Data from: Towards breed formation by island model divergence in Korean cattle

Background: The main cattle breed in Korea is the brown Hanwoo, which has
been under artificial selection within a national breeding program for
several decades. Varieties of the Hanwoo known as Jeju Black and Chikso
were not included in the breeding program and remained isolated from the
effects of recent artificial selection advancements. We analysed the Jeju
Black and Chikso populations in regards to their genetic variability,
state of inbreeding, as well as level of differentiation from the mainland
Hanwoo population. Results: Jeju Black and Chikso were found to have small
estimated effective population sizes (N e ) of only 11 and 7,
respectively. Despite a small N e , higher than expected heterozygosity
levels were observed (0.303 and 0.306), however, lower allelic richness
was found for the two island populations (1.76 and 1.77) compared to the
mainland population (1.81). The increase in heterozygosity could be due to
environmental disease challenges that promoted maintenance of higher
genetic variability; however, no direct proof exists. Increased
heterozygosity due to a first generation crossing of genetically different
populations is not recorded. The differentiation between the Korean
populations had F ST values between 0.014 and 0.036 which is not as high
as the differentiation within European beef or dairy cattle breeds
(0.047–0.111). This suggests that the three populations have not separated
into independent breeds. Conclusion: Results agree with an island model of
speciation where the brown Hanwoo represents the ancestral breed, whilst
the Jeju Black and Chikso diverge from this common ancestor, following
different evolutionary trajectories. Nevertheless, differences are minor
and whether Jeju Black and Chikso cattle will develop into discrete breeds
or reintegrate with the main population has to be seen in the future and
will largely depend on human management decisions. This offers a rare
opportunity to accompany the development of new breeds but also poses
challenges on how to preserve these incipient breeds and ensure their long
term viability.