• Title/Summary/Keyword: Polymorphisms

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Association between Genotypes of the Isocitrate Dehydrogenase 3, beta subunit (IDH3B) Gene and Carcass Traits in an F2 Crossbred Population of Landrace × Jeju (Korea) Black Pigs (제주흑돼지와 랜드레이스 교배 2세대의 도체형질과 IDH3B 유전자형의 상관관계)

  • Kang, Yong-Jun;Jeong, Dong Kee;Cho, In-Cheol;Han, Sang-Hyun
    • Journal of Life Science
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    • v.26 no.4
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    • pp.414-418
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    • 2016
  • This study tested the association between genetic polymorphisms of the isocitrate dehydrogenase 3, beta subunit (IDH3B) gene and economic traits in an F2 crossbred population of Landrace × Jeju (South Korea) Black pigs. A 304-bp insertion/deletion mutation in promoter region was screened for determining genotypes of the IDH3B gene in a total of 1,105 F2 pigs. Three genotypes (AA, AB, and BB) were identified in the founder, F1, and F2 populations. Association analysis showed significant differences in carcass weights (CW), backfat thicknesses in three positions of the body (4th-5th ribs, BF5; 11th-12th ribs, BF12; 13th rib-1st lumbar, BFL), and carcass lengths (CL) (p<0.05), but not in meat color (MC), eye muscle area (EMA), or marbling scores (MARB) (p>0.05). The F2 IDH3B BB homozygotes showed heavier CW (80.790±0.725 kg) and shorter CL (101.875±0.336 cm) than the other genotypes (p<0.05). In addition, the BF levels between the 4th - 5th and 11th - 12th vertebrae were thicker in the carcasses of pigs with the IDH3B BB genotype than with the other genotypes (p<0.05). These results suggested that genetic variations in the IDH3B gene may serve as molecular genetic markers for improving the Landrace × Jeju Black pig crossbreeding systems.

Association of Melanocortin 4 Receptor (MC4R) Genotypes with Fatty Acid Compositions in an Intercross Population between Duroc and Jeju Native Pigs (제주재래돼지와 듀록 참조축군에서 Melanocortin 4 Receptor (MC4R) 유전자형과 지방산 조성간의 관련성 분석)

  • Kang, Yong-Jun;Kim, Sang-Geum;Kim, Su-Yeon;Shin, Moon-Cheol;Woo, Jae-Hoon;Kim, Nam-Young;Shin, Sang-Min;Choi, Jae-Young;Yoo, Ji-Hyun;Park, Nam-Geon;Yang, Byoung-Chul;Cho, In-Cheol
    • Journal of Life Science
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    • v.30 no.1
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    • pp.58-63
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    • 2020
  • This study was conducted to examine association between melanocortin-4-receptor (MC4R) genotypes and fatty acid (FA) composition in an F2 intercross between Duroc and Jeju (South Korea) Native pigs (JNP). Fourteen FA composition traits were measured in more than 290 F2 progeny population produced between Duroc and JNP. All experimental pigs were successfully genotyped for the MC4R c.1426A>G (p.Asp298Asn) single nucleotide polymorphism (SNP) by using Taq I PCR-RFLP methods. We detected three MC4R genotypes, AA, AG, and GG with 0.299, 0.542, and 0.159 genotype frequencies, respectively. The MC4R AA genotype animals showed higher levels in palmitic acid (C16:0, p<0.05), stearic acid (C18:0, p<0.01), eicosenoic acid (C20:1n9, p<0.05), saturated fatty acid (SFA, p<0.01) than GG homozygotes, respectively. Whereas MC4R GG genotype showed higher values in linoleic acid (C18:2n6, p<0.001), linolenic acid (C18:3n3, p<0.001), linolenic acid (C18:3n6, p<0.001), arachidonic acid (C20:4n6, p<0.001) and unsaturated fatty acid (USFA, p<0.01) than AA pigs, respectively. The MC4R GG genotype was associated with increasing USFA and decreasing SFA in the F2 progeny population produced between Duroc and JNP. Our finding suggests that the MC4R polymorphisms can be used as a valuable genetic marker for Duroc and JNP breeding programs to improve meat quality and to control FA compositions.

