• Journal of Plant Biotechnology
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• v.50
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• pp.190-199
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• 2023

Date palm (Phoenix dactylifera L.: Arecaceae) is a dioecious species where only female trees bear fruits. In their natural state, date palms produce dates once a year. However, in Thailand, some trees were observed to produce dates during the off-season, despite no variations in morphology. The availability of such off-season fruits can significantly increase their market value. Interestingly, most female off-season date palms investigated in this study were obtained through micropropagation. Hence, there is an urgent need for genetic markers to distinguish female offseason flowering plantlets within tissue culture systems. In this study, we aimed to develop random amplification of polymorphic DNA-sequence characterized amplified region (RAPD-SCAR) markers for the identification of female off-season flowering date palms cultivated in Thailand. A total of 160 random decamer primers were employed to screen for specific RAPD markers in off-season flowering male and female populations. Out of these, only one primer, OPN-02, generated distinct genomic DNA patterns in female off-season flowering (FOFdp) individuals compared to female seasonal flowering genotypes. Based on the RAPD-specific sequence, specific SCAR primers denoted as FOFdpF and FOFdpR were developed. These SCAR primers amplified a single 517-bp DNA fragment, predominantly found in off-season flowering populations, with an accuracy rate of 60%. These findings underscore the potential of SCAR marker technology for tracking offseason flowering in date palms. Notably, a BLAST analysis revealed a substantial similarity between the SCAR marker sequence and the transcript variant mRNA from Phoenix dactylifera encoding the SET DOMAIN GROUP 40 protein. In Arabidopsis, this protein is involved in the epigenetic regulation of flowering time. The genetic potential of the off-season flowering traits warrants further elucidation.

• Korean Journal of Plant Resources
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• v.26 no.4
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• pp.491-502
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• 2013

Persimmon (Diospyros kaki Thunb) fruit is one of the most important fruit and have been cultivated from ancient times in Korea. In this study, we found 16 EST-SSR markers that contained one or more EST-SSR sites from 246 cDNA sequences. The developing of EST-SSR marker analysis from 42 persimmon cultivars was compared by genetic relationships and morphological relationships using 6 qualitative traits (fruit related 6 traits) and 19 quantitative traits (flower related 19 traits). In this study, 25 primer sets were tested to identify PCR polymorphism and 14 potential EST-SSR primer pairs were selected. The result of morphological relationship EST-SSR marker analysis showed that the coefficient 0.02 was difficult to categorize in several groups. And then, coefficient 0.77 of genetic relationship showed that the group was classified as four groups. The result of correlation distance between genetic relationship and morphological relationship were investigated was low significance (-0.03). Our results also provided an optimized method for improvement of breeding efficiency and introduce of superior character at persimmon cultivars using EST-SSR markers which was useful for further investigation.

• Korean Journal of Agricultural Science
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• v.47 no.3
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• pp.693-705
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• 2020

Grapes (Vitis spp. L.) are the third most produced fruit in the world. Crown gall disease caused by Agrobacterium vitis forms galls in the stems of the grapevines and reduces the vitality of the fruit trees, resulting in reduced yields. This pathogen has occurred in vineyards worldwide and caused serious economic losses. It is a soil-borne disease, so Agrobacterium vitis can survive for several years in vineyards and is difficult to control. Additionally, since there is no effective chemical control method, the most effective control method is the breeding of resistant varieties. To make the resistant variety, marker-assisted selection (MAS) enables fast breeding with low cost. In this study, we applied a genome-wide association study (GWAS), by combining phenotyping and genotyping-by-sequencing (GBS), for the development of a single nucleotide polymorphism (SNP) marker set related to crown gall disease using 350 grapevine varieties. As a result of the GBS based genotyping analysis, about 58,635 SNPs were obtained. In addition, the phenotypic analysis showed 35.2% resistance, 73% moderate susceptibility and 16.4% highly susceptibility. Moreover, after confirmation, two genes (VvARF4 and VvATL6-like) were shown to be related to crown gall disease based on the results of GWAS analysis, using the phenotypic data, and GBS. High-resolution melting analysis (HRMA) was performed using the Luna^® Universal Probe with real-time PCR to distinguish the melting peaks of the resistant and susceptible varieties. Our data show that these SNP markers are expected to be helpful in evaluating resistance against grapevine crown gall disease and in breeding.

