• Genes and Genomics
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• 제40권12호
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• pp.1319-1329
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• 2018

SSRs were successfully isolated from the Perilla crop in our current study, and used to analyze Perilla accessions from East Asia. Analyses of the clear genetic diversity and relationship for Perilla crop still remain insufficient. In this study, 40 new simple sequence repeat (SSR) primer sets were developed from RNA sequences using transcriptome analysis. These new SSR markers were applied to analyze the diversity, relationships, and population structure among 35 accessions of the two cultivated types of Perilla crop and their weedy types. A total of 220 alleles were identified at all loci, with an average of 5.5 alleles per locus and a range between 2 and 10 alleles per locus. The MAF (major allele frequency) per locus varied from 0.229 to 0.943, with an average of 0.466. The average polymorphic information content (PIC) value was 0.603, ranging from 0.102 to 0.837. The genetic diversity (GD) ranged from 0.108 to 0.854, with an average of 0.654. Based on population structure analysis, all accessions were divided into three groups: Group I, Group II and the admixed group. This study demonstrated the utility of new SSR analysis for the study of genetic diversity and population structure among 35 Perilla accessions. The GD of each locus for accessions of cultivated var. frutescens, weedy var. frutescens, cultivated var. crispa, and weedy var. crispa were 0.415, 0.606, 0.308, and 0.480, respectively. Both weedy accessions exhibited higher GD and PIC values than their cultivated types in East Asia. The new SSR primers of Perilla species reported in this study may provide potential genetic markers for population genetics to enhance our understanding of the genetic diversity, genetic relationship and population structure of the cultivated and weedy types of P. frutescens in East Asia. In addition, new Perilla SSR primers developed from RNA-seq can be used in the future for cultivar identification, conservation of Perilla germplasm resources, genome mapping and tagging of important genes/QTLs for Perilla breeding programs.

• BMB Reports
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• 제56권10호
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• pp.569-574
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• 2023

Aberrant DNA methylation plays a pivotal role in the onset and progression of colorectal cancer (CRC), a disease with high incidence and mortality rates in Korea. Several CRC-associated diagnostic and prognostic methylation markers have been identified; however, due to a lack of comprehensive clinical and methylome data, these markers have not been validated in the Korean population. Therefore, in this study, we aimed to obtain the CRC methylation profile using 172 tumors and 128 adjacent normal colon tissues of Korean patients with CRC. Based on the comparative methylome analysis, we found that hypermethylated positions in the tumor were predominantly concentrated in CpG islands and promoter regions, whereas hypomethylated positions were largely found in the open-sea region, notably distant from the CpG islands. In addition, we stratified patients by applying the CpG island methylator phenotype (CIMP) to the tumor methylome data. This stratification validated previous clinicopathological implications, as tumors with high CIMP signatures were significantly correlated with the proximal colon, higher prevalence of microsatellite instability status, and MLH1 promoter methylation. In conclusion, our extensive methylome analysis and the accompanying dataset offers valuable insights into the utilization of CRC-associated methylation markers in Korean patients, potentially improving CRC diagnosis and prognosis. Furthermore, this study serves as a solid foundation for further investigations into personalized and ethnicity-specific CRC treatments.

• Journal of Animal Science and Technology
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• 제53권1호
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• pp.29-34
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• 2011

본 연구에서는 Landrace, Large White와 Duroc 3품종의 3원 교잡 시스템으로 비육돈을 생산하는 9개 농가를 대상으로 Landrace와 Large White 교배를 통해 생산된 $F_1$ 모돈과 Duroc 웅돈 그리고 비육돈을 이용하여 기 보고한 바 있는 돼지 이력추적 및 브랜드육 식별을 위한 13종의 MS marker의 개체판별능과 혈연관계 추정 효율을 실증하였다. 우선 $F_1$ 모돈과 웅돈 즉 부모 집단을 대상으로 API-CALC version 1.0 프로그램을 이용하여 무작위 교배집단, 반형매 교배집단 그리고 전형매 교배집단으로 가정시 개체 판별능이 각 각 $4.94{\times}10^{-34}$, $8.16{\times}10^{-23}$ 그리고 $2.01{\times}10^{-08}$으로 추정되었으며, 비육돈을 포함한 추정치는 $3.74{\times}10^{-35}$, $5.48{\times}10^{-25}$ 그리고 $2.96{\times}10^{-11}$으로 추정되었다. 또한 Cervus version 2.0을 이용하여 친자감별률을 추정한 결과 100% 인 것으로 추정되었다. 이론적으로 산출된 상기의 수치들을 검증하기 위해 PAPA version 2.0 프로그램을 이용하여 비육돈 전체 452두에 대한 친자감별을 실시한 결과 100% 친부모를 확인 할 수 있었으며, Cervus 프로그램을 이용하여 전체 축군에서 동일한 대립유전자형을 가진 개체의 출현을 조사한 결과 동일개체는 존재하지 않는 것을 확인하였다. 비록 개체 판별능에 대한 실증은 제시한 이론적 판별능에 상응하는 두수를 검증하지는 못하였으나, 친자확인의 경우는 제시한 이론적 효율성 100%는 실증적으로 검증되었다. 따라서 현재 국내에서 행해지는 3 품종 교잡에 의한 비육돈 생산 시스템의 경우 본 연구의 결과로 비추어 볼 때 13 MS marker를 이용하여 체계화된 전산정보와 병행하여 계열화된 생산체계하의 브랜드 단위 또는 지역별 권역으로 구분하는 이력추적이 충분히 가능하다고 사료된다.

