• Journal of Applied Biological Chemistry
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• v.59 no.4
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• pp.323-330
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• 2016

Pinellia ternata Breitenbach, the natural medicinal plant of the Araceae family, is a perennial plant originated from the East Asia, but also widely distributed in Europe and North America. Its tuber is used as traditional medicine for treatment of various diseases such as vomiting, inflammation, and traumatic injury. Pharmacological studies revealed that P. ternata possesses anticonvulsant, anti-tumor, insecticidal, and cytotoxic activities. Despite being well-known as the useful medicinal plant, there is no reliable, standardized method for origin discrimination. Ultra performance liquid chromatography-photodiode array detector and quadrupole time of flight-mass spectrometry based metabolite-profiling was applied to explore significant metabolite for origin discrimination between Korean and Chinese P. ternata. One compound was isolated from Korean P. ternata using repeated ODS column chromatography by bioactivity guided fractionation, and determined as [6]-gingerol according to the results of spectroscopic data including nuclear magnetic resonance and MS. This compound was selected as cosmeceutical biomarker by fingerprints, and it was associated to melanin inhibitory effect determining its origin authenticity. Furthermore, the calibration curve of biomarker was prepared using validated method for the comparison of content between Korean and Chinese P. ternata. This is the report to address the selection and successful validation of the discriminant metabolite for confirmation of Korean P. ternata.

• Journal of Life Science
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• v.17 no.11
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• pp.1505-1510
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• 2007

We found 8 single nucleotide polymorphisms (SNPs) in adipocyte fatty acid bonding protein (FABP4) gene as candidate gene of FAT1 locus on pig chromosome 4. With over 800 heads of major commercial pig breeds including Duroc, Landrace, Berkshire and Yorkshire, we analyzed SNPs of FABP4 gene to determine possible effects of FABP4 genotype to economically important traits. $400{\sim}800\;bp$ amplicons in FABP4 gene were used PCR-RFLP for each SNPs and we found that the frequency of some SNPs of this gene was different among the breeds. According to the statistical analyses to determine possible associations of each genotype with economic traits, it was found that subgroup with different genotypes showed significant differences in daily gain, backfat thickness, lean percentage and feed conversion ratio (P<0.05). Thus, as a Part of enhancing the selection competence related to swine growth rate and lean percentage, it is expected that FABP4 gene markers verified in this study will be useful to use for Korean commercial pig industry.

• Korean Journal of Breeding Science
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• v.50 no.4
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• pp.434-441
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• 2018

High-density genetic linkage mapping is critical for undertaking marker-assisted selection and confirming quantitative trait loci, as well as helping to build pseudomolecules of genomes. We constructed a genetic map using 94 $F_1$ populations generated from the interspecific cross between Korean cultivar "Wonwhang" (Pyrus pyrifolia, NCBI BioSample SAMN05196235) and European cultivar "Bartlett" (Pyrus communis). We designed a total of 24,267 SSR markers based on the genome sequences of "Wonwhang" for this. To select the markers that are linked to the traits important in pear breeding programs, SSR-containing genomic sequences were subjected to nucleotide sequence homology searches, which resulted in 510 SSR markers with high similarity to genes encoding proteins with putative functions such as transcription factors, resistance proteins, flowering time, and regulatory genes. Of these, 70 markers showed polymorphisms in parents and segregating populations and were used to construct a genetic linkage map, together with the unpublished 579 SNPs obtained from genotyping by sequencing analysis. The genetic linkage map covered 3,784.2 cM and the average distance between adjacent markers was 5.8 cM. Seventy SSR markers were distributed across 17 chromosomes with more than one locus.

