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

Lee, Wonseok,Ahn, Sojin,Taye, Mengistie,Sung, Samsun,Lee, Hyun-Jeong,Cho, Seoae,Kim, Heebal Korean Society for Molecular and Cellular Biology 2016 Molecules and cells Vol.39 No.12

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 cross-bred 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.

mtDNA Diversity and Phylogenetic Analysis of Korean Native Goats

Jae-Hwan Kim(김재환),Chang-Yeon Cho(조창연),Seong-Bok Choi(최성복),Young Moo Cho(조영무),Seung-Hum Yeon(연성흠),Suk Yang(양보석) 한국생명과학회 2011 생명과학회지 Vol.21 No.9

한국재래염소는 흑모색의 특징을 나타내며, 유일한 염소 품종으로서 오랫동안 한반도에서 사육되어 왔다. 하지만 이들에 대한 유전적 다양성, 계통유전학적 분석 등을 통한 기원 추정 등에 대한 연구는 미비한 실정이다. 본 연구에서 한국재래염소 5개 집단, 60두를 대상으로 mtDNA D-loop 영역 중 HVI 영역의 서열을 이용하여 유전적 다양성 및 계통유전학적 분석을 실시하였다. 한국 재래염소는 다른 나라 염소들에 비해서 haplotype 다양성 지수가 낮게 나타났다. 또한 본 연구에서 분류된 한국재래염소 10개 haplotype 중 현재까지 보고되지 않은 6개의 새로운 haplotype이 확인되었다. 계통유전학적 분석 결과, 분석에 사용된 모든 한국재래염소는 mtDNA 모계혈통 A에 속하였다. 10개의 haplotype 중 8개는 베트남, 일부 중국 염소와 함께 subgroup을 형성하였다. 그러나 나머지 2개 haplotype은 각각 서로 독립적인 계통유전학적 위치를 보였다. 이런 결과들을 토대로 한국재래염소는 상대적으로 높은 근친상황으로 외부 유전자 유입이 적었을 것이라고 추정된다. 한국재래염소의 새로운 mtDNA haplotype의 발견 및 유전자원 보존 및 평가를 위해서 더 많은 분석집단 및 개체를 수집하고, MS 마커를 이용한 추가분석이 필요하다고 사료된다. Korean native goats, which are characterized by black coat color, have existed on the Korean peninsula for a long time. Until now, there has been no comprehensive investigation concerning their genetic diversity, phylogenetic analysis or origin. In this study, we investigated the genetic diversity and verified phylogenetic status of the Korean native goat using the 453-bp fragment of the hypervariable fragment I (HVI) of mitochondrial DNA (mtDNA) D-loop region from 60 individuals among 5 populations. The Korean native goat showed less haplotype diversity when compared with goats from other countries. In addition, 6 haplotypes that had not been previously reported were verified in this study. In phylogenetic analyses with other country"fs goats, 10 haplotypes from Korean native goats were classified into mtDNA lineage A. Moreover, in a phylogenetic tree for goats which contained mtDNA lineage A, 8 of 10 haplotypes could be included in a subgroup with goats from Vietnam and an area of China. However, none of the remaining haplotypes belonged to a major group of Korean native goats and were located on different independent positions. These results suggest that almost Korean native goats aligned more closely to China and Vietnam breeds in mtDNA lineage A and there was no gene flow from other mtDNA lineages. Our results will contribute to conservation strategies and genetic breeding of Korean native goats.

한국재래산양의 핵형분석

오승현,윤영민,윤여성,이준섭,이흥식,성제경,Oh, Seung-hyun,Yun, Young-min,Yoon, Yeo-sung,Lee, Joon-sup,Lee, Heungshik S.,Seong, Je-Kyung 대한수의학회 1999 大韓獸醫學會誌 Vol.39 No.5

We investigated the cytogenetic characteristics of Korean native goat(Capra hircus). Chromosome slides were prepared from peripheral blood cell cultures. GTG, GBG, RBG and CBG-banding techniques were employed on those slides. The high resolution karyotype of Korean native goat could be made with the incorporation of BrdU. Korean native goat has 60 chromosomes composed of 58 autosomes and XY or XX sex chromosomes. All of autosomes of Korean native goat were acrocentric chromosomes. X chromosome was submetacentric and Y chromosome was metacentric. The GTG, GBG and RBG-band patterns of Korean native goat were similar to those of other goats. CBG-band regions were distinct at the proximal portion of the long arms of all autosomes in Korean native goats. According to our investigation, there was no significant difference in chromosomal band patterns between Korean native goat and other goats. It might be necessary to use molecular genetic markers for clarifying the genetical characteristics of Korean native goat whose biological characteristics are not clearly defined.

