Data from: Genomic analyses suggest adaptive differentiation of Northern European native cattle breeds

Native domestic breeds represent important cultural heritage and genetic
diversity relevant for production traits, environmental adaptation and
food security. However, risks associated with low effective population
size, such as inbreeding and genetic drift, have elevated concerns over
whether unique within-breed lineages should be kept separate or managed as
one population. As a conservation genomic case study of the genetic
diversity represented by native breeds, we examined native and commercial
cattle (Bos taurus) breeds including the threatened Danish Jutland cattle.
We examined population structure and genetic diversity within breeds and
lineages genotyped across 770K single nucleotide polymorphism loci to
determine (a) the amount and distribution of genetic diversity in native
breeds, and (b) the role of genetic drift vs. selection. We further
investigated the presence of outlier loci to detect (c) signatures of
environmental selection in native vs. commercial breeds, and (d) native
breed adaptation to various landscapes. Moreover, we included older
cryopreserved samples to determine (e) if cryopreservation allows
(re)introduction of original genetic diversity. We investigated a final
set of 195 individuals and 677K autosomal loci for genetic diversity
within and among breeds, examined population structure with principal
component analyses and a maximum likelihood approach, and searched for
outlier loci suggesting artificial or natural selection. Our findings
demonstrate the potential of genomics for identifying the uniqueness of
native domestic breeds, and for maintaining their genetic diversity and
long-term evolutionary potential through conservation plans balancing
inbreeding with carefully designed outcrossing. One promising opportunity
is the use of cryopreserved samples, which can provide important genetic
diversity for populations with few individuals, while helping to preserve
their traditional genetic characteristics. Outlier tests for native vs.
commercial breeds identified genes associated with climate adaptation,
immunity and metabolism, and native breeds may carry genetic variation
important for animal health and robustness in a changing climate.