• Journal of Korean Medicine Rehabilitation
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• v.31 no.1
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• pp.95-108
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• 2021

Objectives This study was conducted to investigate the beta-glucan, ginsenoside content, antioxidant activity and safety of modified Kyungohkgo added to Sparassis crispa and Hericium erinaceum. Methods The marker compounds contents, antioxidant activity and safety of modified Kyungohkgo were tested. The contents of beta-glucan and ginsenoside Rb1, Rg1, and Rg3 marker compounds were measured, the antioxidant activity was measured using 2,2-diphenyl-1-picrylhydrazyl (DPPH) free radical scavenging activity, and a safety test was conducted via single dose toxicity assessment. Results Analyzing the contents of marker compounds showed 351.75 mg/g of beta-glucan, 0.0327 mg/g of ginsenoside Rb1 and 0.0802 mg/g of ginsenosai Rg3. In the DPPH free radical scavenging activity, the inhibition concentration 50% of modified Kyungohkgo was 0.2880%. The scavenging activity of modified Kyungohkgo was 5.49% activity at 0.05% concentration, 89.66% activity at 0.5% concentration, 94.68% activity at 1% concentration, and 96.06% activity at 5% concentration. In the single dose toxicity test of modified Kyungohkgo, a dose of 2,000 mg/kg B.W. was set at its highest capacity and observed after oral administration to female and male rats. No toxicological findings were recognized. It was observed that the resulting lethal dose can be set to 2,000 mg/kg B.W. or higher for both females and males. Conclusions The results of the experiment on modified Kyungohkgo showed that the marker compounds contents were beta-glucan and ginsenoside Rb1 and Rg3, that antioxidant activity was observed through the DPPH free radical scavenging activity, and safety was confirmed through the single dose toxicity assessment.

• Journal of agriculture & life science
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• v.46 no.4
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• pp.85-92
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• 2012

This study was conducted to develop a set of EST-SSR marker for the purity test of commercial F1 hybrid cultivars in the watermelon. A total of 353 EST-SSR were selected and tested on seven F1 cultivars and their 11 parental lines achieved from NH Seeds Inc., Korea. Among tested 96 primer sets, WMU0056 for 'Orange', WMU0400 for 'Heukbo', WMU0056 and WMU0400 for 'Sindong', and WMU0056 and WMU0400 for 'Serona' revealed polymorphisms between the parental lines and heterozygosity from these F1 cultivers. Of 122 primer sets tested for 'Haedong', WMU0056, WMU0400, WMU0580, WMU1211, WMU4136, and WMU448 showed polymorphisms that were appropriate for the F1 purity test. WMU0056 and WMU0400 can be useful for 'Haedong', as well. Relatively low polymorphisms between parental lines were detected for 'Kulnara'(5%) and 'Hwangpea'(2%), and therefore, all 353 primer sets were tested on these cultivars. As the result, WMU5339 and WMU7003 were found to be useful for the F1 purity test in 'Kulnara' and 'Hwangpea', respectively. Using these EST-SSR markers developed by ICuGI, hybridity of the seeds for four F1 cultivars produced from farmers was evaluated, and levels of the F1 purity higher than 97.5% was observed from all seed populations. Our results indicated that the watermelon EST-SSR marker information posted in ICuGI could be utilized for developing codomiant and locus-specific markers that are highly effective for the F1 purity test.

• Proceedings of the Korean Society of Toxicology Conference
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• 2001.10a
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• pp.35-36
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• 2001

Nutrition influences cancer incidence and offers a variety of preventive dietary factors including non-nutritive plant metabolites. To identify novel potential chemopreventive agents, we have set up cell- and enzyme-based in vitro marker systems relevant for prevention of carcinogenesis in vivo. This experimental approach led to the identification of Xanthohumol (Xn), a prenylated chalcone from hop (Humulus lupulus L.) as a most promising broad-spectrum chemopreventive agent.(omitted)

• The Korea Journal of Herbology
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• v.33 no.3
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• pp.25-35
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• 2018