호남지역의 양축농가에 있어서 UR에 대처한 가축의 생산성 향상에 관한 연구

이주묵,권오덕,채준석,김명철,김흥섭,이성재,이후식,노수일,김길수,Lee, Joo-mook,Kwon, Oh-deog,Chae, Joon-seok,Kim, Myeong-chul,Kim, Heung-seob,Lee, Sung-jae,Lee, Hoo-sik,Roh, Soo-il,Kim, Kil-soo 대한수의학회 1994 大韓獸醫學會誌 Vol.34 No.1

For the purpose to increase productivities of livestock the present investigations were undertaken in order to clarify the clinical and suclinical status of Korean native cattle, dairy cattle(holstein) and Korean native goat. Blood, feces and urine samples were collected from 247 Korean native cattle(222 adult and 25 calf), 224 dairy cattle(211 adult and 13 calf) and 142 Korean native goat rearing at Chonbuk area and analyzed for clinical, serum chemical, hematological and urinary findings. In addition, we were examined the infection rate of theileriosis, internal parasite and ring worm. The mean value for each component was calculated by statistical analysis using Excel computer program. From these investigations the following results were obtained. The mean values for RBC, PCV and etc in 433 adult cow(Korean native cattle and dairy cattle) were similar with other reports. But the mean values for MCHC of all species were lower than normal. Adult Korean native cattle and adult dairy cattle which showed hematologically normal levels were only 9.01% and 9.48%, respectively. Abnormally high values for PCV, RBC and Hb were recorded in 7.66% of adult Korean native cattle, 20% of korean native calf, 15.38% of dairy calf and 13.36% of Korean native goat. Adult Korean native cattle and adult dairy cattle which showed hematologically anemia were 4.95% and 19.43% respectively, but Korean native calf and dairy calf showed normal. Adult Korean native cattle, adult dairy cattle, Korean native calf and dairy calf which showed normal serum protein level 84.0%, 90.8%, 50% and 44.4%, respectively. In present investigations, 50% of Korean native calf and 55.6% of dairy calf were decreased serum protein values under range. These abnormally decreased serum protein values mean the shortage of antibody, and these have a possibility to occurs to pneumonia and diarrhea. From these results, the economical loss caused by pneumonia was calculated as 124,038,833 won in the KNC and 742,703,430 won in the dairy calf rearing in Chonbuk area. Calculated economical loss caused by enteritis was 56,658,690 won in Korean native cattle, 476,775,799 won in dairy calf, and the total loss amount of 533,434,488 won in Chonbuk area. Abnormally high values$(21.7{\pm}4.0mg/dl)$ for serum calcium were recorded 49.6% in dairy cattle. The mean values for serum total cholesterol were $170.8{\pm}99.8mg/dl$ in Korean native cattle, $196.0{\pm}40.6mg/dl$ in Korean native calf, $202.9{\pm}86.0mg/dl$ in adult dairy cattle and $289.4{\pm}97.5mg/dl$ in dairy calf. The infection rate of internal parsite were as follows; adult Korean native cattle: 21.2%, Korean native calf: 8.0%, adult dairy cattle: 67.8% and Korean native goat: 81.5%. The estimated economical loss caused by internal parasites infection were 1,120,855,837 won in Korean native calf, 4,994,959,405 won in adult Korean native cattle, 3,334,751,066 won in adult holstein, and the total loss amount to 9,450,566,308 won. The infection rate of theileriosis were 1.4% in Korean native cattle and 6.6% in dairy cattle. The presumed economical loss by T. sergenti infection were 154,408,482 won in Korean native cattle and 171,577,237 won in dairy cattle rearing at Chonbuk area. The infection rate of ringworm were 0.5% in Korean native cattle, 0.9% adult dairy cattle and 7.7% in dairy calf. The presumed economical loss by dermatomycophyte were 12,061,532 won in Korean native cattle, 16,895,403 won in dairy cattle, and the total estimated loss amount to 28,955,935 won a year in Chonbuk area.

