• KOREAN JOURNAL OF CROP SCIENCE
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• v.59 no.4
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• pp.391-397
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• 2014

Anthocyanins are water-soluble plant pigments that give rise to the red, purple, or blue colors observed in many crops. Especially purple pigment of colored rice represent biological activities has been an increased interest, due to the functional meal as a staple food. These health benefits have been attributed to antioxidant property of anthocyanin. However, there have been little genetic source for development of new and various colored rice variety. A recently developed new variety, 'Jungmo1020', showed an unique characteristic of blue color of rice grain hull. We identified the pigment petunidin-3-O-glucoside (Pt-3-G) as a major compound with a value of $176.3{\pm}2.3mg/100g$ (68.3%) from 80% MeOH with 1% HCl extracts by UPLC/MS/MS. The content of Pt-3-G in the extracts using a solvent of 100% MeOH with 1% HCl was the highest with the values of $183.8{\pm}2.5mg/100g$. In addition, these extracts showed excellent antioxidatative activities by DPPH and ABTs assay.

• Horticultural Science & Technology
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• v.35 no.1
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• pp.98-107
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• 2017

A DNA profile database was constructed to investigate the genetic relatedness of 72 germplasm samples of Pyrus and related cultivars using microsatellite markers. Three P. pyrifolia, four P. commus, and one P. betulifolia cultivars with different morphological traits were screened using 387 pairs of microsatellite primers. A core set of 11 primer pairs was selected to obtain 133 polymorphic amplified fragments meeting three criteria: high polymorphism information contents (PIC), high repeatability, and distinct allele patterns. The number of alleles per locus ranged between 4 and 22. Average PIC was 0.743 (range: 0.557 - 0.879). Cluster analysis using the unweighted pair - group method with arithmetical average (UPGMA) separated the 72 pear cultivars and germplasm samples into four major groups: Chinese, European pears, and a cluster of 55 Asian pears that could be reclassify into two subcluster, I - $1^{st}$ and II - $2^{nd}$, according to pedigree information. Almost all of the cultivars were discriminated by 11 microsatellite marker genotypes. The microsatellite DNA profile database may be utilized as tool to verify distinctness, uniformity, and stability between candidate cultivar, and to verify in the distinctness of existing cultivars.

• The Korean Journal of Mycology
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• v.42 no.2
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• pp.159-164
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• 2014

For development of a method for differentiation of Pleurotus eryngii cultivars, simple sequence repeats (SSR) from whole genomic DNA sequence analysis was used for genotyping and two multiplex-SSR primer sets were developed. These SSR primer sets were employed to distinguish 12 cultivars and strains. Five polymorphic markers were selected based on the genotyping results. PCR using each primer produced one to four distinct bands ranging in size from 200 to 300 bp. Polymorphism information content (PIC) values of the five markers were in the range of 0.6627 to 0.6848 with an average of 0.6775. Unweighted pairgroup method with arithmetic mean clustering analysis based on genetic distances using five SSR markers classified 12 cultivars into two clusters. Cluster I and II were comprised of four and eight cultivars, respectively. Two multiplex sets, Multi-1 (SSR312 and SSR366) and Multi-2 (SSR178 and SSR277) completely discriminated 12 cultivars and strains with 21 alleles and a PIC value of 0.9090. These results might be useful in providing an efficient method for the identification of P. eryngii cultivars with separate PCR reactions.

• Plant Breeding and Biotechnology
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• v.6 no.4
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• pp.391-403
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• 2018

Genome resequencing by next-generation sequencing technology can reveal numerous single nucleotide polymorphisms (SNPs) within a closely-related cultivar group, which would enable the development of sufficient SNP markers for mapping and the identification of useful genes present in the cultivar group. We analyzed genome sequence data from 13 Korean japonica rice varieties and discovered 740,566 SNPs. The SNPs were distributed at 100-kbp intervals throughout the rice genome, although the SNP density was uneven among the chromosomes. Of the 740,566 SNPs, 1,014 SNP sites were selected on the basis of polymorphism information content (PIC) value higher than 0.4 per 200-kbp interval, and 506 of these SNPs were converted to Kompetitive Allele-Specific PCR (KASP) markers. The 506 KASP markers were tested for genotyping with the 13 sequenced Korean japonica rice varieties, and polymorphisms were detected in 400 KASP markers (79.1%) which would be suitable for genetic analysis and molecular breeding. Additionally, a genetic map comprising 205 KASP markers was successfully constructed with 188 $F_2$ progenies derived from a cross between the varieties, Junam and Nampyeong. In a phylogenetic analysis with 81 KASP markers, 13 Korean japonica varieties showed close genetic relationships and were divided into three groups. More KASP markers are being developed and these markers will be utilized in gene mapping, quantitative trait locus (QTL) analysis, marker-assisted selection and other strategies relevant to crop improvement.

