Whole-Genome Sequencing Mapping of Candidate Genes of Cervus Nippon Hortulorum, Presumed to be Sika Deer from the Korean Peninsula
Whole-Genome Sequencing Mapping of Candidate Genes of Cervus Nippon Hortulorum, Presumed to be Sika Deer from the Korean Peninsula
Yong Su Park1a, Dong Won Seo2a, You Sam Kim2, Myung Hum Park2, Min Jee Oh3, Sang Hwan Kim3,4*
ABSTRACT
The deer known as Sika deer, which has been extinct in Korea since 1920, is known to be a very important biological resource in Korea, but it is very difficult to establish a standard for Korean deer due to indiscriminate introduction. In particular, the genetic diversity and phylogenetic relationships of various subspecies of deer are known to be uncertain, so securing deer genes that can represent Korea is very important. We found a document observing Sika deer near the 38th parallel, and we were confident that this deer would inhabit North Korea and the Russian Maritime Province. Therefore, in this study, in order to explore the phylogenetic relationships of various Sika deer, we collected samples of Sika deer living around the Maritime Province and North Korea that had the morphology suggested in the literature, collected mtDNA of the deer, and analyzed whole-genome sequencing (WGS) to determine whether they could be classified as subspecies of Cervus nippon hortulorum in the Korean Peninsula. 11 Sika deer with similar morphology to those presented in ancient literature were finally selected. Most of the sequence reads of the mtDNA gene sequence were mapped to a 2.8 Gbp region, which is 97.6% of the total region in all reads mapping. The average number of reads was confirmed to be 708,020,765. The experimental flower deer group possessed an average of 19,994,130 SNP mutations along with 996,204 insertions and 1,050,106 deletions, thus exhibiting a clear difference from the previously reported Japanese Cervus nippon hortulorum population and suggesting that it may have been a deer native to the Korean Peninsula.
Keywords | Cervus nippon, Whole genome sequencing, Single-nucleotide polymorphism, Sika deer, MtDNA, Korea
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January 2025
Adv. Anim. Vet. Sci., Vol. 13, Iss. 1, pp. 1-216
