• 제목/요약/키워드: SNP markers

검색결과 303건 처리시간 0.023초

소아 IgA 신병증 환자에서 임상병리 양상과 CCL-2 및 CCL-5 유전자 다형성의 연관성 연구 (Association Study between CCL-2 and CCL-5 Polymorphisms and Clinicopathological Characteristics of Childhood IgA Nephropathy)

  • 한원호;서진순;조병수
    • Childhood Kidney Diseases
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    • 제14권1호
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    • pp.51-61
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    • 2010
  • 목 적 : 최근 Chemokine (C-C motif) ligand-2 (CCL-2; also known as MCP-1)와 CCL-5 (also known as RANTES)가 다양한 염증성 및 비염증성 신질환과 연관성을 보인다는 연구결과들이 보고되고 있다. 이에 본 저자들은 CCL-2 및 CCL-5 유전자의 단일염기다형성(single nucleotide polymorphism; SNP)가 소아 IgA 신병증의 발생 및 임상양상과 어떠한 연관성을 보이는지 알아보기 위하여 본 연구를 시행하였다. 방 법 : 경희의료원 소아청소년과에서 학교 검뇨상 이상소견을 보여 전원된 환아 중 신생검을 통해 IgA 신병증으로 확진된 196명의 소아환아와 285명의 건강한 대조군을 대상으로 geneotyping을 통해 6 개의 SNP 대립 유전자 빈도를 조사하여 분석하였다. 또한, 단백뇨(>4 mg/$m^2$/hour), 병리 소견 상 족세포의 족돌기 융합과 병리학적 진행성 병변의 유무에 따라 환자군을 다시 세 개의 하위그룹으로 세분화하여 비교하였다. 결 과 : IgA 신병증 환아 및 대조군의 SNP 대립 유전자 빈도를 분석하였을 때, CCL-2 및 CCL-5 유전자 모두에서 질환의 발생과 연관성을 보이는 SNP는 발견되지 않았다. 두 개의 linkage disequilibrium block이 형성되었으나 하플로타입 분석에서는 유의한 하플로타입을 찾을 수 없었다. 또한, 환자의 하위그룹을 비교하였을 때에도 단백뇨, 병리 소견 상 족세포의 족돌기 융합과 병리학적 진행성 병변과 연관성을 보이는 SNP는 발견되지 않았다. 결 론 : 한국 소아 환자를 대상으로 시행한 본 연구에서 CCL-2 및 CCL-5유전자 다형성과 IgA 신병증의 임상병리 양상 간에 유의한 연관성은 없었다.

닭의 모색 연관 유전자인 MC1R, MITF, TYRP1의 SNP(Single Nucleotide Polymorphism) 규명 (Identification of SNP(Single Nucleotide Polymorphism) from MC1R, MITF and TYRP1 associated with Feather Color in Chicken)

  • 김병기;변윤화;하재정;정대진;이윤석;형기은;여정수;오동엽
    • 한국가금학회지
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    • 제41권1호
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    • pp.29-37
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    • 2014
  • 닭을 구분하는데 있어 가장 눈에 띠는 것이 모색이며, 모색 관련 유전자인 MC1R, MITF, TYRP1의 SNP에 따른 유전자형을 확인하고, 각 품종별로 구별이 가능한 SNP 마커를 개발하고자 하는데, 본 연구의 목적이 있다. 마커들을 조합으로 haplotype을 보았을 때, MC1R 유전자의 SNP 조합에서 CGG type일 경우, 재래닭 만을 특별히 구별할 수 있었으며, TAG, TGG, TAA type일 경우에는 아라카나 만을 구별할 수 있었고, CAA type의 경우, 레그혼 만을 특이적으로 구별할 수 있었다. TYRP1 유전자의 SNP 조합에서는 TTTCA, CCTCA type의 경우, 레그혼 만을 구별할 수 있으며, CTTTA type의 경우, 오골계 만을 특이적으로 구별할 수 있었다. MC1R 유전자의 SNP 조합으로 재래닭, 레그혼, 아라카나를 구별할 수 있었고, TYRP1 유전자의 각각의 SNP 및 조합으로 4가지 품종 모두 구별할 수 있었다. 이렇게 품종 간의 유전적 다형성에 대한 연구가 더 많이 진행된다면, 단순 모색만으로 품종을 구별하기보다는 분자생물학적으로 품종 간의 차이를 이해할 수 있게 될 것이라고 생각된다.