Association between SNPs on equine chromosomes 3 and body conformation of 12 month of age in Jeju crossbred horses (Jeju crossbred에서 3번 염색체 단일염기변이와 12개월령 체형과의 연관관계)

  • Kim, Nam-Young;Choi, Jung-Woo;Chae, Hyun-Seok;Baek, Kwang-Soo;Son, Jun-Kyu;Shin, Sang-Min;Woo, Jae-Hoon;Park, Seol-Hwa;Hong, Hyun-Jun;Kim, Su-Yeon;Yang, Young-Hoon
    • Journal of Embryo Transfer
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    • v.31 no.3
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    • pp.227-233
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    • 2016
  • This study was conducted to analyze the effect of single nucleotide polymorphisms (SNPs) on the equine chromosomes (ECA) 3 for the body conformations of 12 month of age in Jeju crossbred (Jeju horses ${\times}$ Thoroughbred). A total of 199 Jeju crossbred horse samples were obtained from the National Institute of Subtropical Livestock Research Institute for this study. To correctly estimate the body conformations, we measured thirteen elements relevant to the body conformation such as body weight, wither height, body length for all the 199 horses at 12 month of age. Furthermore, all the horses were genotyped using four SNPs including the BIEC2-808466, BIEC2-808543, BIEC2-808967, BIEC2-809370, of which genomic coordinates range approximately from 105.1Mbp to 110 Mbp in the ECA3. For the phenotypic data sets, the average body weight was $193.7{\pm}24.5kg$ and the height was $124.5{\pm}4.0cm$. As for the genotypic data, the miner allele frequencies of the SNPs were shown to be varied from 0.01 to 0.291. Using the phenotypic and genotypic data sets, analysis of covariance was performed to find any association between those SNP genotypes and body conformations, using year of birth, month of birth, sex, and parity as the covariance components. The result showed that alternative genotypes in the BIEC2-808967 and BIEC2-809370 SNPs were significantly associated with the body length (P<0.05) and the wither height (P<0.05) respectively in the Jeju crossbred horses. Therefore, it is estimated that there are significant associations in the body conformation of 12 month of age of Jeju crossbred for those two SNPs used in this study.

QTL Analysis of Concerned on Ideal Plant Form in Rice (벼의 이상적인 초형에 관여하는 QTL 분석)

  • Chung, Il Kyung;Kim, Kyung-Min
    • Korean Journal of Plant Resources
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    • v.30 no.2
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    • pp.213-218
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    • 2017
  • Rice is the staple food of at least half of the world's population. Due to global warming, the weather is difficult to forecast nowadays. Therefore, it is necessary to breed various breeding to respond to such changes in the environment. This study was conducted to analyze the QTL about plant form, culm length, ear number and ear length by using 120 lines by anther culture, a cross between the Indica variety Cheongcheong and Japonica variety Nagdong. DNA marker was selected on the QTLs gene, and the following results were obtained. CNDH (Cheongcheong Nagdong Doubled Haploid) lines frequency distribution table curves about culm length, ear number and ear length exhibited showed a continuous variation close to a normal distribution. QTL analysis result, on culm length qPlL1-1 and qPlL1-2 were detected on the chromosome 1 and qPlL5 was detected on the chromosome 5. However, on ear length qPL2, qPL3 and qPL10, were detected on the chromosome 2, 3 and 10, while on ear number qPN1-1 and qPN1-2 were detected on the chromosome 1, qPN9 was detected on the chromosome 9. The QTLs related to culm length was found to chromosomes 5 and LOD scores were 3.81. The QTLs related to ear length was found to chromosomes 2 and 3 LOD scores were 7.13 and 3.20. The QTLs related to ear number was found to chromosome 9 and LOD scores were 4.27. Twenty two (22) Japonica cultivars and 12 Indica cultivars were analyzed polymorphisms, using selected 9 markers from the result about plant form analysis. RM5311, RM555 and RM8111 about the culm length, the ear length and number of ear were selected on the standard of Cheongcheong and Nagdong. Each rate of concordances about the culm length, the ear length and number of ear are 44.11%, 41.17% and 44.11%.

