• Journal of Crop Science and Biotechnology
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• v.11 no.3
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• pp.163-170
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• 2008

The detection, characterization and use of quantitative traits loci, QTL, have significant potential to improve the efficiency of selective breeding of species. Therefore, a population with 59 advanced backcross lines($BC_2F_5$), derived from a cross between IR64 and Tarome molaei, were studied in Tonekabon Rice Research Station of Iran in order to map QTLs for panicle length, number of grain per panicle, and panicle grain sterility in rice. The parental screening wtih 235 SSR markers in agarose and polyacrylamide gels revealed 114 markers with clear polymorphic bands. To search for QTLs associated with panicle length, number of grain per panicle, and panicle grain sterility, we constructed a genetic linkage map using 114 microsatellite markers. Positive and negative transgressive segregations were observed in $BC_2F_5$ lines for all traits. Using multiple interval mapping(MIM), a total of 20 putative QTLs were detected, of which eight were for panicle length, three for number of grains, and nine for panicle grain sterility. The maximum number of QTLs were mapped on chromosomes 1 and 2 with eight QTLs. These QTL markers could possible be utilized for marker-assisted selection.

• Journal of Plant Biotechnology
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• v.5 no.4
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• pp.201-207
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• 2003

Tissue culture techniques arguably are an important approach for ex situ conservation of rare and endangered plant species. However, there is utmost importance on maintaining the genetic integrity of the introduced plants especially in tree species. To examine the genetic integrity of the micropropagated plants, we randomly screened few hardened plants of Syzygium travancoricum, a critically endangered tree taxon, using Randomly Amplified Polymorphic DNA (RAPD) markers. Twenty-three random. primers were tried and twenty-five polymorphic loci were identified. The dendrogram based on the Unweighted Pair-Group Method Arithmetic Average and Nei's similarity index depicted about 97% homology between the mother plants and micropropagated plants. Further, an attempt was made to reintroduce the micropropagated plants in the wild. Over three hundred small trees could be successfully established.

• Journal of Microbiology
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• v.34 no.2
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• pp.166-171
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• 1996

Genetic analysis was conducted on newly isolated coliphages form soil by using a RAPD assay. From the initial result, the coliphages were turned out to be different form one another but were closely related to .psi..lambda. due to the fact that they shared the samed RAPD maker in which other T phage testings failed to show. By using the primers EC01 or EC02, a fast genetic mutation of .psi.C1 was found by producing specific RAPD markers on the phages from the first filial progeny to the second filial progeny. When we made a RAPD assay with combined primers (EC01, EC05 and EC08), the genetic mutation was again confirmed in .psi.C1. The assay detection showed mutations in other coliphages such as .psi.C2 and .psi.C3 by revealing specific RAPD bands among different progeny phages, where genetic instability of the coliphages in implied.

• Journal of Life Science
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• v.11 no.1
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• pp.65-67
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• 2001

In order to develop a rapid and simple method for testing the purity of radish hybrid seeds using a procedure based on the PCR(Polymerase chain reaction), eighty random primers were screened with the genomic DNA extracted from five day old seedlings of inbred parent lines and their F1 hybrids. Two primers, HRM-02 (5'-GAGACCAGAC-3') and HRM-19(5'-TGAGGCGTGT-3'), generate reproducible unique PCR patterns which can identify each parent lines as well as their hybrids. In actual test of randomly selected hybrid seeds using the two marker primers, the purity tested by one primer was exactly same as that of other primer. It suggests that one marker primer selected in this experiment is enough for the purity test of radish hybrid seeds. We demonstrates the use of RAPD(randomly amplified polymorphic DNAs) markers to identify each of inbred parent lines and hybrids by rapid and simple method.

• Animal Bioscience
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• v.35 no.9
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• pp.1314-1326
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• 2022

Objective: Alongside the rise of animal-protection awareness in Taiwan, the public has been paying more attention to dog genetic deficiencies due to inbreeding in the pet market. The goal of this study was to isolate novel microsatellite markers for monitoring the genetic structure of domestic dog populations in Taiwan. Methods: A total of 113 DNA samples from three dog breeds-beagles (BEs), bichons (BIs), and schnauzers (SCs)-were used in subsequent polymorphic tests applying the 14 novel microsatellite markers that were isolated in this study. Results: The results showed that the high level of genetic diversity observed in these novel microsatellite markers provided strong discriminatory power. The estimated probability of identity (P_(ID)) and the probability of identity among sibs (P_(ID)sib) for the 14 novel microsatellite markers were 1.7×10^-12 and 1.6×10^-5, respectively. Furthermore, the power of exclusion for the 14 novel microsatellite markers was 99.98%. The neighbor-joining trees constructed among the three breeds indicated that the 14 sets of novel microsatellite markers were sufficient to correctly cluster the BEs, BIs, and SCs. The principal coordinate analysis plot showed that the dogs could be accurately separated by these 14 loci based on different breeds; moreover, the Beagles from different sources were also distinguished. The first, the second, and the third principal coordinates could be used to explain 44.15%, 26.35%, and 19.97% of the genetic variation. Conclusion: The results of this study could enable powerful monitoring of the genetic structure of domestic dog populations in Taiwan.

