• Korean Journal of Breeding Science
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• v.43 no.5
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• pp.399-404
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• 2011

Genetic diversity among 28 Cymbidium varieties was evaluated by using a sequence-related amplified polymorphism (SRAP) marker system. The SRAP marker which was based on the open reading frames (ORFs) regions was developed primarily for Brassica species, but has been applied to various crops. A total of 30 SRAP primer combinations were initially screened. Twenty-eight SRAP primer combinations showed high polymorphism among the 28 Cymbidium varieties, which were consisted of breeding varieties and their parents in National Institute of Horticultural & Herbal Science (NIHHS). The amplified DNA fragments were separated by denaturing acrylamide gels and detected silver staining method. One hundred ninety six polymorphic bands (7 per primer) were generated and ranged from 0.3 to 1.0 kb in size. Polymorphic fragments were scored for calculating simple matching coefficient of genetic similarity and cluster analysis with multi-variate statistical package (MVSP) 3.1. The mean genetic similarity coefficient value was 0.588. The results showed that the correlation between $F_1$ varieties and their parents was high. These studied SRAP markers will be useful tools for genotype identification, germplasm conservation, genetic relationships in Cymbidium.

• Animal Bioscience
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• v.34 no.11
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• pp.1757-1765
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• 2021

Objective: The swine leukocyte antigen (SLA) gene group, which is closely linked and highly polymorphic, has important biomedical significance in the protection and utilization of germplasm resources. However, genetic polymorphism analyses of SLA microsatellite markers in Chinese miniature pigs are limited. Methods: Eighteen pairs of microsatellite primers were used to amplify the SLA regions of seven miniature pig breeds and three wild boar breeds (n = 346) from different regions of China. The indexes of genetic polymorphism, including expected heterozygosity (He), polymorphic information content (PIC), and haplotype, were analyzed. The genetic differentiation coefficient (Fst) and neighbor-joining methods were used for cluster analysis of the breeds. Results: In miniature pigs, the SLA I region had the highest numbers of polymorphisms, followed by the SLA II and SLA III regions; the region near the centromere had the lowest number of polymorphisms. Among the seven miniature pig breeds, Diannan small-ear pigs had the highest genetic diversity (PIC value = 0.6396), whereas the genetic diversity of the Hebao pig was the lowest (PIC value = 0.4330). The Fst values in the Mingguang small-ear, Diannan small-ear, and Yunnan wild boars were less than 0.05. According to phylogenetic cluster analysis, the South-China-type miniature pigs clustered into one group, among which Mingguang small-ear pigs clustered with Diannan small-ear pigs. Haplotype analysis revealed that the SLA I, II, and III regions could be constructed into 13, 7, and 11 common haplotypes, respectively. Conclusion: This study validates the high genetic diversity of the Chinese miniature pig. Mingguang small-ear pigs have close kinship with Diannan small-ear pigs, implying that they may have similar genetic backgrounds and originate from the same population. This study also provides a foundation for genetic breeding, genetic resource protection, and classification of Chinese miniature pigs.

• Animal Bioscience
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• v.36 no.9
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• pp.1357-1366
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• 2023

Objective: This study aimed to identify the single-nucleotide polymorphisms (SNPs) in the dual-specificity phosphatase 8 (DUSP8) and insulin-like growth factor 2 (IGF2) genes and to explore their effects on inosine-5'-monophosphate (IMP), inosine, and hypoxanthine contents in Korean native chicken -red-brown line (KNC-R Line). Methods: A total sample of 284 (males, n = 127; females n = 157) and 230 (males, n = 106; females, n = 124) aged of 10 weeks old KNC-R line was used for genotyping of DUSP8 and IGF2 genes, respectively. One SNP (rs313443014 C>T) in DUSP8 gene and two SNPs (rs315806609A/G and rs313810945T/C) in IGF2 gene were used for genotyping by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and KASP methods, respectively. The Two-way analysis of variance of the R program was used to associate DUSP8 and IGF2 genotypes with nucleotide contents in KNC-R chickens. Results: The DUSP8 (rs313443014 C>T) was polymorphic in KNC-R line and showed three genotypes: CC, CT, and TT. The IGF2 gene (rs315806609A/G and rs313810945T/C) was also polymorphic and had three genotypes per SNP, including GG, AG, and AA for the SNP rs315806609A/G and genotypes: CC, CT, and TT for the SNP rs313810945T/C. Association resulted into a strong significant association (p<0.01) with IMP, inosine, and hypoxanthine. Moreover, the significant effect of sex (p<0.05) on nucleotide content was also observed. Conclusion: The SNPs in the DUSP8 and IGF2 genes might be used as genetic markers in the selection and production of chickens with highly flavored meat.

