data from Swedish native
breeds (Fjäll, Rödkulla and SRB) and international breeds such as Holstein and Jersey. ROH
defined as continuous stretches of homozygous genotypes, serve as genomic markers of
inbreeding and selection and offer insights into both recent and ancient demographic processes.
Simulations were conducted using msprime to model historical population structures, and ROH
were detected using PLINK in both simulated and empirical data. The results revealed distinct
ROH patterns between native and commercial breeds. Swedish native breeds exhibited several
short ROH segments, consistent with historical bottlenecks and small effective population sizes. In
contrast, Holstein and Jersey cattle showed fewer but longer ROH segments, indicating more
recent inbreeding due to intensive selection.
ROH islands, genomic regions consistently homozygous across individuals, were identified in
both data types and further investigated for gene content. These regions might display selection for
traits like disease resistance, environmental adaptability and fertility.
This demonstrates the value of ROH analysis in revealing the demographic and selective histories
of cattle populations. It provides with insights for the preservation of rare breeds and the
management of breeding programs.