Genetic Relationships of Panax Species by RAPD and ISSR Analyses

Dong-Su In,Young-Chang Kim,Kyong-Hwan Bang,Jong-Wook Chung,Ok-Tae Kim,Dong-Yoon Hyun,Seon-Woo Cha,Tae-Soo Kim,Nak-Sul Seong 韓國藥用作物學會 2005 한국약용작물학회지 Vol.13 No.5

This study was carried out to develop convenient and reproducible methods for identifying the genetic relationship among germplasms of Panax species based on molecular genetics. Using random amplified polymorphic DNA (RAPD) and inter simple sequence repeat (ISSR) analyses, genetic polymorphism of the Panax species was investigated with following cultivars and accessions, such as Chunpoong, Yunpoong, Kopoong, Sunpoong, and Kumpoong in domestic cultivars, Hwangsuk, Jakyung and Suckju in domestic accessions, and Panax quinquefolius L. and Panax japonicus C.A. Meyer in foreign introduced accessions, respectively. Specific DNA fragments ranging from 200 to 3,000 base pairs in size could be obtained with various ISSR and RAPD primers under the optimized PCR conditions. The dissimilarity coefficients among the genetic polymorphisms of ginseng cultivars and accessions were calculated from 0.26 to 0.90 in RAPD and from 0.12 to 0.89 in ISSR analysis, respectively. Eleven plant samples were grouped siblings together with cultivars and parents based on cluster analysis of genetic distance depending on genetic property such as origin of the species. In results, both RAPD and ISSR analyses were useful for identifying the genetic relationship among cultivars and accessions of Panax species at DNA level.

DNA Polymorphism and Assessments of Genetic Relationships in genus Zoysia Based on Simple Sequence Repeat Markers

Man Kyu Huh(허만규) 한국생명과학회 2015 생명과학회지 Vol.25 No.3

한국에서 채집한 잔디속(genus Zoysia) 식물 종의 유전적 변이를 단순 서열 반복(Inter-Simple Sequence Repeat Markers, ISSR) 마커 시스템으로 조사하였다. 8개의 ISSR 시발체를 이용한 중합효소 사슬 증폭반응에서 86개의 분절의 증폭물을 얻었으며 이 중 76(87.1%)개 분절이 다형성을 나타내었다. ISSR 마커 시스템에서 다형성 정보지수(PIC)는 0.848이었다. 다형성 대립유전자좌위의 퍼센트(Pp)는 41.2%에서 44.7%까지 나타내었다. 네이(Nei)의 유전자 다양성(H)은 0.149에서 0.186까지 이며 평균은 0.170이었다. 샤논(Shannon)의 정보 지수(I)의 평균값은 0.250이었다. 대립유전자좌위에 근거하여 전체 변이에서 종 간 차이를 나타내는 변이의 몫(GST)은 0.601였다. 이는 전체변이의 약 60.1%는 종 간에 있음을 의미한다. 따라서 변이의 약 39.9%는 종 내에 있었다. GST에 근거한 유전자 흐름(이동)은 잔디속 간에는 대단히 낮았다(Nm = 0.332). 계통도는 3개의 뚜렷한 분지군으로 분리되었다. 왕잔디(Zoysia macrostachya)와 금잔디(Z. tenuifolia) 분지군, 갯잔디(Z. sinica) 단독 분지군, 잔디(Z .japonica) 단독 분지군이었다. 결론적으로 잔디속 식물에 대한 ISSR 분석은 유전적 변이를 탐지하는데 유용하며, 종을 구분하는 유전자형의 대한 식별력을 주었다. The genetic variability of four species of the genus Zoysia collected from South Korea was analyzed using an inter-simple sequence repeat (ISSR) marker system. Polymerase chain reactions (PCR) with eight ISSR primers generated 86 amplicons, 76 (87.1%) of which were polymorphisms. The polymorphism information content (PIC) value of the ISSR marker system was 0.848. The percentage of polymorphic loci (Pp) ranged from 41.2% to 44.7%. Nei’s gene diversity (H) ranged from 0.149 to 0.186, with an average overall value of 0.170. The mean of Shannon’s information index (I) value was 0.250. Total genetic diversity values (HT) varied between 0.356 (ISSR-1) and 0.418 (ISSR-16), for an average overall polymorphic loci of 0.345. Interlocus variation in within-species genetic diversity (HS) was low (0.170). On a per-locus basis, the proportion of total genetic variation due to differences among species (GST) was 0.601. This indicated that about 60.1% of the total variation was among species. Thus, about 39.9 of genetic variation was within species. The estimate of gene flow, based on GST, was very low among species of the genus Zoysia (Nm = 0.332). The phylogenic tree showed three distinct groups: Z. macrostachya and Z. tenuifolia clades and other species were formed the separated clusters. In conclusion, the ISSR assay was useful for detecting genetic variation in the genus Zoysia, and its discriminatory power was comparable to that of other genotyping tools.