• Journal of Korean Society of Forest Science
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• v.102 no.4
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• pp.560-565
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• 2013

Population genetic structure and diversity of Ulmus davidiana var. japonica in South Korea were studied using ISSR markers. A total of 45 polymorphic ISSR amplicons were cropped from 7 ISSR primers and 171 individuals of 7 populations. The average of effective alleles and the proportion of polymorphic loci were 1.5 and 89% respectively. The Shannon's diversity index (I) was 0.435 and the expected heterozygosity from the frequentist's method ($H_e$) and the Bayesian inference (hs) were 0.289 and 0.323 respectively. From AMOVA, 4.2% of total genetic variation in the elm populations was explained with the difference among populations (${\Phi}_{ST}=0.042$) and the other 95.8% was distributed within populations. The ${\theta}^{II}$ value by Bayesian method which was comparable to the FST was 0.043. So the level of genetic diversity in the elm populations was similar to that in Genus Ulmus and the level of genetic differentiation was lower than that of others. No population showed a significant difference in the population-specific fixation indices (average of $PS-F_{IS}=0.822$) or the population-specific genetic differentiations (average of $PS-F_{ST}=0.101$). Seven populations were allocated into 3 groups in the UPGMA and the PCA, but the grouping patterns were different. Also, we could not confirm any geographic trend from Bayesian clustering.

• Horticultural Science & Technology
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• v.31 no.3
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• pp.337-343
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• 2013

The aims of this study were to compare genetic distances among 14 Phalaenopsis varieties using simple sequence repeat (SSR) and sequence-related amplified polymorphism (SRAP) marker systems and to determine the discrimination using SSR. A total of 111 SSR primers and 30 SRAP combinations were initially screened. Twelve SSR primers and thirty SRAP combinations showed high polymorphism among the 14 Phalaenopsis varieties including domestic breeding varieties, conserved in National Institute of Horticultural & Herbal Science (NIHHS). The amplified DNA fragments were separated by denaturing acrylamide gels and detected by silver staining method. A total of 474 polymorphic bands, including 55 by SSRs and 419 by SRAPs, were identified and used for genetic diversity analysis. Polymorphic bands were scored for calculating a simple matching coefficient of genetic similarity and cluster analysis with multi-variate statistical package (MVSP) 3.1. Fourteen Phalaenopsis varieties were classified into three major groups at similarity coefficient value of 0.683 and 0.66 using SRAP and SSR, respectively. Also we could discriminate these domestic breeding Palaenopsis varieties using only SSR 20 and SSR 22. The results indicate that SSR analysis is effective for discrimination among Phalaenopsis varieties and SRAP is useful for genetic diversity when there is no sequence information. These studied SSR and SRAP markers will be useful tools for genotype identification, germplasm conservation and genetic relationship study in Phalaenopsis.

• Journal of Life Science
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• v.17 no.6 s.86
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• pp.756-761
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• 2007

Cenus Malus is a long-lived woody species primarily distributed throughout Asia. Many species of this genus are regarded as agriculturally and ecologically important. The phynetics and genetic diversity among eight species of genus Malus were reconstructed using the random amplified polymorphic DNA (RAPD) markers. In a simple measure of intraspecies variability by the percentage of polymorphic bands, the M. micromalus exhibited the lowest variation (34.7%). The M. pumila showed the highest (50.0%). Mean number of alleles per locus (A) ranged from 1.347 to 1.500 with a mean of 1.437. The phenotypic frequency of each band was calculated and used in estimating genetic diversify (H) within species. The mean of H was 0.190 across species, varying from 0.155 to 0.220. In particular, two cultivated species, M. pumila and M. asiatica, had high expected diversity, 0.314 and 0.307, respectively. On a per locus basis, the proportion of total genetic variation due to differences among species ranged from 0.388 to 0.472 with a mean of 0.423, indicating that 42.3% of the total variation was found among species. The phylogenetic tree showed three distinct elates. One includes M. sieversii, M. pumila, and M. asiatica. Another includes three M. baccata taxa. The other includes M. sieboldii, M. floribunsa, and M. micromalus. One variety and one form of M. sieboldii were well separated each other. RAPD markers are useful in germ-plasm classification of genus Malus and evolutionary studies.

• Horticultural Science & Technology
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• v.19 no.1
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• pp.29-33
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• 2001

This study was carried out to discriminate potato cultivars and breeding lines by specific molecular markers using random amplified polymorphic DNA (RAPD) analysis. The genotypes of potatoes used for analysis were eight cultivars and five breeding lines. Some of those show much phenotypic resemblances among them because 'Jopung', 'Daekwan70', 'Gawon', and 'Daekwan72' have immediate parental relationship with 'Superior', 'Irish Cobbler', 'Namsuh', and 'Atlantic', respectively. So, there are many difficulties to distinguish the varieties by the morphological characteristics. Three URP primers, URP2, URP4, and URP8 were selected for promising primers to discriminate potato genotypes or cultivars. The three URP primers were shown very high reproducibility because of the relatively high annealing temperature and long primer size. Although the results of similarity analyses did not always reflect the genetic relationship between potato varieties, the reproducible pattern of amplified DNA bands by URP primers showed possibility for molecular markers for discrimination of potato genotype or cultivar.