• Animal Bioscience
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• v.36 no.6
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• pp.861-868
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• 2023

Objective: Loin muscle area (LMA) is an important target trait of pig breeding. This study aimed to identify single nucleotide polymorphisms (SNPs) and genes associated with LMA in the Duroc×(Landrace×Yorkshire) crossbred pigs (DLY). Methods: A genome-wide association study was performed using the Illumina 50K chip to map the genetic marker and genes associated with LMA in 511 DLY pigs (255 boars and 256 sows). Results: After quality control, we detected 35,426 SNPs, including six SNPs significantly associated with LMA in pigs, with MARC0094338 and ASGA0072817 being the two key SNPs responsible for 1.77% and 2.48% of the phenotypic variance of LMA, respectively. Based on previous research, we determined two candidate genes (growth hormone receptor [GHR] and 3-oxoacid Co A-transferase 1 [OXCT1]) that are associated with fat deposition and muscle growth and found further additional genes (MYOCD, ARHGAP44, ELAC2, MAP2K4, FBXO4, FBLL1, RARS1, SLIT3, and RANK3) that are presumed to have an effect on LMA. Conclusion: This study contributes to the identification of the mutation that underlies quantitative trait loci associated with LMA and to future pig breeding programs based on marker-assisted selection. Further studies are needed to elucidate the role of the identified candidate genes in the physiological processes involved in LMA regulation.

• Asian-Australasian Journal of Animal Sciences
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• v.27 no.5
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• pp.616-627
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• 2014

The Lanyu is a miniature pig breed indigenous to Lanyu Island, Taiwan. It is distantly related to Asian and European pig breeds. It has been inbred to generate two breeds and crossed with Landrace and Duroc to produce two hybrids for laboratory use. Selecting sets of informative genetic markers to track the genetic qualities of laboratory animals and stud stock is an important function of genetic databases. For more than two decades, Lanyu derived breeds of common ancestry and crossbreeds have been used to examine the effectiveness of genetic marker selection and optimal approaches for individual assignment. In this paper, these pigs and the following breeds: Berkshire, Duroc, Landrace and Yorkshire, Meishan and Taoyuan, TLRI Black Pig No. 1, and Kaohsiung Animal Propagation Station Black pig are studied to build a genetic reference database. Nineteen microsatellite markers (loci) provide information on genetic variation and differentiation among studied breeds. High differentiation index ($F_{ST}$) and Cavalli-Sforza chord distances give genetic differentiation among breeds, including Lanyu's inbred populations. Inbreeding values ($F_{IS}$) show that Lanyu and its derived inbred breeds have significant loss of heterozygosity. Individual assignment testing of 352 animals was done with different numbers of microsatellite markers in this study. The testing assigned 99% of the animals successfully into their correct reference populations based on 9 to 14 markers ranking D-scores, allelic number, expected heterozygosity ($H_E$) or $F_{ST}$, respectively. All miss-assigned individuals came from close lineage Lanyu breeds. To improve individual assignment among close lineage breeds, microsatellite markers selected from Lanyu populations with high polymorphic, heterozygosity, $F_{ST}$ and D-scores were used. Only 6 to 8 markers ranking $H_E$, $F_{ST}$ or allelic number were required to obtain 99% assignment accuracy. This result suggests empirical examination of assignment-error rates is required if discernible levels of co-ancestry exist. In the reference group, optimum assignment accuracy was achievable achieved through a combination of different markers by ranking the heterozygosity, $F_{ST}$ and allelic number of close lineage populations.

• KOREAN JOURNAL OF CROP SCIENCE
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• v.60 no.3
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• pp.293-299
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• 2015

High temperature is one of major environmental stress. Heat tolerance managing is difficult through the phenotypic selection, so marker assistant selection (MAS) using molecular markers like as RAPD, SSR etc. was tried to select useful traits for heat tolerance. Fourteen SSR markers reported by previous research were selected for this research. We tried to evaluate 14 SSR markers for MAS using 31 useful wheat resources including 24 crossing line from Turkey, six Korean wheat cultivars and Chinese spring. The average of the number of alleles and PIC values in this study were 6.14 and 0.64, respectively. Two major clades and four sub clades were grouped by phylogenetic tree using UPGMA. Four Korean wheat cultivars were distinct from other Turkey resources in the phylogenetic dendrogram. From the results, we expected that these markers were able to adapt to screening wheat genotyping for heat tolerance.