Variability in Drug Interaction According to Genetic Polymorphisms in Drug Metabolizing Enzymes

  • Jang, In-Jin;Yu, Kyung-Sang;Cho, Joo-Youn;Chung, Jae-Yong;Kim, Jung-Ryul;Lim, Hyeong-Seok;Shin, Sang-Goo
    • Environmental Mutagens and Carcinogens
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    • v.24 no.1
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    • pp.15-18
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    • 2004
  • There are significant differences in the extent of drug interactions between subjects. The influence of the genetic make up of drug metabolizing enzyme activities (CYP3A5, CYP2C19 and UDP-glucuronosyl transferase) on the pharmacokinetic drug interaction potential were studied in vivo. Nineteen healthy volunteers were grouped with regard to the $CYP3A5^{*}3$ allele, into homozygous wild-type (CYP3A5^{*}1/1^{*}1$, n=6), heterozygous $(CYP3A5^{*}1/^{*}3$, n=6), and homozygous variant-type $(CYP3A5^{*}3/^{*}3$, n=7) subject groups. The pharmacokinetic profile of intravenous midazolam was characterized before and after itraconazole administration (200 mg once daily for 4 days), and also following rifampin pretreatment (600 mg once daily for 10 days), with a washout period of 2 weeks in between. For omeprazole and moclobemide pharmacokinetic interaction study 16 healthy volunteers were recruited. The volunteer group comprised 8 extensive metabolizers and 8 poor metabolizers of CYP2C19, which was confirmed by genotyping. Subjects were randomly allocated into two sequence groups, and a single-blind, placebo-controlled, two-period crossover study was performed. In study I, a placebo was orally administered for 7 days. On the eighth morning, 300 mg of moclobemide and 40 mg of placebo were coadministered with 200 mL of water, and a pharmacokinetic study was performed. During study n, 40 mg of omeprazole was given each morning instead of placebo, and pharmacokinetic studies were performed on the first and eighth day with 300 mg of moclobemide coadministration. In the UGT study pharmacokinetics and dynamics of 2 mg intravenous lorazepam were evaluated before and after rifampin pretreatment (600 mg once daily for 10 days), with a washout period of 2 weeks in between. The subjective and objective pharmacodynamic tests were done before and 1, 2, 4, 6, 8, and 12 hrs after lorazepam administration. The pharmacokinetic profiles of midazolam and of its hydroxy metabolites did not show differences between the genotype groups under basal and induced metabolic conditions. However, during the inhibited metabolic state, the $CYP3A5^{*}3/^{*}3$ group showed a greater decrease in systemic clearance than the $CYP3A5^{*}1/^{*}1$ group $(8.5\pm3.8$ L/h/70 kg vs. $13.5\pm2.7$ L/h/70 kg, P=0.027). The 1'-hydroxymidazolam to midazolam AUC ratio was also significantly lower in the $CYP3A5^{*}3/^{*}3$,/TEX> group $(0.58\pm0.35,$ vs. $1.09\pm0.37$ for the homozygous wild-type group, P=0.026). The inhibition of moclo-bemide metabolism was significant in extensive metabolizers even after a single dose of omeprazole. After daily administration of omeprazole for 1 week, the pharmacokinetic parameters of moclobemide and its metabolites in extensive metabolizers changed to values similar to those in poor metabolizers. In poor meta-bolizers, no remarkable changes in the pharmacokinetic parameters were observed. The area under the time-effect curves of visual analog scale(VAS), choice reaction time, and continuous line tracking test results of lorazepam was reduced by 20%, 7%, 23% respectively in induced state, and in spite of large interindividual variablity, significant statistical difference was shown in VAS(repeated measures ANOVA, p=0.0027).