A Study on the Dry Matter Yield and Nutritive Values of Wild Korean Lespedeza (Lespedeza stipulacea Maxim.)

Lee, Hyung Suk,Lee, In-Duk Asian Australasian Association of Animal Productio 2002 Animal Bioscience Vol.15 No.3

This study was conducted to evaluate the dry matter (DM) yield, quality and utilization of nutrients in Korean lespedeza (Lespedeza stipulacea Maxim.) swards as a roughage source. DM yield in various stages, chemical composition, and DM digestibility were observed, and DM intake, digestibility and utilization of nitrogen and energy by Korean native goat were determined. Experimental diets include three treatments: mixture hay (MH) 100%, MH (80%)+wild Korean lespedeza hay (LH) 20% and MH (60%)+LH (40%). As growth stage advanced, the DM yield of Korean lespedeza tended to increase significantly (p<0.05). The mean DM yield of all growing stages was observed as 7,336 kg/ha. Crude protein (CP) content of Korean lespedeza tended to decrease, but fibrous contents tended to increase when the growth stage advanced. The tannin content of Korean lespedeza was the highest at the bud stage (64.7 mg/g). However, it showed a tendency to decrease as the growth stage advanced, and thus it was the lowest at the ripe seed stage (26.8 mg/g) (p<0.05). With increasing level of LH, voluntary DM intake by Korean native goats slightly increased, but no differences were observed between diets. The digestibility of DM, cellular constituents and NDF was slightly higher in LH containing diets than that of MH 100% diet (p<0.05). There was no significant difference in apparently digested N% among all diets, but retained N% and retained N% of the absorbed were higher in MH (60%)+LH (40%) than those of other diets (p<0.05). A difference in the utilization of energy was not detected. In conclusion, Juvenile LH improved the digestibility of nutrients, presumably due to its high CP content and low fibrous compound. Especially, tannin in LH did not affect in DM intake, but increased the nitrogen utilization of Korean native goats. Accordingly, it could be suggested that Korean lespedeza has a potential to be provided as a roughage source for Korean native goats.

PCR 기법을 이용한 한국재래산양 β-casein 유전자의 특성

김지애,류승희,유성란,이준헌,서길웅,김선균,상병찬 충남대학교 농업과학연구소 2002 농업과학연구 Vol.29 No.2

본 연구는 한국 재래 산양 112두와 유산양인 Saanen종 7두의 혈액으로부터 genomic DNA를 추출하고, PCR-RFLP 방법에 의해 β-casein 유전자의 특성을 분석하여 한국재래산양의 효율적인 유전자원의 보전 및 개량을 위한 기초 자료로 제공하고자 실시하였다. 한국재래산양의 genomic DNA로부터 PCR기법을 이용하여 β-casein의 유전자좌를 증폭한 결과 각각 481bp 크기의 단편이 양호하게 증폭되었음을 확인하였다. β-casein 유전자좌의 증폭산물에 대한 Bal Ⅰ의 제한효소를 처리한 결과, β-casein AB형은 481bp, 284bp 및 197bp의 단편을, 그리고 BB형은 284BP와 197BP의 단편을 한국재래산양과 유산양인 Saanen 종에서 확인 할 수 있었다, 유전자형 빈도에 있어서는 한국재래산양에서 β-casein AB 및 BB의 빈도는 각각 6.25 및 93.75%이었고, 유산양인 Saanen 종은 각각 57.14 및 42.86%이었다. 유전자빈도에 있어서는 한국재래산양의 β-casein A 및 B의 빈도가 각각 0.031 및 0.969이었고, Saanen 종에서는 각각 0.286 및 0.714의 빈도를 보였다 한국재래산양의 β-casein 유전자의 염기서열과 이미 보고되어 있는 goat의 염기서열(GeneBank accession Number M90556)간에는 총 11개의 염기서열에 차이를 나타내어 97.71%의 상동성을 보였다, 따라서 한국재래산양의 β-casein 유전자의 다형성과 염기서열 분석에 의한 분자유전학적 특성의 규명은 한국재래산양의 유전자원의 보전 및 개량을 위한 기초 및 응용 자료로 이용될 수 있을 것으로 생각된다. This study was performed to provide the basic data for preservation and improvement of genetic resources according to finding genetic construction obtained from analysis of genetic characteristics of β-casein gene in Korean Native goat and Saanen using the PCR-RFLP. This study confirmed the amplified products of 481bp fragments obtained from the amplification of β-casein loci by PCR. The β-casein AB genotype showed 481, 284 and 197bp, and β-casein BB genotype showed 284 and 197bp fragments in Korean Native goat and Saanen. The frequencies of β-casein genotype in Korean Native goat were 6.25 and 93.75% for AA and AB and the frequencies of β-casein genotype in Saanen were 57.14 and 42.86% for AA and AB types. The frequencies of β-casein A and B alleles were 0.031 and 0.969 in Korean Native goat and the frequencies of β-casein A and B alleles are 0.286 and 0.714 in Saanen, respectively. The nucleotide sequence of β-casein gene of Korean Native goat was 97.71% higher homology with 11 nucleotide sequences difference of that of goat reported in GeneBank (M90556). Therefore, this study of molecular genetic characteristics by the analysis of genetic polymorphism and sequencing for β-casein gene should be used as basic and applying data for preservation and improvement of genetic resources in Korean Native goat breeding.