• Journal of Mushroom
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• v.19 no.1
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• pp.76-80
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• 2021

To develop a method for the differentiation of Pleurotus ostratus cultivars, the multiplex-simple sequence repeat (SSR) primer set based on the SSRs obtained from whole genomic DNA sequence analysis was designed with two polymerase chain reaction (PCR) primer sets. These SSR primer sets were employed to distinguish 10 cultivars and strains. Twenty polymorphic markers were selected based on the genotyping results. PCR with each primer produced 1-4 distinct bands ranging in size from 150 to 350 bp, which was within the expected range. However, since a sole SSR marker was unable to detect polymorphisms in every cultivar, multiplex PCRs with composite PCR primer sets were employed. The multiplex primer, "166+115," completely discriminated 12 cultivars and strains with 40 loci, which were 12 more than the simple arithmetic addition of each locus of the primers 115 and 166. These results might be useful to provide an efficient method for the differentiation of P. ostreatus cultivars with separate PCRs for the quality control of spawn and protection of breeders' rights.

• Journal of The Korean Society of Grassland and Forage Science
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• v.40 no.4
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• pp.259-264
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• 2020

The aim of this study was to investigate the feasibility of discrimination 12 different cultivar of sorghum × sudangrass hybrid (Sorghum genus) seed through near infrared spectroscopy (NIRS). The amount of samples for develop to the best discriminant equation was 360. Whole samples were applied different three spectra range (visible, NIR and full range) within 680-2500 nm wavelength and the spectrastar 2500 Near near infrared was used to measure spectra. The calibration equation for discriminant analysis was developed partial least square (PLS) regression and discrimination equation (DE) analysis. The PLS discriminant analysis model for three spectra range developed with mathematic pretreatment 1,8,8,1 successfully discriminated 12 different sorghum genus. External validation indicated that all samples were discriminated correctly. The whole discriminant accuracy shown 82 ~ 100 % in NIR full range spectra. The results demonstrated the usefulness of NIRS combined with chemometrics as a rapid method for discrimination of sorghum × sudangrass hybrid cultivar through seed.

• Korean Journal of Agricultural Science
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• v.38 no.2
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• pp.285-294
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• 2011

Glucosinolate (GSL) contents were investigated (i) at 1~7 days after sowing (DAS) in seed sprouts and (ii) at 3-7 weeks after sowing for the time-course. Moreover, (iii) They were compared with five different cultivars of rocket salad (Eruca sativa). Seventeen GSLs were separated by HPLC analysis, and 10 GSLs among them were identified as glucoraphanin, sinigrin, glucoalyssin, diglucothiobeinin, glucobrassicanapin, glucoerucin, glucobrassicin, dimeric, 4-mercaptobutyl GSL, 4-methoxy glucobrassicin, gluconasturttin by using LC-APCI-MS analysis, but 7 compounds were not identified. (i) The total GSL content in seed sprouts initially increased up to 3 DAS and then decreased according to their seedling growth. In particular, glucoraphanin known as a strong anti-cancer reagent was found the highest level (5.05 ${\mu}mol/g$ dry wt.) at 3 DAS. The most abundant GSL was glucoerucin ranged from 26.0~49.6 ${\mu}mol/g$ dry wt. (ii) In the time-course, the total GSL contents increased dramatically from 3-week (5.91 ${\mu}mol/g$ dry wt.) to 7-week after sowing (32.2 ${\mu}mol/g$ dry wt.). The major GSLs were glucoraphanin, glucoerucin and 4-methoxy glucobrassicin. (iii) By comparing GSL contents with five different cultivars, the total GSL contents increased from 4-week to 6-week after sowing, regardless of cultivar. In 4-week-old, the order with the total GSL content was "Rucola" > "Rocket Herbs" ${\geqq}$ "Odyssey" > "Takii" > "Herb", but in 6-week-old it is changed as "Takii" > "Herb" > "Odyssey" > "Rucola" > "Rocket Herbs" even there was almost no significantly difference between them.