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Genetic polymorphisms of the $Fc{\gamma}R$ genes in periodontally healthy Korean population (치주적으로 건강한 한국인에서 $Fc{\gamma}R$ 유전자의 유전자 다형성 발생빈도에 관한 연구)

  • Shin, Seung-Yun;Kim, Kyoung-Hwa;Park, Ok-Jin;Kim, Kak-Kyun;Chung, Chong-Pyoung;Yoshie, Hiromasa;Ku, Young
    • Journal of Periodontal and Implant Science
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    • v.33 no.4
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    • pp.747-753
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    • 2003
  • 면역글로불린의 Fc 부분에 대한 수용기인 $Fc{\gamma}R$는 세균에 대한 인식, 결합과 포식작용과정에서 중요한 역할을 한다. 이 $Fc{\gamma}R$에서 $Fc{\gamma}R$IIa, $Fc{\gamma}R$IIIa, $Fc{\gamma}R$IIIb의 유전자 다형성이 치의학 분야에서 연구되고 있다. $Fc{\gamma}R$IIa에서는 두 번째 세포외 면역글로불린 유사 영역의 131번째 아미노산에서 아르기닌($Fc{\gamma}R$IIa-R131) 혹은 히스티딘($Fc{\gamma}R$IIa-H131)을 갖고 있으며, $Fc{\gamma}R$IIIa에서는 두번째 세포외 영역의 158번째 아미노산이 발린($Fc{\gamma}R$IIIa-158V) 혹은 페닐알라닌($Fc{\gamma}R$IIIa-158F)을 갖고 있다. $Fc{\gamma}R$IIIb에서는 첫 번째 세포외 면역글로불린 유사영역의 4개의 아미노산의 유전자 다형성으로 인해서 $Fc{\gamma}R$IIIb-NA1과 $Fc{\gamma}R$IIIb-NA2의 두가지 유전자 다형성을 보이고 있다. 이번 연구는 치주적으로 건강한 한국인에서 $Fc{\gamma}R$IIa, $Fc{\gamma}R$IIIa, $Fc{\gamma}R$IIIb에 대한 유전자형의 분포를 조사하고자 한 것으로 서울대학교 치과병원에 근무하는 치과의사, 치과위생사, 간호조무사 및 서울대학교 치과대학 4학년 학생 중 치주낭 깊이와 부착소실이 4mm 이하인 치주적으로 건강한 한국인 65명을 대상으로 하였다. $Fc{\gamma}R$IIa, $Fc{\gamma}R$IIIa, $Fc{\gamma}R$IIIb의 유전자 다형성은 분리한 DNA에 각 대립유전자에 특이성을 지닌 primer를 넣고 PCR(polymerase Chain Reaction)법을 이용하여 증폭시킨후 전기영동법을 이용하여 각 대립유전자의 존재를 확인함으로써 결정하였다. $Fc{\gamma}R$IIa의 유전자 다형성은 R/R131, R/H131, H/H131의 유전자형에 대하여 각각 7.7%, 38.5%, 53.8%의 분포를 보였으며, $Fc{\gamma}R$IIIa의 158V/V, 158V/F, 158F/F 유전자형에 대하여 각각 7.7%, 35.4%, 56.9%의 분포를 보였다. 또한 $Fc{\gamma}R$IIIb의 NA1/NA1, NA1/NA2, NA2/NA2 유전자형은 각각 33.9%, 53.8%, 12.3%의 분포를 보였다. 이를 바탕으로 각 대립유전자의 발생빈도 계산한 결과 $Fc{\gamma}R$IIa의 R131과 H131이 26.9% 73.1%로 나타났으며, $Fc{\gamma}R$IIIa의 158V, 158F의 유전자형이 25.4%, 74.6%로 나타났다. $Fc{\gamma}R$IIIb의 NA1, NA2 유전자형의 발생빈도는 60.8%, 29.2%로 나타났다. 이번 연구는 치주적으로 건강한 한국인에서의 $Fc{\gamma}R$IIa, $Fc{\gamma}R$IIIa, $Fc{\gamma}R$IIIb에 대한 유전자형의 분포를 조사한 것으로, 이후 치주질환자의 유전자형 분포와의 비교로 치주질환과 $Fc{\gamma}R$IIa, $Fc{\gamma}R$IIIa, $Fc{\gamma}R$IIIb의 유전자다형성과의 관련성에 관한 추가적인 연구가 필요할 것으로 여겨진다.

