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.

背景：韩国的主要肉牛品种为褐韩牛（Hanwoo），数十年来一直处于国家级育种计划的人工选择之下。韩牛的两个地方类群——济州黑牛（Jeju Black）与奇科索牛（Chikso）——并未被纳入该育种计划，且长期与近期人工选择技术的影响相隔绝。本研究针对济州黑牛与奇科索牛种群的遗传变异程度、近交状态，以及与大陆韩牛种群的遗传分化水平展开了分析。
结果：研究发现，济州黑牛与奇科索牛的估计有效种群大小（effective population size，N_e）分别仅为11与7。尽管有效种群规模较小，但二者的观测杂合度却高于预期值（分别为0.303与0.306）；然而相较于大陆韩牛种群（1.81），这两个岛屿种群的等位基因丰富度更低（分别为1.76与1.77）。杂合度升高可能源于环境病原压力维持了较高的遗传变异，但目前尚无直接证据支持这一假说。此外，本研究未记录到因遗传分化种群的第一代杂交而导致杂合度升高的现象。韩国三类牛种群间的遗传分化F_ST值介于0.014至0.036之间，这一水平低于欧洲肉牛或奶牛品种内部的遗传分化程度（0.047~0.111），表明这三个种群尚未分化为独立的品种。
结论：本研究结果符合物种形成的岛屿模型——褐韩牛为祖先种群，济州黑牛与奇科索牛则从该共同祖先分化而来，遵循各自不同的演化路径。不过，三者间的遗传差异仍较小，济州黑牛与奇科索牛未来是否会演化为独立品种，或是与核心种群重新整合，仍有待观察，且这在很大程度上取决于人类的管理决策。这一研究对象为我们提供了伴随新品种培育的罕见契机，但同时也带来了如何保护这些初期分化类群、保障其长期存续的挑战。