• Journal of Animal Science and Technology
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• 제46권4호
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• pp.525-536
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• 2004

본 연구는 돼지의 염색체 7번에 존재하는 주요 경제형질에 관여하는 양적형질 유전자좌위(Quantitative trait loci; QTL)를 밝히기 위해 초성위체 표지인자를 이용하여 유전자지도(연관지도) 작성을 수행하였다. 기준집단의 조성은 이형접합성이 높은 기준집단을 조성하기 위하여 유전적 특성이 현격히 다른 우리나라의 재래돼지와 Landrace를 전형매 교배하여 생산된 $F_2$ 183두를 사용하였으며 기준집단에 대해 도축 24시간 후의 pH, 육색, 육즙손실량, 전단력, 가열감량, 조지방, 조회분, 수분, 조단백질 등 육질형질을 조사 및 분석하였다. 염색체 7번의 연관지도는 총 23개의 표지인자로 작성되었으며 암수평균 연관지도 길이는 154.6 cM 이었으며 수컷과 암컷의 연관지도 길이는 각각 169.2 cM과 141.4 cM로 수컷의 연관지도 길이가 암컷의 것보다 27.8 cM 더 길었다. 표지인자간의 최소간격은 SW175와 S0066 표지인자사이로 1.6 cM이었고, 최대간격은 SW2002와 SWR773표지인자사이로서 15.9 cM이었으며 평균간격은 7.02 cM이었다. 본 연구에서는 9개의 육질관련 형질 중 육색과 연관된 2개의 QTL이 확인되었는데 적색도(CIE-a)와 연관된 QTL은 45 cM 영역에서 1% 수준의 통계적 유의성을 나타내었고(Fig. 2), 이 영역에서 불과 3${\sim}$4 cM 떨어진 위치에서 황색도(CIE-b)와 연관된 QTL이 확인되었다. 향후에 본 연구에서 탐색된 QTL 영역에 대하여 고밀도의 유전자 지도 작성을 통하여 특정 형질과 연관된 부분을 계속해서 추적해 나간다면 육색형질을 조절하는 주유전자의 클로닝 및 특성 구명이 가능할 것으로 사료되며 궁극적으로는 돼지의 개량에 효율적으로 활용할 수 있는 표지인자(MAS)의 개발 등도 가능 할 것으로 사료된다.

• 한국어류학회지
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• 제32권4호
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• pp.199-209
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• 2020

본 연구는 예전부터 혼란스러웠던 한국산 대주둥치속, Macroramphosus 어류의 분류학적 위치를 명확히 하기 위해, 한국산 18개체를 일본/대만산 35개체 및 지중해산 M. scolopax와 형태 및 분자 변이를 비교 분석하였다. 한국, 일본 및 대만산 대주둥치속 어류는 제1등지느러미 극조 길이(A-type은 22.8~32.1%, B-type은 15.6~21.4%), 제1등지느러미와 제2등지느러미 사이 길이(A-type은 6.4~9.7%, B-type은 8.6~13.3%), 체고(A-type은 20.0~28.0%, B-type은 17.3~22.6%)에서 두 type으로 명확히 구분되었으나, 유전적으로는 구분되지 않았다(CR에서 0.0~3.3%, cyt b에서 0.0~1.3%, COI에서 0.0~0.5%). 한편, 한국산 대주둥치는 지중해산 M. scolopax와 유전적으로 명확히 구분되어(CR에서 9.9~11.5%, cyt b에서 3.8~4.6%, COI에서 1.2~3.6%), 최근 사용하고 있는 학명 M. scolopax를 M. japonicus (및/또는 M. sagifue)로 변경해야 할 것이다. 그러나, 본 연구에서 두 type 간 형태변이와 분자변이 간 일치성을 찾지 못했으며, 이는 아마도 그들간에 분화가 상당히 최근에 일어났음을 시사한다. 두 type 간 유전자 교류 정도를 파악하려면 향후 microsatellite와 같은 보다 민감한 마커를 이용한 후속 연구가 필요할 것이다.

