• Mycobiology
• /
• v.29 no.1
• /
• pp.43-47
• /
• 2001

Genetic diversity of 21 Korean Phytophthora capsici isolates was analyzed by using several molecular markers such as random amplified polymorphic DNA(RAPD), M-13, microsatellite and random amplified microsatellite sequences(RAMS). The overall average similarity coefficient among the isolates was 86% based on the combined data obtained by the molecular markers. No molecular markers were found to be associated with hosts or geographic regions. In addition to RAPD, analysis based on repeated sequences such as $(GTG)_5$, M-13 and RAMS could be used to assess population structure of P. capsici.

• Journal of Microbiology
• /
• v.33 no.3
• /
• pp.171-177
• /
• 1995

Random amplified polymorphic DAN markers were characterized for three taxonomically problematic Penicillium species : P. aurantiogriseum var. Aurantiogriseum, P. verrucosum and P. puberulum, as well as for 25 species of mono, bi-, and terverticillate Penicillia. The relationships among mono, bi-, and terverticillate Penicillium species were determined from these RAPD markers. Eight species from mono-, eight from bi-, and nine from terverticilate Penicillia were examined. With 14 randomly chosen 10-mer primes, a 310 character by 25 species matrix was generated. Phenetic analysis separated the 25 species into three genetically distinct groups that correspond to the different arrangements of penicilli (mono-, bi-, and terverticillate). The results of this study suggest that P. aurantiogriseum var. aurantiogriseum, P. VERRUCOSUM, AND P. puberulum represent genetically distinct species, and that P. vulpinum should be included in terverticilate Penicillia. Phenogram branching patterns indicated that biverticillate species are genetically more similar to monoverticilate species than they are to terverticillate species.

• Journal of Korean Society of Forest Science
• /
• v.87 no.3
• /
• pp.422-428
• /
• 1998

Polymerase chain reaction(PCR)-based inter-simple sequence repeats(I-SSR) markers were analyzed in 48 megagametophytes of a single tree of Abies koreana $W_{ILS}$. Nineteen of the 35 primers, screened with 6 megagametophyte DNA and produced the clearest amplification products in the preliminary experiment, were used for PCR with 48 megagametophyte DNAs sampled from a single tree. On the basis of the chi-square test, a total of 51 amplicons, amplified by the 19 primers, were revealed to be segregated according to the Mendelian ratio(i.e., 1 : 1 segregation ratio) in the 48 megagametophytes at 5% significance level. Based on the linkage analysis, the observed 51 Mendelian loci turned out to be unlinked each other, which suggested that they are evenly distributed in the genome. However, majority of RAPD markers are known to belong to the independent linkage blocks, which frequently results in the amplification of RAPD markers from the restricted regions of the genome. Owing to the nature of even distribution of the 51 loci observed in this study, the I-SSR markers could give better resolution of estimating genetic diversity from the whole genome than RAPD markers. And I-SSR markers are also more suitable than RAPD markers for reconstructing phylogenetic relationship by a cladistic method which requires to fulfil the assumption of independent evolution of the different characters.

• Journal of Korean Society of Forest Science
• /
• v.89 no.4
• /
• pp.536-542
• /
• 2000

A linkage map for Japanese red pine (Pinus densiflora) was constructed on the basis of two DNA marker systems of random amplified polymorphic DNAs (RAPDs) and inter-simple sequence repeats (I-SSR). Haploid genomic DNAs were extracted from megagametophyte tissues of 96 individual seeds in a single tree. A total of 98 DNA markers including 52 RAPD markers amplified by 25 primers and 46 I-SSR markers amplified by 18 primers were verified as Mendelian loci showing 1 : 1 segregation in 96 megagametophytes which were ${\chi}^2$-tested at 5% significance level. Of them, 63 segregating loci turned out to be linked into 20 linkage groups by the two-point analysis. However, 35 loci (17 RAPD and 18 I-SSR) of the 98 segregating loci did not coalesced into any linkage groups at a LOD of 3.0. The linked 63 loci were separated by an average distance of about 25.5 cM, which were spanned 1097.8 cM as a whole. The minimum and maximum map distances of the linkage groups were 4.3 cM and 54.9 cM, respectively. Incorporation of I-SSR loi into linkage map of RAPD loci resulted in extended and partially more saturated linkage blocks.