전북지역 염소에서 Coxiella burnetii 감염실태 조사

강수진 ( Su-jin Gang ),정재명 ( Jae-myong Jeong ),김현관 ( Hyun-kwan Kim ),이재욱 ( Jae-wook Lee ),손구례 ( Ku-rye Shon ),박태욱 ( Tae-wook Park ) 한국가축위생학회 2016 韓國家畜衛生學會誌 Vol.39 No.4

The prevalence of Coxiella burnetii in native Korean goats in Jeonbuk province was investigated using ELISA (sera) and PCR (vaginal mucus). A total of 798 blood samples from 189 farms were collected in 2013 and 2015. Sero-prevalence was 13.6% in 2013 and 15.7% in 2015. Tracking survey of six seropositive farms on the prevalence of C. burnetii was conducted. 137 (41.4%) out of 331 goats were seropositive and 47 (17.6%) out of 267 goats were positive in PCR. The higher seropositivity observed in adult goats and female goats significantly, the seroprevalence of C. burnetii was higher as age increased (<1 y=13.2%∼≥5 y=100%)(P<0.05) and female goats (44.8%) was higher than male goats (24.1%) on the seroprevalence (P<0.05). 21 (7.9%) goats positive in PCR was seronegative. The prevalence of C. burnetii in native Korean goats in slaughter house was 30.0% in ELISA and 11.5% in PCR. Significantly, female goats (62.8%) was higher than male goats (12.3%) on the seroprevalence (P<0.05). Based on these data, C. burnetii was easily exposed in domestic animals: native Korean goats-related areas such as farms and slaughter house.

The Use of Apple Pomace in Rice Straw Based Diets of Korean Native Goats(Capra hircus)

Ahn, J.H.,Jo, I.H.,Lee, J.S. Asian Australasian Association of Animal Productio 2002 Animal Bioscience Vol.15 No.11

In this study, three different experiments were conducted to evaluate the nutritional value of apple pomace produced in southern areas of the Republic of Korea (South Korea). The effects of combining apple pomace in different ratios with commercial concentrates and rice straw in the diets of Korean native goats (Capra hircus) were examined. In experiment I, in situ DM and CP disappearances from nylon bags incubated in the rumen of goats showed that greater amounts of DM and CP were released from apple pomace than those from concentrates at the later stages of incubation, but only after 48 h for DM and CP, respectively. This was reflected in the higher 'b' value of the slowly degradable fraction of the apple pomace compared to the concentrates. Prior to these times the trend was reversed. In experiment II, Korean native goats were fed a diet containing apple pomace with either rice straw or rice straw and concentrates, and the in vivo nutrient digestibilities compared to animals receiving an alfalfa hay. DM digestibility in the animals given apple pomace plus concentrates with rice straw (66.86%) were similar to the goats given alfalfa hay only (69.09%) but significantly greater than for a diet of rice straw plus concentrates. In experiment III, an in vivo study was conducted to investigate the inclusion of 30 to 60% apple pomace pre-mixed with rice straw, rice bran and concentrates on the nutritional value for Korean native goats. Apple pomace mixed diets had higher DM intakes, nutrient digestibility and nitrogen retention than diets without apple pomace, which may have been due to the higher non-structural carbohydrates (NSC) and less ADF and NDF than those in other treatments. Replacement of concentrates with apple pomace in rice straw based diets of Korean native goats fed either separately (experiment II) or by pre-mixing (experiment III) gave satisfactory feed intake, digestibility, pH of ruminal fluid and production of $NH_3$-N and VFA in the rumen of goats. The results of this study infer that apple pomace can be included at levels of up to 60% in the diets of goats without dramatic effect on the animal.

