Identifying Loci Under Positive Selection in Yellow Korean Cattle (Hanwoo)

Abstract

Jeju Black cattle is one of the aboriginal Korean cattle breeds that has been isolated in Jeju island for a long time, while Yellow Hanwoo cattle has been extensively selected for beef production traits for the last several decades. Aiming to investigate broader patterns of selection, we genotyped 352 Yellow Hanwoo and 169 Jeju Black cattle using a customized 150 K bovine chip. Our composite selection signals' analysis to identify selection signatures (cross-population extended haplotype homozygosity [XP-EHH], ΔSAF, and F _ST) identified recent and strong signature of selection near many loci with mutations affecting the traits under strong selection as outlier in Yellow Hanwoo, including SCP2 (P = 8.41 × 10^-10) that may be involved in the meat quality. We found nine candidate regions with significant clusters of selection signals, and further bioinformatics analyses of the genes located within these regions revealed mainly genes involved in G-protein coupled receptor signaling pathway (GO:0007186) or olfactory transduction (bta04740), which may be due to adaptation to natural environments in Jeju island. Based on the stronger correlation of Ne₁₀/Ne₁₀₀ ratio between Yellow Hanwoo (0.61) and Jeju Black (0.66) cattle, our results suggest that the difference of chromosomal regions of selection signature between the 2 cattle breeds was due to a consequence of selection processes to adapt to environmental differences between Jeju island and the main inland, Korean peninsula.

Keywords: Jeju black cattle; Yellow Hanwoo; effective population size; positive selection.

Figure 1.

Principal component analysis between Hanwoo (red circles) and Jeju Black (blue circles) cattle breeds, 392 animals plotted.

Figure 2.

Genetic effective population size trends for Hanwoo and Jeju Black cattle in the last 1000 generations.

Figure 3.

Manhattan plot of genome-wide autosomal composite selection signal (CSS) analyses of Hanwoo cattle. Red line in the CSS plots represents the genome-wide 0.5% thresholds based on the Bonferroni threshold correction.

Figure 4.

Composite selection signals, XP-EHH, ΔSAF, and F_ST in Hanwoo. Vertical dashed red lines represent the position of the SNP detected as highly significant in Hanwoo (Chr3: 93936476 bp, P = 8.41 × 10⁻¹⁰). The horizontal blue line marks the selective region (Chr3: 92.62-93.94 Mb).