• Plant Biotechnology Reports
• /
• v.2 no.3
• /
• pp.191-198
• /
• 2008

Germplasm characterization and evolutionary process in viable populations are important links between the conservation and utilization of plant genetic resources. Here, an investigation is made, based on molecular and biochemical techniques for assessing and exploiting the genetic variability in germplasm characterization of taro, which would be useful in plant breeding and ex situ conservation of taro plant genetic resources. Geographical differentiation and phylogenetic relationships of Indian taro, Colocasia esculenta (L.) Schott, were analyzed by random amplified polymorphic DNA (RAPD) and isozyme of seven enzyme systems with specific reference to the Muktakeshi accession, which has been to be proved resistant to taro leaf blight caused by P. colocasiae. The significant differentiations in Indian taro cultivars were clearly demonstrated by RAPD and isozyme analysis. RAPD markers showed higher values for genetic differentiation among taro cultivars and lower coefficient of variation than those obtained from isozymes. Genetic differentiation was evident in the taro accessions collected from different regions of India. It appears that when taro cultivation was introduced to a new area, only a small fraction of genetic variability in heterogeneous taro populations was transferred, possibly causing random differentiation among locally adapted taro populations. The selected primers will be useful for future genetic analysis and provide taro breeders with a genetic basis for selection of parents for crop improvement. Polymorphic markers identified in the DNA fingerprinting study will be useful for screening a segregating population, which is being generated in our laboratory aimed at developing a taro genetic linkage map.

• Plant Biotechnology Reports
• /
• v.4 no.3
• /
• pp.237-242
• /
• 2010

Six parent and their 12 gamma ray-induced somatic flower colour mutants of garden rose were characterized to discriminate the mutants from their respective parents and understanding the genetic diversity using Random amplification of polymorphic DNA (RAPD) markers. Out of 20 primers screened, 14 primers yielded completely identical fragments patterns. The other 7 primers gave highly polymorphic banding patterns among the radiomutants. All the cultivars were identified by using only 7 primers. Moreover, individual mutants were also distinguished by unique RAPD marker bands. Based on the presence or absence of the 48 polymorphic bands, the genetic variations within and among the 18 cultivars were measured. Genetic distance between all 18 cultivars varied from 0.40 to 0.91, as revealed by Jaccard's coefficient matrix. A dendrogram was constructed based on the similarity matrix using the Neighbor Joining Tree method showed three main clusters. The present RAPD analysis can be used not only for estimating genetic diversity present in gamma ray-induced mutants but also for correct identification of mutant/new varieties for their legal protection under plant variety rights.

• Journal of The Korean Society of Grassland and Forage Science
• /
• v.18 no.1
• /
• pp.35-42
• /
• 1998

Eleven Italian ryegrass cultivars were examined for their genetic polymorphisms and phylogenetic relationships using randomly amplified polymorphic DNA (RAPD) markers. In RAPD analysis of 34 random primers, 96 of total 162 bands obtained from 16 primers were polymorphic and sizes of polymorphic band ranged between 0.5 and 1.5kb. Number of bands amplified per primer was varied from 3 to 16 and average number was 14.8. Phylogenetic relationship among cultivars based on the RAPD analysis was examined using UPGMA computer program. In pairwise genetic similarity test of 11 Italian ryegrass cultivars, Grazer and Orlando showed highest coefficient of genetic similarity as 0.740, whereas Marshall and Orlando was lowest as 0.438. Eleven Italian ryegrass cultivars were grouped into 3 major clusters and genetic distance of clusters ranged between 0.567 and 0.646, indicating low level of genetic variation.