Relationships between Single Nucleotide Polymorphism Markers and Meat Quality Traits of Duroc Breeding Stocks in Korea

  • Choi, J.S.;Jin, S.K.;Jeong, Y.H.;Jung, Y.C.;Jung, J.H.;Shim, K.S.;Choi, Y.I.
    • Asian-Australasian Journal of Animal Sciences
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    • 제29권9호
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    • pp.1229-1238
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    • 2016
  • This study was conducted to determine the relationships of five intragenic single nucleotide polymorphism (SNP) markers (protein kinase adenosine monophosphate-activated ${\gamma}3$ subunit [PRKAG3], fatty acid synthase [FASN], calpastatin [CAST], high mobility group AT-hook 1 [HMGA1], and melanocortin-4 receptor [MC4R]) and meat quality traits of Duroc breeding stocks in Korea. A total of 200 purebred Duroc gilts from 8 sires and 40 dams at 4 pig breeding farms from 2010 to 2011 reaching market weight (110 kg) were slaughtered and their carcasses were chilled overnight. Longissimus dorsi muscles were removed from the carcass after 24 h of slaughter and used to determine pork properties including carcass weight, backfat thickness, moisture, intramuscular fat, $pH_{24h}$, shear force, redness, texture, and fatty acid composition. The PRKAG3, FASN, CAST, and MC4R gene SNPs were significantly associated with the meat quality traits (p<0.003). The meats of PRKAG3 (A 0.024/G 0.976) AA genotype had higher pH, redness and texture than those from PRKAG3 GG genotype. Meats of FASN (C 0.301/A 0.699) AA genotype had higher backfat thickness, texture, stearic acid, oleic acid and polyunsaturated fatty acid than FASN CC genotype. While the carcasses of CAST (A 0.373/G 0.627) AA genotype had thicker backfat, and lower shear force, palmitoleic acid and oleic acid content, they had higher stearic acid content than those from the CAST GG genotype. The MC4R (G 0.208/A 0.792) AA genotype were involved in increasing backfat thickness, carcass weight, moisture and saturated fatty acid content, and decreasing unsaturated fatty acid content in Duroc meat. These results indicated that the five SNP markers tested can be a help to select Duroc breed to improve carcass and meat quality properties in crossbred pigs.

Application of Linkage Disequilibrium Mapping Methods to Detect QTL for Carcass Quality on Chromosome 6 Using a High Density SNP Map in Hanwoo

  • Lia, Y.;Lee, J.H.;Lee, Y.M.;Kim, J.J.
    • Asian-Australasian Journal of Animal Sciences
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    • 제24권4호
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    • pp.457-462
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    • 2011
  • The purpose of this study was to detect QTL for carcass quality on bovine chromosome (BTA) 6 using a high density SNP map in a Hanwoo population. The data set comprised 45 sires and their 427 Hanwoo steers that were born between spring of 2005 and fall of 2007. The steers that were used for progeny testing in the Hanwoo Improvement Center in Seosan, Korea, were genotyped with the 2,535SNPs on BTA6 that were embedded in the Illumina bovine SNP 50K chip. Four different linkage disequilibrium (LD) mapping models were applied to detect significant SNPs for carcass quality traits; the fixed model with a single marker, the random model with a single marker, the random model with haplotype effects using two adjacent markers, and the random model at hidden state. A total of twelve QTL were detected, for which four, one, three and four SNPs were detected on BTA6 under the respective models (p<0.001). Among the detected QTL, four, two, five and one QTL were associated with carcass weight, backfat thickness, longissimus dorsi muscle area, and marbling score, respectively (p<0.001). Our results suggest that the use of multiple LD mapping approaches may be beneficial in increasing power to detect QTL given a limited sample size and magnitude of QTL effect.

QTL Scan for Meat Quality Traits Using High-density SNP Chip Analysis in Cross between Korean Native Pig and Yorkshire

  • Kim, S.W.;Li, X.P.;Lee, Y.M.;Choi, Y.I.;Cho, B.W.;Choi, B.H.;Kim, T.H.;Kim, J.J.;Kim, Kwan-Suk
    • Asian-Australasian Journal of Animal Sciences
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    • 제24권9호
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    • pp.1184-1191
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    • 2011
  • We attempted to generate a linkage map using Illumina Porcine 60K SNP Beadchip genotypes of the $F_2$ offspring from Korean native pig (KNP) crossed with Yorkshire (YS) pig, and to identify quantitative trait loci (QTL) using the line-cross model. Among the genotype information of the 62,136 SNPs obtained from the high-density SNP analysis, 45,308 SNPs were used to select informative markers with allelic frequencies >0.7 between the KNP (n = 16) and YS (n = 8) F0 animals. Of the selected SNP markers, a final set of 500 SNPs with polymorphic information contents (PIC) values of >0.300 in the $F_2$ groups (n = 252) was used for detection of thirty meat quality-related QTL on chromosomes at the 5% significance level and 10 QTL at the 1% significance level. The QTL for crude protein were detected on SSC2, SSC3, SSC6, SSC9 and SSC12; for intramuscular fat and marbling on SSC2, SSC8, SSC12, SSC14 and SSC18; meat color measurements on SSC1, SSC3, SSC4, SSC5, SSC6, SSC10, SSC11, SSC12, SSC16 and SSC18; water content related measurements in pork were detected on SSC4, SSC6, SSC7, SSC10, SSC12 and SSC14. Additional QTL of pork quality traits such as texture, tenderness and pH were detected on SSC6, SSC12, SSC13 and SSC16. The most important chromosomal region of superior pork quality in KNP compared to YS was identified on SSC12. Our results demonstrated that a QTL linkage map of the $F_2$ design in the pig breed can be generated with a selected data set of high density SNP genotypes. The QTL regions detected in this study will provide useful information for identifying genetic factors related to better pork quality in KNP.

