Detecting Positive Selection of Korean Native Goat Populations Using Next-Generation Sequencing.

Goats (Capra hircus) are one of the oldest species of domesticated animals. Native Korean goats are a particularly interesting group, as they are indigenous to the area and were raised in the Korean peninsula almost 2,000 years ago. Although they have a small body size and produce low volumes of milk and meat, they are quite resistant to lumbar paralysis. Our study aimed to reveal the distinct genetic features and patterns of selection in native Korean goats by comparing the genomes of native Korean goat and crossbred goat populations. We sequenced the whole genome of 15 native Korean goats and 11 crossbred goats using next-generation sequencing (Illumina platform) to compare the genomes of the two populations. We found decreased nucleotide diversity in the native Korean goats compared to the crossbred goats. Genetic structural analysis demonstrated that the native Korean goat and crossbred goat populations shared a common ancestry, but were clearly distinct. Finally, to reveal the native Korean goat's selective sweep region, selective sweep signals were identified in the native Korean goat genome using cross-population extended haplotype homozygosity (XP-EHH) and a cross-population composite likelihood ratio test (XP-CLR). As a result, we were able to identify candidate genes for recent selection, such as the CCR3 gene, which is related to lumbar paralysis resistance. Combined with future studies and recent goat genome information, this study will contribute to a thorough understanding of the native Korean goat genome.

Molecular and serologic detection of Coxiella burnetii in native Korean goats (Capra hircus coreanae).

The occurrence of Q fever in native Korean goats (Capra hircus coreanae) was investigated for the first time in the country using ELISA and PCR. A total of 597 blood samples were collected from goats belonging to five different provinces of Korea. To detect Coxiella burnetii, sera were separated from the whole blood and analysed by ELISA; DNA was extracted directly from the whole blood and analysed by PCR. Overall, 114 (19.1%, 95% C.I.=16.1-22.4) and 57 goats (9.5%, 95% C.I.=7.5-12.2) tested positive for C. burnetii in the ELISA- and PCR-based screening, respectively, while 18 goats (3.0%, 95% C.I.=1.9-4.7) tested positive in both the assays. There was a significant difference between the number of ELISA- and PCR-positive goats (P<0.05). The seroprevalence of Q fever was significantly higher among the adult goats (≥1y, 22.0%) than among the young goats (<1y, 13.8%) (P<0.05). While the results of the serologic analysis showed no seasonal variation, data from the PCR-based assay indicated that there were a higher number of positive cases during the cold seasons. Because Q fever infection has high rates of prevalence in native Korean goats, further studies on humans at a high risk of contracting this disease should be conducted. The PCR-based assay used in this study is a useful method for the direct detection of C. burnetii in blood samples from small ruminants.