• BMB Reports
• /
• v.37 no.2
• /
• pp.213-222
• /
• 2004

A randomly amplified polymorphic DNA (RAPD) analysis was used to identify the species- and population-specific markers of abalone; Haliotis asinina, H. ovina, and H. varia in Thai waters. Fifteen species-specific and six population-specific RAPD markers were identified. In addition, an 1650 bp band (UBC195) that was restricted to H. ovina from the Gulf of Thailand (east) was also found. All of the specific RAPD markers were cloned and sequenced. Twenty pairs of primers were designed and specificity-tested (N = 12 and 4 for target and non-target species, respectively). Seven primer pairs (CUHA1, 2, 4, 11, 12, 13, and 14) were specifically amplified by H. asinina DNA, whereas a single pair of primers showed specificity with H. ovina (CUHO3) and H. varia (CUHV1), respectively. Four primer pairs, including CUHA2, CUHA12, CUHO3, and CUHV1, were further examined against 216 individuals of abalone (N = 111, 73, and 32, respectively). Results indicated the species-specific nature of all of them, except CUHO3, with the sensitivity of detection of 100 pg and 20 pg of the target DNA template for CUHA2 and CUHA12 and CUHV1, respectively. The species-origin of the frozen, ethanol-preserved, dried, and boiled H. asinina specimens could also be successfully identified by CUHA2.

• Asian-Australasian Journal of Animal Sciences
• /
• v.19 no.9
• /
• pp.1234-1239
• /
• 2006

Murrah and NiliRavi are the important North Indian buffalo breeds occupying the prominent position of being the highest milk producers. These breeds are more or less similar at morphological as well as physiological levels. The technique of RAPD-PCR was applied in the present study to identify a battery of suitable random primers to detect genetic polymorphism, elucidation of the genetic structure and rapid assessment of the differences in the genetic composition of these two breeds. A total of 50 random primers were screened in 24 animals each of Murrah and NiliRavi buffaloes to generate RAPD patterns. Of these, 26 (52%) primers amplified the buffalo genome generating 263 reproducible bands. The number of polymorphic bands for the 26 chosen RAPD primers varied from 3 (OPG 06 and B4) to 26 (OPJ 04) with an average of 10.1 bands per primer and size range of 0.2 to 3.2 kb. DNA was also pooled and analyzed to search for population specific markers. Two breed specific RAPD alleles were observed in each of Murrah (OPA02 and OPG16) and NiliRavi (OPG09) DNA pools. RAPD profiles revealed that 11 (4.2%) bands were common to all the 48 individuals of Murrah and NiliRavi buffaloes. Pair-wise band sharing calculated among the individual animals indicated considerable homogeneity of individuals within the breeds. Within breed, band sharing values were relatively greater than those of interbreed values. The low genetic distance (Nei's) value (0.109) estimated in this study is in accordance with the origin and geographical distribution of these breeds. The RAPD analysis indicated high level of genetic similarity between these two important North Indian buffalo breeds.

• Journal of Physiology & Pathology in Korean Medicine
• /
• v.18 no.3
• /
• pp.825-829
• /
• 2004

This study was carried out to differentiate the origins of Astragalus membranaceus Bunge and A. membranaceus Bunge var. mogholicus Nakai. To identify the variation of the RAPD patterns between domestic and foreign Astragalus species, 40 random primers were applied to ten accessions of A. membranaceus and six accessions of A. membranaceus var. mogholicus genomic DNA, respectively, Ten primers of 40 primers could be used to discriminate the origins and 33 polymorph isms among 44 scored DNA fragments (33 fragments are specific for A. membranaceus and A. membranaceus var. mogholicus) were generated using these primers, 75.0 % of which were polymorphic. Especially, three primers of ten primers, OPA17, OPA11 and OPB11, were useful to differentiate between domestic and foreign Astragalus species. RAPD data from the 10 primers were used for cluster analysis and cluster analysis of RAPD markers showed that the two groups are distinct genetically. Consequently, RAPD analysis was a useful method to discriminate between A. membranaceus and A. membranaceus var. mogholicus.