Determination of Genetic Divergence Based on DNA Markers Amongst Monosporidial Strains Derived from Fungal Isolates of Karnal Bunt of Wheat

Seneviratne, J.M.,Gupta, Atul K.,Pandey, Dinesh,Sharma, Indu,Kumar, Anil The Korean Society of Plant Pathology 2009 Plant Pathology Journal Vol.25 No.4

Genetic variation among the base isolates and monosporidial strains derived from these isolates of Tilletia indica- the causal agent of Karnal bunt (KB) in wheat, was analyzed by morphological, growth behaviors and RAPD-ISSR based molecular polymorphism. Genetic make up of fungal cultures vary among each other. The magnitude of variation in KBPN group is less (narrow genetic base) when compared to the other groups KB3, KB9 and JK (broad genetic base) reflecting that variability is a genetically governed process. The generation of new variation with different growth characteristics is not a generalized feature and is totally dependant on the original genetic make-up of the base isolate generating new monosporidial strains. Thus, it can be concluded that monosporidial strains derived from mono-teliosporic isolate, consists of genetically heterogeneous population. The morphological and genetic variability further suggests that the variation in T. indica strains is predominantly derived through the genetic rearrangements through para sexual means.

Genetic Relationships of Panax Species by RAPD and ISSR Analyses

In, Dong-Su,Kim, Young-Chang,Bang, Kyong-Hwan,Chung, Jong-Wook,Kim, Ok-Tae,Hyun, Dong-Yoon,Cha, Seon-Woo,Kim, Tae-Soo,Seong, Nak-Sul The Korean Society of Medicinal Crop Science 2005 韓國藥用作物學會誌 Vol.13 No.5

This study was carried out to develop convenient and reproducible methods for identifying the genetic relationship among germplasms of Panax species based on molecular genetics. Using random amplified polymorphic DNA (RAPD) and inter simple sequence repeat (ISSR) analyses, genetic polymorphism of the Panax species was investigated with following cultivars and accessions, such as Chunpoong, Yunpoong, Kopoong, Sunpoong, and Kumpoong in domestic cultivars, Hwangsuk, Jakyung and Suckju in domestic accessions, and Panax quinquefolius L. and Panax japonicus C.A. Meyer in foreign introduced accessions, respectively. Specific DNA fragments ranging from 200 to 3,000 base pairs in size could be obtained with various ISSR and RAPD primers under the optimized PCR conditions. The dissimilarity coefficients among the genetic polymorphisms of ginseng cultivars and accessions were calculated from 0.26 to 0.90 in RAPD and from 0.12 to 0.89 in ISSR analysis, respectively. Eleven plant samples were grouped siblings together with cultivars and parents based on cluster analysis of genetic distance depending on genetic property such as origin of the species. In results, both RAPD and ISSR analyses were useful for identifying the genetic relationship among cultivars and accessions of Panax species at DNA level.