흑염소의 林內放牧이 산림에 미치는 영향(豫報)

전문장,송해범,임해수 대구대학교 농업과학연구소 1992 農業科學硏究論文集 Vol.6 No.-

This study investigated the effects of forest-grazing of the Korean Native goats, Capra hircus, at three different areas of Kyung-sangbuk-do(Province) for a year(Oct. 1991 to Oct. 1992). The grazing of the Korean Native goats were led by leaders of the three areas. From this study, there were no significant damages of gnawing or peeling of standing trees. At the same time, soil erosion by forest-grazing was not observed either. But this study found that some damages on the browse of undergrowth trees and the herbaceous plants were observed. Especially, twiners such as arrowroot, Pueraria lobata, were favorite food for the Korean Native goats. If various field survey and researches on the forest-grazing of the Korean Native goats are performed in the future, it is possible to establish efficient management system for the forest-grazing of the Korean Native goats.

재래흑염소의 형태적 특징 및 생육특성

이상훈(Sang-Hoon Lee),이진욱(Jinwook Lee),전다연(Dayeon Jeon),김승창(Seungchang Kim),김관우(Kwan-Woo Kim) 한국산학기술학회 2019 한국산학기술학회논문지 Vol.20 No.8

본 연구는 우리나라 고유 재래흑염소 유전자원인 당진계통, 장수계통 및 통영계통의 특성을 조사하였다. 재래흑염소 형태적 특징을 조사한 결과 장수계통과 통영계통의 모색은 전신 흑색을 나타내었으며 당진계통은 흑색 또는 흑갈색으로 긴 털의 특징이 뚜렷하게 나타났다. 일부 개체에서 이모색이 출현하였고 당진계통, 장수계통 및 통영계통 순으로 그 비율이 높게 조사되었다. 재래흑염소의 계통별 육염과 뿔의 유무를 조사한 결과 통영계통에서만 육염이 출현하지 않았으며 당진계통의 암염소와 숫염소에서 각각 1개체씩 무각의 특성을 보였다. 또한 귀의 길이와 꼬리의 길이는 암염소와 숫염소가 거의 비슷한 경향을 보였으나 뿔의 길이와 수염의 길이는 숫염소가 암염소에 비해 긴 것으로 조사되었다. 재래흑염소의 체중을 조사한 결과 생시체중은 평균 2 kg이며, 숫염소가 암염소 보다 조금 높은 경향을 보였으며 3개월령의 이유 시 체중은 모든 계통에서 숫염소가 암염소 보다 조금 높았으며 12개월령의 체중도 암염소가 계통별 16.5~19.3kg, 숫염소가 18.3~22.2 kg으로 높게 조사되었다. 재래흑염소의 체형을 조사한 결과 계통별 체장과 체고는 숫염소가 암염소보다 약간 컸으며, 흉폭과 흉위는 계통 및 성별간의 차이가 나타나지 않았다. 본 연구 결과는 재래종 염소와 교잡종 염소를 구분할 수 있는 기준 마련과 나아가 재래흑염소 개량을 위한 기초자료로 이용될 것이다. This study aims to provide basic data for investigating the phenotypic traits and growth characteristics of Korean native black goats. The Jangsu and Tongyoung strains were shown to have black hair, while the Dangjin strain was shown to have black or dark brown long hair. Only the Tongyeong strain was found to have no wattle and one goat each from the females and males of the Dangjin strain was found to have no horns. The lengths of the ears and tails were similar for the female and male goats, while the lengths of horns and beards were longer in the male goats. The birth weight was 2 kg on average, with that of male goats tending to be slightly heavier than that of the females. Weights at the weaning period were found to be slightly heavier for the males. Also, at 12 months, the weights of the male goats by strain were shown to be heavier than that of the females. The body length and depth by strain were found to be higher for the male goats, while no differences in the chest width and girth between the strains or gender were found. These findings are expected to be used as a basis for differentiating between native and crossbred Korean black goat strains and for improving Korean native black goats.