• 원예과학기술지
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• 제30권5호
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• pp.557-567
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• 2012

본 연구는 마커이용여교잡(marker-assisted backcross, MAB)을 통한 내병성 토마토 신품종육성에 필요한 기초 정보를 얻기 위해 수행되었다. TYLCV, 시들음역병, 청고병, 흰가루병에 내병성인 공여친 계통 10종과 이병성이지만 우수 원예형질을 지닌 회복친 계통 4종에 대해 병리검정과 TYLCV 내병성 연관 분자마커 분석을 수행하였다. MAB를 위한 회복친 유전자 선발(background selection)용 마커개발을 목표로 SOL Genomics Network에 공시된 토마토 유전자지도(reference map)로부터 전 게놈에 균등히 분포된 108개(염색체 당 평균 9개) SSR 마커를 분석하여, 총 303개의 다형성 마커를 기반으로 공여친, 회복친 계통 간 유연관계를 분석하였다. 그 결과, 유사도 값의 전체 범위는 0.33-0.80으로계통 간 가장 높은 유사도 값(0.80)을 나타낸 것은 청고병에 저항성인 '10BA333'와 '10BA424'이었고, 가장 낮은 유사도 값(0.33)을 나타낸 것은 시들음역병에 내병성인 야생종 L3708(Solanum pimpinelliforium L.)과 청고병에 저항성인 '10BA424'이었다. 유사도 값을 이용하여 UPGMA 분석한 결과, 유사도 0.58를 기준으로 나누었을 때 3개의 군(cluster)으로 분류되었는데, 대부분 동일한 내병성을 지닌 공여친계통 간 유전적 거리가 가까워 이들은 공통된 저항성 재료를 이용한 육성과정에서 파생된 계통일 것이라 판단되었다. 계통수(dendrogram)를 기준으로 유전적 거리가 지나치게 멀지 않으면서 비교적 다수의 회복친 유전자 선발용 SSR 마커의 확보가 가능한 여교배 조합(공여친 ${\times}$ 회복친)은 TYLCV 내병성의 경우 'TYR1' ${\times}$ 'RPL1', 청고병의 경우 '10BA333' 또는 '10BA424' ${\times}$ 'RPL2', 흰가루병의 경우 'KNU12' ${\times}$ 'AV107-4' 또는 'RPL2'로 판단되었다. 시들음역병의 경우 내병성 공여친인 'L3708'은 야생종으로서 모든 회복친 계통들과 유전적 거리가 매우 멀었으며, 적절한 조합은 유사도 값이 0.41이며 계통 간 45개의 다형성 SSR 마커가 선발된 'L3708' ${\times}$ 'AV107-4'로 판단되었다.

• Asian-Australasian Journal of Animal Sciences
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• 제22권10호
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• pp.1351-1358
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• 2009

Parentage tests using polymorphic DNA marker are commonly performed to avoid incorrect recording of the parental information of livestock animals, and single-nucleotide polymorphisms (SNPs) are becoming the method of choice. In Japanese Black cattle, parentage tests based on the exclusion method using microsatellite markers are currently conducted; however, an alternative SNP system aimed at parentage tests has recently been developed. In the present study, two types of simulations were conducted using the pedigree data of two subpopulations in the breed (subpopulations of Hyogo and Shimane prefectures) in order to examine the effect of actual genetic and breeding structures. The first simulation (simulation 1) investigated the usefulness of SNPs for excluding a close relative of the true sire; the second one (simulation 2) investigated the accuracy of sire identification tests for multiple full-sib putative sires by a combined method of exclusion and paternity assignment based on the LOD score. The success rates of excluding a single fullsib and sire of the true sires were, respectively, 0.9915 and 0.9852 in Hyogo and 0.9848 and 0.9852 in Shimane, when 50 SNPs with minor allele frequency (MAF: q) of 0.25${\leq}$q${\leq}$0.35 were used in simulation 1. The success rates of sire identification tests based solely on the exclusion method were relatively low in simulation 2. However, assuming that 50 SNPs with MAF of 0.25${\leq}$q${\leq}$0.35 or 0.45${\leq}$q${\leq}$0.5 were available, the total success rates including achievements due to paternity assignment were, respectively, 0.9430 and 0.9681 in Hyogo and 0.8999 and 0.9399 for Shimane, even when each true sire was assumed to compete with 50 full-sibs.