Association of rs10757274 and rs2383206 Polymorphisms on 9p21 locus with Coronary Artery Disease in Turkish Population

Çağrı Yayla,Kaan Okyay,Asife Şahinarslan,Akın Yılmaz,Atiye Seda Yar Sağlam,Azmi Eyiol,Hasan Ata Bolayır,Burak Sezenöz,Sevda Menevşe,Atiye Çengel 대한심장학회 2016 Korean Circulation Journal Vol.46 No.5

Background and Objectives: Genetic predisposition is an important risk factor for coronary artery disease (CAD). In this study, we aimed to evaluate the impact of rs10757274 and rs2383206 polymorphisms in chromosome 9p21 on presence and severity of CAD in a Turkish population. Subjects and Methods: A total of 646 patients who underwent coronary angiography were included in this study. Coronary vessel score and Gensini score were calculated to assess the angiographic severity of CAD. Alleles of AA, AG, and GG were determined for rs10757274 (polymorphism-1) and rs2383206 (polymorphism-2) polymorphisms located in chromosome 9p21 from the blood samples. Results: There was a significant difference between the alleles in polymorphism-1 in the presence of coronary artery disease (38.9% in AA, 48.0% in GG and 56.4% in AG, p=0.017). However, there was no difference between the alleles in polymorphism-2. According to vessel scores, there was a significant difference between the alleles in polymorphism-1 (AA 0.71±1.04, GG 0.88±1.07, AG 1.06±1.12, p=0.018). In polymorphism-2, vessel scores did not show a difference between the alleles. In polymorphism-1, there was a significant difference in Gensini score (p=0.041). Gensini scores did not differ between the alleles in polymorphism-2 (p>0.05 for all). In multivariate analyses, none of the alleles was an independent factor for presence of CAD. Conclusion: The presence of rs10757274 polymorphism including AG allele in chromosome 9p21 was related to CAD. However, this relationship was not independent of other cardiovascular risk factors.

Single nucleotide polymorphism-based analysis of the genetic structure of the Min pig conserved population

Meng Fanbing,Cai Jiancheng,Wang Chunan,Fu Dechang,Di Shengwei,Wang Xibiao,Chang Yang,Xu Chunzhu 아세아·태평양축산학회 2022 Animal Bioscience Vol.35 No.12

Objective: The study aims to uncover the genetic diversity and unique genetic structure of the Min pig conserved population, divide the nucleus conservation population, and construct the molecular pedigree. Methods: We used KPS Porcine Breeding Chip v1 50K for SNP detection of 94 samples (31♂, 63♀) in the Min pig conserved population from Lanxi breeding Farm. Results: The polymorphic marker ratio (PN), the observed heterozygosity (Ho), and the expected heterozygosity (He) were 0.663, 0.335, and 0.330, respectively. The pedigreebased inbreeding coefficients (FPED) was significantly different from those estimated from runs of homozygosity (FROH) and single nucleotide polymorphism (FSNP) based on genome. The Pearson correlation coefficient between FROH and FSNP was significant (p<0.05). The effective population content (Ne) showed a continuously decreasing trend. The rate of decline was the slowest from 200 to 50 generations ago (r = 0.95), then accelerated slightly from 50 to 5 generations ago (1.40<r<1.50) and increased significantly in the last 5 generations (r = 2.6). According to the composition of Chinese lineage, we separated the nucleus conservation population (81 individuals) and the candidate conservation population (13 individuals) of Min pig, then the nucleus conservation population of Min pig was divided into 9 families by genomic information matrix. Conclusion: Our study indicated that the genetic diversity of the Min pig conserved population was inadequate. Due to the introgression of European commercial pig breeds and the unscientific breeding process, it is necessary to construct the molecular pedigree of the nucleus conservation population for the Min pig. Objective: The study aims to uncover the genetic diversity and unique genetic structure of the Min pig conserved population, divide the nucleus conservation population, and construct the molecular pedigree.Methods: We used KPS Porcine Breeding Chip v1 50K for SNP detection of 94 samples (31♂, 63♀) in the Min pig conserved population from Lanxi breeding Farm.Results: The polymorphic marker ratio (PN), the observed heterozygosity (Ho), and the expected heterozygosity (He) were 0.663, 0.335, and 0.330, respectively. The pedigree-based inbreeding coefficients (F_PED) was significantly different from those estimated from runs of homozygosity (F_ROH) and single nucleotide polymorphism (FSNP) based on genome. The Pearson correlation coefficient between F_ROH and F_SNP was significant (p<0.05). The effective population content (Ne) showed a continuously decreasing trend. The rate of decline was the slowest from 200 to 50 generations ago (r = 0.95), then accelerated slightly from 50 to 5 generations ago (1.40<r<1.50) and increased significantly in the last 5 generations (r = 2.6). According to the composition of Chinese lineage, we separated the nucleus conservation population (81 individuals) and the candidate conservation population (13 individuals) of Min pig, then the nucleus conservation population of Min pig was divided into 9 families by genomic information matrix.Conclusion: Our study indicated that the genetic diversity of the Min pig conserved population was inadequate. Due to the introgression of European commercial pig breeds and the unscientific breeding process, it is necessary to construct the molecular pedigree of the nucleus conservation population for the Min pig.