SSR Marker Related to Major Characteristics Affected Kernel Quality in Waxy Corn Inbred Lines (찰옥수수 자식계통의 주요 품질특성과 관련된 SSR마커)

  • Jung, Tae-Wook;Moon, Hyeon-Gui;Son, Beom-Young;Kim, Sun-Lim;Kim, Soon-Kwon
    • KOREAN JOURNAL OF CROP SCIENCE
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    • v.51 no.spc1
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    • pp.185-192
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    • 2006
  • This experiment was conducted to assess genetic diversity of waxy corn inbred lines and to identify SSR markers related to major characteristics affected kernel quality for improving waxy corn $F_1$ hybrid with good quality. Diversity of 64 waxy com inbred lines was evaluated using 30 microsatellite markers. The 30 microsatellite markers representing 30 loci in the maize genome detected polymorphisms among the 64 inbred lines and revealed 225 alleles with a mean of 7.5 alleles per primer. The polymorphism Information content (PIC) value ranged from 0.14 to 0.87, with an average of 0.69. Based on Nei's genetic distances, the 64 inbred lines were classified into 9 groups by the cluster analysis. The group I included 26 inbred lines (41%), other groups included 3 to 9 inbred lines. One-way analysis of variance was conducted to identify significant relationship between individual markers and major characteristics that affect kernel quality. The analysis showed that umc1019 was related to amylopectin and crude protein content, me 1020 to amylopectin content and peak viscosity, and bnlg1537 to 100-kernel weight, kernel length, and kernel width.

Genetic and Agronomic Analysis of a Recombinant Inbred Line Population to Map Quantitative Trait Loci for Blast Resistance and Select Promising Lines in Rice (벼 RIL집단의 유전 분석과 농업형질 분석을 통한 도열병 저항성 QTL 탐색 및 유망계통 선발)

  • Ha, Su-Kyung;Jeung, Ji-Ung;Jeong, Jong-Min;Kim, Jinhee;Mo, Youngjun
    • KOREAN JOURNAL OF CROP SCIENCE
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    • v.65 no.3
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    • pp.172-181
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    • 2020
  • Koshihikari has been one of the most popular rice cultivars with good eating quality since the 1960s despite its susceptibility to blast disease and lodging. To map the genes controlling blast resistance and to develop promising blast-resistant breeding lines inheriting Koshihikari's high eating quality, a recombinant inbred line (RIL) population was developed from a cross between Koshihikari and a blast resistance donor with early maturity, Baegilmi. A total of 394 Koshihikari × Baegilmi RILs (KBRIL), and the two parents, were evaluated for blast resistance and major agronomic traits including heading date, culm length, panicle length, and tiller number. A linkage map encompassing 1,272.7 cM was constructed from a subset of the KBRIL (n = 142) using 130 single nucleotide polymorphisms. Two quantitative trait loci (QTL) for blast resistance, qBL1.1 harboring Pish/Pi35 and qBL2.1 harboring Pib, were mapped onto chromosomes 1 and 2, respectively. qBL1.1 was detected in both of the experimental sites, Namwon and Jeonju, while qBL2.1 was only detected in Namwon. qBL1.1 and qBL2.1 did not affect agronomic traits, including heading date, culm length, panicle length, and tiller number. From the 394 KBRILs, lines that were phenotypically similar to Koshihikari were selected according to heading date and culm length and were further divided into the following two groups based on blast resistance: Koshishikari-type blast resistant lines (KR, n = 15) and Koshishikari-type blast susceptible lines (KS, n = 15). Although no significant differences were observed in the major agronomic traits between the two groups, the KR group produced a greater mean head rice ratio than the KS group. The present study provides useful materials for developing blast-resistant cultivars that inherit both Koshihikari's high eating quality and Baegilmi's blast resistance.

