Figure 1.
Korean cattle breeds used in this study.
(A) Hanwoo. (B) Jeju Heugu. (C) Korean Holstein. (D) Chikso. (E) Mural painting in the Anak tomb no. 3 (A.D. 357) in the Goguryeo age: a stable illustrating three cattle in black, yellow, and brindle colors (courtesy of Dr. Ho-Tae Jeon). F: Eighteenth century painting by Hong-Do Kim (1745–1806), Joseon Dynasty, depicting farmers ploughing a rice field using Korean native cattle (at the National Museum of Korea).
Table 1.
Summary of sequencing results for Hanwoo, Jeju Heugu, and Korean Holstein cattle breeds.
Table 2.
Functional classification and novelty status of the detected single nucleotide polymorphisms (SNPs) and insertion–deletions (InDels).
Table 3.
Homozygous-to-heterozygous and transition-to-transversion ratios for the single nucleotide polymorphism (SNP) datasets.
Table 4.
Concordance between single nucleotide polymorphism (SNP) genotypes derived from the BovineSNP50 BeadChip and genotypes from whole-genome sequencing (WGS).
Figure 2.
Venn diagram showing the overlap of all detected single nucleotide polymorphisms in the Hanwoo, Jeju Heugu, Chikso, and Korean Holstein genomes.
Figure 3.
Length distribution of insertions–deletions (InDels) in this study.
(A) Total insertion length distribution. (B) Distribution of insertions in coding regions. (C) Total deletion length distribution. (D) Distribution of deletions in coding regions.
Figure 4.
Distribution of copy number variation regions (CNVRs) on the chromosomes.
Pink diamonds on the left of each chromosome indicate CNVR gains in Korean Holstein relative to Hanwoo, Jeju Heugu, and Chikso. Blue squares, green circles, and yellow triangles on the right represent CNVR gains in Hanwoo, Jeju Heugu, and Chikso, respectively.
Table 5.
Distributions and characteristics of putative copy number variation regions (CNVRs) in genome comparisons of Hanwoo, Jeju Heugu, and Chikso with Korean Holstein.
Figure 5.
Copy number variation regions (CNVRs) overlapping the NOS2 gene region.
(A) Log2 ratio plot of the CNVRs overlapping the NOS2 gene region for Hanwoo, Jeju Heugu, and Chikso versus Holstein, respectively. Each point presents the log2 ratio of the number of reads mapped in Korean Holstein versus the Korean native cattle breed. The color gradient indicates the log10 p-value obtained from CNV-seq. (B) NOS2 gene regions in the UCSC Genome Browser. The colors pink, blue, and green indicate genic CNVR gains in Hanwoo, Jeju Heugu, and Chikso, respectively.
Figure 6.
The size distribution of runs of homozygosity (ROHs).
The total ROHs in each breed were plotted with respect to the five size categories (<1 MB, 1–5 MB, 5–10 MB, 10–15 MB, and >15 MB). Breeds from left to right in each size category are Hanwoo, Jeju Heugu, Chikso, and Korean Holstein, which are also highlighted with different colors corresponding to the legend in this figure.