RAPD Polymorphism and Genetic Distance among Phenotypic Variants of Tamarindus indica

( A Mayavel ),( B Vikashini ),( S Bhuvanam ),( A Shanthi ),( R Kamalakannan ),( Ki-won Kim ),( Kyu-suk Kang ) 한국산림과학회(구 한국임학회) 2020 한국산림과학회지 Vol.109 No.4

Tamarind (Tamarindus indica L.) is one of the multipurpose tree species distributed in the tropical and sub-tropical climates. It is an important fruit yielding tree that supports the livelihood and has high social and cultural values for rural communities. The vegetative, reproductive, qualitative, and quantitative traits of tamarind vary widely. Characterization of phenotypic and genetic structure is essential for the selection of suitable accessions for sustainable cultivation and conservation. This study aimedto examine the genetic relationship among the collected accessions of sweet, red, and sour tamarind by using Random Amplified Polymorphic DNA (RAPD) primers. Nine accessions were collected from germplasm gene banks and subjected to marker analysis. Fifteen highly polymorphic primers generated a total of 169 fragments, out of which 138 bands were polymorphic. The polymorphic information content of RAPD markers varied from 0.10 to 0.44, and the Jaccard’s similarity coefficient values ranged from 0.37 to 0.70. The genetic clustering showed a sizable genetic variation in the tamarind accessions at the molecular level. The molecular and biochemical variations in the selected accessions are very important for developing varieties with high sugar, anthocyanin, and acidity traits in the ongoing tamarind improvement program.

Meta-analysis of Association Studies of CYP1A1 Genetic Polymorphisms with Digestive Tract Cancers Susceptibility in Chinese

Liu, Chang,Jiang, Zheng,Deng, Qian-xi,Zhao, Ya-nan Asian Pacific Journal of Cancer Prevention 2014 Asian Pacific journal of cancer prevention Vol.15 No.11

Background: A great number of studies have shown that cytochrome P450 1A1 (CYP1A1) genetic polymorphisms, CYP1A1 Msp I and CYP1A1 Ile/Val, might be risk factors for digestive tract cancers, including esophageal cancer (EC), gastric cancer (GC), hepatic carcinoma (HC), as well as colorectal cancer (CC), but the results are controversial. In this study, a meta-analysis of this literature aimed to clarify associations of CYP1A1 genetic polymorphisms with digestive tract cancers susceptibility in Chinese populations. Materials and Methods: Eligible case-control studies published until December 2013 were retrieved by systematic literature searches from PubMed, Embase, CBM, CNKI and other Chinese databases by two investigators independently. The associated literature was acquired through deliberate search and selection based on established inclusion criteria. Fixed-effects or random-effects models were used to estimate odds ratios (ORs and 95%CIs). The meta-analysis was conducted using Review Manager 5.2 and Stata 12.0 softwares with stability evaluated by both stratified and sensitivity analyses. Moreover, sensitivity analysis and publication bias diagnostics confirmed the reliability and stability. Results: Eighteen case-control studies with 1,747 cases and 2,923 controls were selected for CYP1A1 MspI polymorphisms, and twenty case-control studies with 3, 790 cases and 4, 907 controls for the CYP1A1 Ile/Val polymorphisms. Correlation associations between CYP1A1 Ile/Val polymorphisms and digestive tract cancers susceptibility were observed in four genetic models in the meta-analysis (GG vs AA:OR= 2.03, 95%CI =1.52- 2.72; AG vs AA: OR=1.26, 95%CI =1.07-1.48; [GG+AG vs AA] :OR =1.42, 95%CI=1.20-1.68, [GG vs AA+AG]:OR=1.80, 95%CI =1.40-2.31). There was no association between CYP1A1 Msp I polymorphisms and digestive tract cancers risk. Subgroup analysis for tumor type showed a significant association of CYP1A1 Ile/Val genetic polymorphisms with EC in China. However, available data collected by the study failed to reveal remarkable associations of GC or HC with CYP1A1 Ile/Val genetic polymorphisms and EC, GC or CC with CYP1A1 MspI genetic polymorphisms. Conclusions: Our results indicated that CYP1A1 Ile/Val genetic polymorphisms, but not CYP1A1 Msp I polymorphisms, are associated with an increased digestive tract cancers risk in Chinese populations. Additional well-designed studies, with larger sample size, focusing on different ethnicities and cancer types are now warranted to validate this finding.