Development and Characterization of EMS-induced Mutants with Enhanced Salt Tolerance in Silage Maize (EMS 유도 내염성 증진 사료용 옥수수 돌연변이체 선발 및 특성 분석)

  • Cho, Chuloh;Kim, Kyung Hwa;Seo, Mi-Suk;Choi, Man-Soo;Chun, Jaebuhm;Jin, Mina;Kim, Dool-Yi
    • KOREAN JOURNAL OF CROP SCIENCE
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    • v.65 no.4
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    • pp.406-415
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    • 2020
  • Maize (Zea mays L.) is one of the most valuable agricultural crops and is grown under a wide spectrum of environmental conditions. However, maize is moderately sensitive to salt stress, and soil salinity is a serious threat to its production worldwide. In this study, we used ethyl methane sulfonate (EMS) to generate salt-tolerant silage maize mutants. We screened salt-tolerant lines from 203 M3 mutant populations by evaluating the morphological phenotype after salt stress treatment and selected the 140ES91 line. The 140ES91 mutant showed improved plant growth as well as higher proline content and leaf photosynthetic capacity compared with those of wild-type plants under salt stress conditions. Using whole-genome re-sequencing analysis, 1,103 single nucleotide polymorphisms and 71 insertions or deletions were identified as common variants between KS140 and 140ES91 in comparison with the reference genome B73. Furthermore, the expression patterns of three genes, which are involved in salt stress responses, were increased in the 140ES91 mutant under salt stress. Taken together, the mutant line identified in our study could be used as an improved breeding material for transferring salt tolerance traits in maize varieties.

Development of Disease-resistant Japonica Rice Varieties and Effects of Pyramiding Resistance Genes (내병성 자포니카 벼 계통 육성과 저항성 유전자 집적효과)

  • Kim, Woo-Jae;Baek, Man-Kee;Park, Hyeon-Su;Lee, Geon-Mi;Lee, Chang-Min;Kim, Seok-Man;Cho, Young-Chan;Seo, Jeong-Phil;Jeong, O-Young
    • KOREAN JOURNAL OF CROP SCIENCE
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    • v.65 no.4
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    • pp.314-326
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    • 2020
  • This study was carried out to develop a resistant variety against the K3a race of bacterial blight, Xanthomonas oryzae pv. oryzae, through expansion and pyramiding of resistance genes. To develop an elite bacterial blight-resistant cultivar, the breeding process and bacterial blight resistance reactions in advanced backcross lines (ABLs) were analyzed. ABLs21 which contain Xa3 and Xa21, were developed by double backcrossing japonica cultivar Hwanggeumnuri, which has bacterial blight resistant Xa3 gene, and indica variety IRBB21, which havs Xa21 gene, followed by disease resistance bioassay and marker-assisted selection. The resistance genes of ABLs21 were amplified by PCR with the molecular markers 9643.T4 (Xa3) and U1/I1 (Xa21). Hwanggeumnuri and IRBB3 showed resistance reactions against K1, K2, and K3 races, and a susceptible reaction against K3a, K4, and K5 races. IRBB21 showed resistance reactions against K2, K3, K3a, K4 and K5 races, and a susceptible reaction against K1 race. Hwanggeumnuri showed susceptible reactions at the seedling, tillering and adult stages (all stages), whereas ABL21-1 showed moderate resistance at the tillering stage. ABL21-1 showed stable resistance against 18 isolates of K3a race, and the lesion length was shorter than that of the donor parents. In cluster analysis, the HB4032 isolate showed the highest pathogenicity among the 18 isolates. The molecular marker polymorphisms and average substituted chromosome segment lengths of ABLs21 were 63.2 % and 86.1 cM, respectively. Insertion of the donor chromosomal segments occurred in the predicted region of the Xa21 gene of ABLs21.