• Korean Journal of Agricultural Science
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• v.45 no.3
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• pp.385-400
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• 2018

Marker-assisted backcrossing (MABC) is useful for selecting offspring with a highly recovered genetic background for a recurrent parent at early generation unlike rice and other field crops. Molecular marker sets applicable to practical MABC are scarce in vegetable crops including tomatoes. In this study, we used the National Center for Biotechnology Information- short read archive (NCBI-SRA) database that provided the whole genome sequences of 234 tomato accessions and selected 27,680 tag-single nucleotide polymorphisms (tag-SNPs) that can identify haplotypes in the tomato genome. From this SNP dataset, a total of 143 tag-SNPs that have a high polymorphism information content (PIC) value (> 0.3) and are physically evenly distributed on each chromosome were selected as a MABC marker set. This marker set was tested for its polymorphism in each pairwise cross combination constructed with 124 of the 234 tomato accessions, and a relatively high number of SNP markers polymorphic for the cross combination was observed. The reliability of the MABC SNP set was assessed by converting 18 SNPs into Luna probe-based high-resolution melting (HRM) markers and genotyping nine tomato accessions. The results show that the SNP information and HRM marker genotype matched in 98.6% of the experiment data points, indicating that our sequence analysis pipeline for SNP mining worked successfully. The tag-SNP set for the MABC developed in this study can be useful for not only a practical backcrossing program but also for cultivar identification and F1 seed purity test in tomatoes.

• Molecules and Cells
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• v.41 no.4
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• pp.342-350
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• 2018

Flowering time is determined by florigens. These genes include, Heading date 3a (Hd3a) and Rice FT 1 (RFT1) in rice, which are specifically expressed in the vascular tissues of leaves at the floral transition stage. To study the cis-regulatory elements present in the promoter region of Hd3a, we generated transgenic plants carrying the 1.75-kb promoter fragment of Hd3a that was fused to the ${\beta}$-glucuronidase (GUS) reporter gene. Plants expressing this construct conferred a vascular cell-specific expression pattern for the reporter gene. However, GUS was expressed in leaves at all developmental stages, including the early seedling stage when Hd3a was not detected. Furthermore, the reporter was expressed in roots at all stages. This suggests that the 1.75-kb region lackings cis-elements that regulate leaf-specific expression at the appropriate developmental stages. Deletion analyses of the promoter region indicated that regulatory elements determining vascular cell-specific expression are present in the 200-bp region between -245 bp and -45 bp from the transcription initiation site. By transforming the Hd3a-GUS construct to rice cultivar 'Taichung 65' which is defective in Ehd1, we observed that Ehd1 is the major regulatory element that controls Hd3a promoter activity.

• Korean Journal of Plant Resources
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• v.24 no.3
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• pp.272-279
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• 2011

It is very crucial to evaluate the genetic diversity of peanut genetic resources for identification of peanut germplasm accessions and variety improvement. Cultivated peanut generally has two subspecies, hypogaea and fastigiata. In this study, we identified peanut into three plant types, virginia (var. hypogaea), spanish (var. vulgaris), and valencia (var. fastigiata). Former one belongs to ssp. hypogaea and latter two are involved in ssp. fastigiata. Twenty SSR markers were used to assess the genetic variation of three sets, hypogaea, vulgaris, and fastigiata, respectively. Out of variety-specific SSR primers tried in this study, ten pairs of SSR primers showed polymorphisms. Each accession could be identified by a specific set of polymorphic SSR primers, and allele number was evaluated among accessions, with an average of 6.7 in var. hypogaea and 5.4 in var. vulgaris and fastigiata. For evaluation of genetic diversity, gene diversity ranged from 0.336 to 0.844 and PIC (polymorphism information contents) ranged from 0.324 to 0.827 were investigated. Dendrograms based on genetic distances were constructed, which showed the existence of three different clusters. And these three different clusters might be associated with the genes involved in three plant types. The results also suggested that there were plentiful SSR polymorphisms among peanut germplasm accessions in RDA (Rural Development Administration, Korea) Genebank and SSRs might play an important role in evaluating peanut accessions and cultivar improvement.