Objectives : Lepidii seu Descurainiae Semen has been frequently adulterated with the seeds of several inauthentic plant species. However, the accurate identification of these plant seeds is very difficult. To develop a reliable genetic authentication tool for Lepidii seu Descurainiae Semen, we analyzed matK sequence. Methods : To obtain the matK sequences of plant materials, genomic DNA was extracted from 24 samples and PCR amplification was carried out using matK-AF/matK-8R universal primer set and matK-LDSF/matK-LDSR primer set. For identifying species-specific nucleotides and phylogenetic analysis, matK regions were sequenced and comparatively analyzed by the ClustalW and Maximum Likelihood method. Results : We developed a new primer set to amplify matK region in Lepidii seu Descurainiae Semen and closely related plant samples. From the comparative analysis of matK sequences, we identified species-specific marker nucleotides for D. sophia, L. apetalum, L. latifolium, E. cheiranthoides, E. macilentum, and D. nemorosa, respectively. Furthermore, phylogenetic analysis revealed clear classification depending on the species. These results indicated that the matK sequence obtained a new primer set in this study was useful to identify Lepidii seu Descurainiae Semen in species level. Conclusions : We developed a primer set and identified species-specific marker nucleotides enough to distinguish authentic Lepidii seu Descurainiae Semen and adulterants at the species level based on the matK sequences. These genetic tool will be useful to prevent adulteration and to standardize the quality of Lepidii seu Descurainiae Semen.

• Journal of Animal Science and Technology
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• v.51 no.5
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• pp.353-360
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• 2009

When 14 microsatellite (MS) markers were applied in the identifying test for 480 Hanwoo, the discriminating power was estimated as $3.43{\times}10^{-27}$ based on the assumption of a random mating group (PI). This rate is 1,000 times higher than that of 60 single nucleotide polymorphism (SNP) markers. On the other hand, the power of the 60 SNP markers was estimated as $4.69{\times}10^{-20}$ and $8.02{\times}10^{-12}$ on the assumption of a half-sib mating group ($PI_{half-sibs}$) and a full-sib mating group ($PI_{sibs}$), respectively. These powers were 10 times and 10,000 times higher than those of the 14 MS markers. The results indicated that the total number of alleles (MS vs SNP = 146 vs 120) acted as a key factor for the discriminating power in a random mating population, and the total number of markers (MS vs SNP = 14 vs 60) was a dominant influence on the power in half-sib and full-sib populations. In the Hanwoo population, in which it was assumed that the entire population is the enormous half-sib group formed by the absolute genetic contribution of a few nuclear bulls, there will be only a 10 times difference in the discriminating power between the 14 MS markers and the 60 SNP makers. However, the probability of not excluding a candidate parent pair from the parentage of an arbitrary offspring, given that only the genotype of the offspring ($PNE_{pp}$) was 1,000 times higher as shown by the 14 MS markers than that by the 60 SNP markers. The strong points of SNP makers are the stability of the variation (low mutation rate) and automation of high-throughput genotyping. In order to apply these merits for the practical and constant Hanwoo identity test, research and development are required to set a cost-effective platform and produce a homemade apparatus for SNP genotyping.

• Journal of Life Science
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• v.20 no.3
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• pp.381-387
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• 2010

To find offspring of Jeju Black cattle (JBC) produced by embryo transfer (ET) and artificial insemination (AI), a molecular genetic study was carried out in candidate cattle populations collected from cattle farms in Jeju Island, Korea. The genetic marker set was composed of 11 ISAG microsatellite (MS) markers, 11 SAES MS markers selected by our preliminary analysis for population diversity of JBC and two major coat color related genes: MC1R and ASIP. The results showed a combined non-exclusion probability for first parent (NE-P1) that was higher than that recommended by ISAG (above 0.9995), and a combined non-exclusion probability for sib identity of $5.3{\times}10^{-10}$. Parentage analysis showed that the cases identified the candidate's father only (77.0%), mother only (54.0%), and both parents (40.5%) in the candidate offspring population. The ET and AI calves were identified as 14.7% in the in vitro fertilized eggs provided and 32.4% in total population, respectively. However, the result from ISAG marker analysis showed 3 identical allele-combinations in 7 calves, and that from ISAG/SAES MS marker combination also showed 1 identical allele-combination in 2 calves. Data from MS and coat-color gene analyses provided information for complete identification of all animals tested. Because the present JBC population was mostly bred using small nuclear founders through bioengineering techniques such as AI and ET, the genetic diversity levels obtained from MS analysis in the JBC population were relatively lower than those of other cattle populations, including Hanwoo. The results suggested that the more efficient marker combinations, including coat color related genotypes, should be studied and used for constructing a system for identification and molecular breeding of JBC as well.

• 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.