Analysis of genetic diversity and inbreeding levels in the Korean native black goat population using whole-genome sequencing

Background The Korean native black goat (KNG) is the sole indigenous goat genetic resource of the Korean Peninsula, adapted to local environmental conditions. However, because it has been managed as a closed population over a long period, a sustainability assessment of the population is necessary. Results Consistent with the results of previous MS marker-utilizing studies, KNG and Korean crossbred goat (KCB) were clearly distinguished by population, with similar clustering trends. Although nucleotide diversity (pi) peaks existed at specific sites per contig in the KNG population, in most contigs, pi demonstrated a uniformly low aspect. The general observed heterozygosity (Ho) value of the KNG population was lower than that of the KCB population; however, the variation width between contigs was relatively larger than the average Ho. Therefore, among the four populations, the Jangsu (JS) and Tongyeong (TY) lineages are the most genetically similar, whereas KCB is the most diverse. Runs of homozygosity (ROH) analysis was used to assess the inbreeding levels and genomic fixation patterns of the KNG and KCB populations, determining that the KNG population had a high ROH total per individual, with a predominance of short-range ROH. In contrast, the total number of ROH in the KCB population was relatively small, and the proportions of medium-range and long-range ROH were higher than that of short-range ROH in the KNG population. Conclusions Compared to the KCB, the KNG showed overall lower pi and Ho, the patterns of homozygosity confirmed through ROH length distribution and inbreeding coefficient based on runs of homozygosity (F _ROH ) analysis reflect the demographic history of a closed population maintained for a long period rather than that of recent rapid inbreeding. In particular, the pattern where short ROHs are distributed in large numbers across the entire genome shows that the KNG population has been maintained as an independent population for a long time. This is not a simple inbreeding risk signal but a genomic structure unique to native breeds.