Effects of genetic polymorphisms of apolipoprotein A1 on serum HDL cholesterol level in postmenopausal Korean women

Jang-Soo Hong, Sang-Yong Eom, Yong-Dae Kim, Heon Kim 충북대학교 동물의학연구소 2013 Journal of Biomedical and Translational Research Vol.14 No.2

Apolipoprotein A1 (ApoA1) is the major protein component of high density lipoprotein (HDL) cholesterol in blood, and ApoA1 genetic polymorphisms modulate the blood lipid profiles. This study was conducted in order to investigate the association between three genetic polymorphisms (rs670, rs5069, and rs5070) of ApoA1 and blood lipid profiles in postmenopausal Korean women. A total of 130 postmenopausal women who visited a hospital in order to undergo screening tests were subjects of this study. Genetic polymporphisms and blood lipid profiles were determined using a direct sequencing and spectrophotometric assay, respectively. A significant linkage disequilibrium was observed between all tested single nucleotide polymorphisms. ApoA1 rs5070 genetic polymorphism showed a marginally significant association with HDL cholesterol levels (p=0.066). After adjusting for age, body mass index, smoking, alcohol drinking, medication, hypertension, and diabetes mellitus, we found that the ApoA1 rs5070 genetic polymorphism is a significant determinant of HDL cholesterol levels (β=4.421, p=0.037). According to the results of this study, ApoA1 rs5070 genetic polymorphism may be an important genetic marker associated with HDL cholesterol in postmenopausal Korean women.

Effects of genetic polymorphisms of apolipoprotein A1 on serum HDL cholesterol level in postmenopausal Korean women

엄상용,김용대,김헌,홍장수 충북대학교 동물의학연구소 2013 Journal of Biomedical and Translational Research Vol.14 No.2

Apolipoprotein A1 (ApoA1) is the major protein component of high density lipoprotein (HDL) cholesterol in blood, and ApoA1 genetic polymorphisms modulate the blood lipid profiles. This study was conducted in order to investigate the association between three genetic polymorphisms (rs670, rs5069, and rs5070) of ApoA1 and blood lipid profiles in postmenopausal Korean women. A total of 130 postmenopausal women who visited a hospital in order to undergo screening tests were subjects of this study. Genetic polymporphisms and blood lipid profiles were determined using a direct sequencing and spectrophotometric assay, respectively. A significant linkage disequilibrium was observed between all tested single nucleotide polymorphisms. ApoA1 rs5070 genetic polymorphism showed a marginally significant association with HDL cholesterol levels (p=0.066). After adjusting for age, body mass index, smoking, alcohol drinking, medication, hypertension, and diabetes mellitus, we found that the ApoA1 rs5070 genetic polymorphism is a significant determinant of HDL cholesterol levels (β=4.421, p=0.037). According to the results of this study, ApoA1 rs5070 genetic polymorphism may be an important genetic marker associated with HDL cholesterol in postmenopausal Korean women.