• Horticultural Science & Technology
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• v.34 no.1
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• pp.142-153
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• 2016

The present study investigated identification of cultivars through phylogenetic analysis of 108 Citrus varieties and related cultivars using simple sequence repeat (SSR) markers. Two hundred three SSR primer pairs were used to detect polymorphic markers among 8 Citrus cultivars consisting of 4 mandarins, 1 orange, 1 tangor, 1 tangelo, and 1 pumelo. Eighteen SSR primer pairs were reproducible and showed highly polymorphic alleles. These markers were applied to assess genetic variations of the 108 varieties. Each marker detected 5-14 alleles, with an average of 9.28. The polymorphism information content varied from 0.417 to 0.791 with an average of 0.706. Cluster analysis with SSR markers resulted in 13 major groups reflecting cultivar types and pedigree information. Twelve orange cultivars in the $I-1^{st}$ sub-cluster and 23 mandarin cultivars in the $II-1^{st}$ sub-cluster, respectively, were not discriminated using the SSR markers. This could be due to narrow genetic backgrounds originated through bud mutation or nucellars seedlings. The SSR profile database of Citrus cultivars will be useful as a tool for protection of plant breeders' intellectual property rights in addition to assessing genetic diversity in Citrus cultivars and germplasms.

• Journal of Life Science
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• v.22 no.4
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• pp.466-471
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• 2012

Sixty individuals of the scallop $Patinopecten$ $yessoensis$ (Genus Pecten) were sampled to examine the genetic diversity and population structure of this species. Random amplified polymorphic DNA (RAPD) identified 109 genotypes and produced 79 polymorphic loci (72.8%). Total genetic diversity values ($H_T$) and interlocus variation in the within-population genetic diversity ($H_S$) were 0.254 and 0.178, respectively. On a per-locus basis, the proportion of total genetic variation due to differences among populations ($G_{ST}$) was 0.299. This indicated that about 70.1% of the total variation was within populations. The unique loci and bands of $P.$ $yessoensis$ were shown in only one population among the three countries. RAPD markers were very effective in classifying the natural population levels of $P.$ $yessoensis$ in Korea, China, and Japan. In addition, insights into the relative gene diversity among and within populations of $P.$ $yessoensis$ would be useful in breeding and for the development of strategies for animal genetic resources.

• Journal of Korean Society of Forest Science
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• v.105 no.2
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• pp.186-192
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• 2016

This study was conducted to develop microsatellite markers in Quercus variabilis using next generation sequencing. A total of 305,771 reads (384 bp on average) were generated on a Roche GS-FLX system, yielding 117 Mbp of sequences. The de novo assembly resulted in 7,346 contigs. A total of 606 contigs (20.75%) including 911 microsatellite loci were derived from the 2,921 contigs longer than 500 bp. A total of 180 primer sets were designed from the 911 microsatellite loci and screened in eight Q. variabilis individual trees sampled from a natural stand to obtain polymorphic loci. As a result, a total of thirteen polymorphic microsatellite loci were selected and used for estimating population genetic parameters in the 54 individual trees. The mean number of effective alleles was 4.996 ranging from 2.439 to 7.515. The observed heterozygosity and the expected heterozygosity ranged between 0.731 and 1.000 with an average of 0.873 and from 0.590 to 0.867 with an average of 0.766, respectively. Null alleles were not detected in all loci. No significant linkage disequilibrium was detected after Bonferroni correction in all loci. In the near future, these novel polymorphic microsatellite markers will be used to study population and conservation genetics of Q. variabilis of Korea in more detail.

• Journal of Life Science
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• v.22 no.12
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• pp.1644-1650
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• 2012

The aim of this study was to screen the polymorphisms and distribution of each genotype of insertion/ deletion (indel) markers which were found in a preliminary comparative study of bovine genomic sequence databases. Comparative bioinformatic analyses were first performed between the nucleotide sequences of Bovine Genome Project and those of expressed sequence tag (EST) database, and a total of fifty-one species of indel markers were screened. Of these, forty-two indel markers were evaluated, and nine informative indel markers were ultimately selected for population analysis. Nucleotide sequences of each marker were re-sequenced and their polymorphic patterns were typed in six cattle breeds: Holstein, Angus, Charolais, Hereford, and two Korean native cattle breeds (Hanwoo and Jeju Black cattle). Cattle breeds tested in this study showed polymorphic patterns in eight indel markers but not in the Indel-15 marker in Charolais and Holstein. The results of analysis for Jeju Black cattle (JBC) population indicated an observed heterozygosity (Ho) that was highest in HW_G1 (0.600) and the lowest in Indel_29 (0.274). The PIC value was the highest in HW_G4 (0.373) and lowest in Indel_6 (0.305). These polymorphic indel markers will be useful in supplying genetic information for parentage tests and traceability and to develop a molecular breeding system for improvement of animal production in cattle breeds as well as in the JBC population.

• The Plant Pathology Journal
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• v.23 no.2
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• pp.45-50
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• 2007

Genetic diversity among selected isolates of Macrophomina phaseolina, a causal agent of charcoal rot (stalk rot) disease in sorghum was studied using PCR-RAPD markers. A set of ten isolates, from ten different rabi sorghum genotypes representing two traditional sorghum growing situations viz., Dharwad- a transitional high rainfall region and Bijapur- a semi-arid low rainfall region in South India. From a set of 40 random primers tested, amplicon profiles of 15 were reproducible. A total of 149 amplicon levels, with an average of 9.9 bands per primer, were available for analysis, of which 148 were polymorphic (99.3%). It was possible to discriminate all the isolates with any of the 15 primers employed. UPGMA clustering of data indicated that the isolates shared varied levels of genetic similarity within a range of 0.14 to 0.72 similarity coefficient index and it was suggestive that grouping of isolates was not related to sampling location in anyway. A high level of genetic heterogeneity of 0.28 was recorded among the isolates.