토마토 유전자연관지도 상의 DarT 마커 분포 (Distribution of DArT Markers in a Genetic Linkage Map of Tomato)

  • Truong, Hai Thi Hong;Graham, Elaine;Esch, Elisabeth;Wang, Jaw-Fen;Hanson, Peter
    • 원예과학기술지
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    • 제28권4호
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    • pp.664-671
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    • 2010
  • 토마토풋마름병에 저항성인 $Solanum$ $lycopersicum$ H7996와 극도감수성인 $S.$ $pimpinellifolium$ WVa700 간의 교배를 통해 획득한 재조합순계계통 $F_9$ 세대의 188개체를 이용하여 유전자연관지도를 작성하였다. 유전자지도는 DarT 260종, AFLP 74종, RFLP 4종, SNP 1종 및 SSR 22종 등 총 361종의 마커로 구성되었다. 작성된 유전자지도는 총 13개의 연관군(LG)에 2042.7cM을 포함하였으며 마커간의 평균지도거리는 5.7cM이고 이중 DArT마커는 평균 7.9cM당 1개가 분포하였다. SSR 마커의 분포를 기초로 작성된 11개 연관군들은 토마토 염색체의5번과 12번을 제외한 10개 염색체에 해당하였다. DArT 마커는 다른 마커들처럼 토마토 유전체 상에 고르게 분포하였으며, 인접 마커와의 상호분석(${\leq}$ 0.5cM) 결과 클러스터링 빈도가 13.5%인 AFLP 마커보다 3배 정도 높은 38.8%의 빈도로 최고치를 나타내었다. 본 연구를 통해 토마토에서 최초로 DarT 마커를 이용한 유전자연관지도를 작성하였다.

Genetic Diversity and Population Structure of Peanut (Arachis hypogaea L.) Accessions from Five Different Origins

  • Zou, Kunyan;Kim, Ki-Seung;Lee, Daewoong;Jun, Tae-Hwan
    • 한국작물학회지
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    • 제65권4호
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    • pp.447-456
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    • 2020
  • Peanut is an allotetraploid derived from a single recent polyploidization. Polyploidization has been reported to have caused significant loss in genetic diversity during the domestication of cultivated peanuts. Single nucleotide polymorphism (SNP)-based markers such as cleaved amplified polymorphic sequences (CAPS) derived from next-generation sequencing (NGS) have been developed and widely applied for breeding and genetic research in peanuts. This study aimed to identify the genetic diversity and population structure using 30 CAPS markers and 96 peanut accessions from five different origins. High genetic dissimilarities were detected between the accessions from Korea and those from the other three South American origins generally regarded as the origin of peanuts, while the accessions from Brazil and Argentina presented the lowest genetic dissimilarity. Based on the results of the present study, accessions from Korea have unique genetic variation compared to those from other countries, while accessions from the other four origins are closely related. Our study identified the genetic differentiation in 96 peanut accessions from five different origins, and this study also showed the successful application of SNP information derived from re-sequencing based on NGS technology.

Molecular identification of sweet potato accessions using ARMS-PCR based on SNPs

  • Park, Hyungjun;Kim, Sujung;Nie, Hualin;Kim, Jiseong;Lee, Jeongeun;Kim, Sunhyung
    • Journal of Plant Biotechnology
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    • 제47권2호
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    • pp.124-130
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    • 2020
  • The sweet potato (Ipomoea batatas [L.] Lam.) is the sixth-most important crop in the world following rice, wheat, potato, maize, and cassava. Four varieties ('Beniharuka', 'Annobeni', 'Pungwonmi', 'Hogammi') and their Japanese cultivars are broadly distributed in South Korea. In the Korean marketplace, sweet potatoes are classified by color and shape, not by variety, making it necessary to differentiate varieties for uniform production and consumption. In this study, molecular markers were developed to distinguish the four varieties of sweet potato using SNPs and genotyping-by-sequencing (GBS) analysis via a tetra-primer amplification refractory mutation system (ARMS)-PCR. The results revealed that three variety-specific fragments (164 bp and 241 bp of SNP 04-27457768 and 292 bp of SNP 03-16195623) were amplified in the 'Beniharuka', 'Pungwonmi', and 'Annobeni' sweet potato varieties. There were instances where some varieties produced three bands within the gel electrophoresis, indicating heterozygosity at the given SNPs loci. DNA sequencing analysis also confirmed the results of electrophoresis at the SNPs loci. Overall, these molecular markers would provide a useful, rapid, and, simple evaluation method for the Korean sweet potato marketplace, where the mixing of varieties is a serious issue.