• 한국자원식물학회지
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• 제25권6호
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• pp.762-772
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• 2012

The objective of this study was to analyze the genetic diversity using SSR marker and investigate the fatty acid composition of perilla (P. frutescens var. frutescens) germplasm. Genetic diversity among 95 accessions, which consisted of 29 weedy types and 66 landrace accessions, was evaluated based on 12 SSR markers carrying 91 alleles. The mean values of observed ($H_O$) and expected heterozygosities ($H_E$) were 0.574 and 0.640, respectively, indicating a considerable amount of polymorphism within this collection. A genetic distance-based phylogeny grouped into two distinct groups, which were the landrace, moderate and weedy type, genetic distance (GD) value was 0.609. The physicochemical traits about crude oil contents and fatty acid compositions were analyzed using GC. Among tested germplasm, the total average oil contents (%) showed a range from 28.57 to 49.67 %. Five fatty acids and their contents in the crude oils are as follows: ${\alpha}$-linolenic acid (41.12%-51.81%), linoleic acid (15.38%-16.43%), oleic acid (18.93%-27.28%), stearic acid (2.56%-4.01%), and palmitic acid (7.38%-10.77%). The average oil content of wild types was lower than landrace, and the oil content of middle genotype accessions was higher than other germplasm, but no significant variation between landrace and wild types was shown. Nevertheless, IT117174, landrace of Korea, was highest in crude oil content (47.11%) and linolenic acid composition (64.58%) among the used germplasm. These traits of the selected accessions will be helped for new functional plant breeding in perilla crop.

• Asian-Australasian Journal of Animal Sciences
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• 제16권7호
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• pp.946-951
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• 2003

The Genetic diversity and relationship of native Siri (Bos indicus) cattle populations of Bhutan were evaluated using 20 microsatellite markers. A total of 120 Siri cattle were sampled and were grouped into four populations according to their geographical locations which were named Siri West, Siri South, Siri Central and Siri East cattle. For each, 30 individuals were sampled. In addition, 30 samples each of Indian Jaba (B. indicus), Tibetan Goleng (B. taurus), Nepal Hill cattle (B. indicus), Holstein Friesian (B.taurus) and Mithun (B. frontalis) were typed. The mean number of alleles per loci (MNA) and observed heterozygosity (Ho) were high in the Siri populations ($MNA=7.2{\pm}0.3$ to $8.9{\pm}0.5$ and $Ho=0.67{\pm}0.04$ to $0.73{\pm}0.03$). The smallest coefficient of genetic differentiation and genetic distance ($F_{ST}=0.015$ and $D_A=0.073$) were obtained between Siri West and Siri Central populations. Siri East population is genetically distinct from the other Siri populations being close to the Indian Jaba ($F_{ST}=0.024$ and $D_A=0.084$). A high bootstrap value of 96% supported the close relationship of Siri South, Siri Central and Siri West, while the relationship between Siri East and Jaba was also supported by a high bootstrap value (82%). Data from principal component analysis and individual assignment test were in concordance with the inference from genetic distance and differentiation. In conclusion we identified two separate Siri cattle populations in Bhutan at the genetic level. One population included Siri cattle sampled from the West, Central and South of the country and the other Siri cattle was sampled from the East of the country. We suggest that Siri cattle conservation program in Bhutan should focus on the former population as it has received less genetic influence from other cattle breeds.

• Asian-Australasian Journal of Animal Sciences
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• 제30권8호
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• pp.1061-1065
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• 2017

Objective: This study was conducted to locate quantitative trait loci (QTL) influencing fatty acid (FA) composition in a large $F_2$ intercross between Landrace and Korean native pigs. Methods: Eighteen FA composition traits were measured in more than 960 $F_2$ progeny. All experimental animals were genotyped with 165 microsatellite markers located throughout the pig autosomes. Results: We detected 112 QTLs for the FA composition; Forty seven QTLs reached the genome-wide significant threshold. In particular, we identified a cluster of highly significant QTLs for FA composition on SSC12. QTL for polyunsaturated fatty acid on pig chromosome 12 (F-value = 97.2 under additive and dominance model, nominal p-value $3.6{\times}10^{-39}$) accounted for 16.9% of phenotypic variance. In addition, four more QTLs for C18:1, C18:2, C20:4, and monounsaturated fatty acids on the similar position explained more than 10% of phenotypic variance. Conclusion: Our findings of a major QTL for FA composition presented here could provide helpful information to locate causative variants to improve meat quality traits in pigs.