• Korean Journal of Plant Resources
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• v.17 no.3
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• pp.227-238
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• 2004

Rhododendron micranthum is an endangered species in Korea. In order to develop the strategy of gene diversity conservation, estimation of the amount of genetic diversity, the genetic variation and relationship in the native populations of Rh. micranthum was performed on the basis of AFLP and RAPD analysis. Analysis of 56 accessions derived from 6 populations of Rh. micranthum with four AFLP primer combinations and ten RAPD primers detected a total of 33 polymorphic AFLP fragments and 15 polymorphic RAPD fragments, respectively. By UPGMA cluster analysis with molecular markers, the 56 accessions were grouped into three major clusters at 73.3% genetic similarity; group I consists of most accessions of populations I, II, IV, V and Ⅵ, group II consists of 7 accessions of population III, and group III consists of only two accessions of population IV. The geographic locations of the most accessions derived from six populations were not related to their position in the UPGMA cluster analysis, except for several accessions of populations III and IV. The genetic similarity of among six populations measured by AFLP and RAPD markers ranged from 0.66 to 0.99. Among them, population Ⅵ showed the highest GS with means of 0.87, while population I showed the lowest GS with means of 0.78. This result will be useful for designing the strategy of conservation in the native populations of Rh. micranthum.

• Journal of Life Science
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• v.32 no.8
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• pp.595-600
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• 2022

Water dropworts, Oenanthe javanica and O. javanica var. japonica are called "minari" in Korea and are eaten as a vegetable. Cicuta virosa is common European water hemlock and has toxic properties, such as cicutoxin. Molecular variations of water dropwort species in Korea were investigated using random amplified polymorphic DNA (RAPD). The six populations were studied with 10 primers (Operon, OPB) for RAPD analysis. The 72 DNA fragments (bands) were found among six populations. Among these 72 bands, 61 (84.7%) bands were polymorphic. The typical populations of Cicuta virosa in Korea were small, isolated, and patchily distributed for natural populations and they maintained a high level of genetic diversity. However, when cultivated populations of O. javanica var. japonica were large and widely grown in rice paddies as vegetables, they maintained a lower genetic diversity than those of C. virosa and wild populations of O. javanica. Although the diversity indices of wild populations were shown to be higher than those of cultivated populations, no significant difference for measures of genetic variability was shown. Total genetic diversity value (H_T) was 0.342. The interlocus variation in the within-population genetic diversity (H_S) was 0.201. The proportion of total genetic variation due to differences among populations (G_ST) range was 0.414, indicating that 41.4% of the total variation was among populations. In conclusion, the RAPD technique was a useful method for discrimination between C. virosa and O. javanica. In addition, RAPD-OPB markers could further distinguish the strains from different food sources.

• Korean Journal of Breeding Science
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• v.42 no.5
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• pp.525-533
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• 2010

In this study, random amplified polymorphic DNA (RAPD) and simple sequence repeat (SSR) analyses were utilized for evaluation of genetic diversity of 34 Korean bred and introduced apple cultivars. Thirty-seven RAPD primers detected a total of 193 polymorphic bands (36.2%) with an average of 5.6. Twenty-six SSR markers generated a total of 112 alleles with an average 4.3 alleles per locus. Genetic diversity of 34 cultivars estimated by polymorphic information content (PIC) value ranged from 0.536 (CH03d12) to 0.952 (CH04c06) with an average of 0.843. By UPGMA (unweighted pair-group method arithmetic average) cluster analysis with 305 polymorphic bands, the apple cultivars were classified four groups by similarity index of 0.640. The 'Seokwang' was included in group I. Group II consisted of 12 cultivars which have 'Golden Delicious' in their pedigree, with the exception of 'Spur Earliblaze' and 'Jonathan'. Group III included 13 cultivars which have usually 'Fuji' in their ancestry and bud sport of 'Fuji' cultivars. Group IV consisted of 8 cultivars with 'Hongro', 'Gamhong', and 'Saenara'. Similarity values among the tested apple cultivars ranged from 0.529 to 0.987, and the average similarity value was 0.647. The similarity index was the highest (0.987) between 'Hwarang' and 'Danhong', and the lowest (0.529) between 'Seokwang' and 'Hwarang'. The genetic relationships among the 34 studied apple cultivars were basically consistent with the known pedigree.