• Horticultural Science & Technology
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• v.29 no.4
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• pp.345-351
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• 2011

This study was carried out to develop a model system using selection method for disease resistant plant breeding programs using a herbicide bialaphos-resistant patII gene as a gene-based marker. Spraying bialaphos could eliminate the susceptible plants from the segregating populations such as ${F_2}^{\prime}s$ and thereafter. Tomato cv. Momotaro-yoke was transformed with patII gene 60 independent transformants were acquired. Total 42 transformants were analyzed in transgene copy numbers by Southern blotting and the segregation ratios for the bialaphos resistance. Statistical analysis revealed that the transgene copy numbers and the segregation ratios were not always coincided, especially having the tendency of underestimating the real numbers of the transgenes in the multicopy lines. A two-stepwise screening method was applied to select $T_1$ tomato plants which linked the transgenic patII to a disease resistance gene (I2 and Ve). Based on the resistant to susceptible ratios, T-20 plant was finally selected due to the estimated linkage 12-13 cM between the patII gene to the I2 gene on chromosome 11. This newly developed system could be applied to any economical crop in breeding programs.

• Horticultural Science & Technology
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• v.29 no.5
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• pp.461-466
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• 2011

In genetic and molecular breeding studies of plants, researchers need to design various kinds of primers based on their research purposes. So far many kinds of web- or script-based non-commercial programs for primer design are available. Because most of them do not include user interface for multipurpose usage including gene structure prediction and direct target selection on sequences, it has been a laborious work to design primers targeting on the exon or intron regions of interesting genes. Here we report a primer designing graphic user interface program, Pickprimer, that includes gene structure prediction and primer design modules by combining source codes of the Spidey and Primer3 programs. This program provides simple graphic user interface to input sequences and design primers. Genomic sequence and mRNA or coding sequence of genes can be copy and pasted or input as fasta or text files. Based on alignment of the input sequences using the Spidey module, a putative gene structure is graphically visualized along with exon-intron sequences of color codes. Primer design can be easily performed by dragging mouse on the displayed sequences or input primer targeting position with desirable values of primers. The output of designed primers with detailed information is provided by the Primer3 module. PCR evaluation of 24 selected primer sets successfully amplified single amplicons from six Brassica rapa cultivars. The Pickprimer will be a convenient tool for genetic and molecular breeding studies of plants.

• Korean Journal of Environmental Agriculture
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• v.29 no.3
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• pp.287-292
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• 2010

We aimed to investigate the responses of soil organisms to cover plants and to provide information for the selection of proper plant species. We studied the effects of 7 cover plants, including rye, oat, rattail fescue, Chinese milk vetch, red clover, crimson clover, and hairy vetch, on soil organisms in an apple orchard. An increase in the microbial phospholipid fatty acids (PLFA) and in the number of nematodes and microarthropods in the soil under the cover plants reflects elevated activities of soil organisms. A decrease in the level of some marker PLFA, which is an indicator of environmental stress, suggests that cover plants provide favorable environments for soil organisms. The population of fungi and animals that feed on fungi increased in the soil surface under red clover. The population density of nematodes and mites increased in the soil surface under rattail fescue, and that of mites and omnivorous nematodes increased in the soil surface under Chinese milk vetch. The level of microbial PLFA in the soil surfaces under the tested cover plants was higher than that under clean culture system. These results suggest that proper selection of the cover plants can facilitate the creation of favorable environments for soil organisms.

• Journal of Plant Biotechnology
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• v.43 no.3
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• pp.272-280
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• 2016

Chrysanthemum is one of the top floriculture species with ornamental and medicinal value. Although chrysanthemum breeding program has contributed to the development of various cultivars so far, it needs to be advanced from the traditional phenotype-based selection to marker-assisted selection (molecular breeding) as shown in major cereal and vegetable crops. Molecular breeding relies on trait-linked molecular markers identified from genetic, molecular, and genomic studies. However, these studies in chrysanthemum are significantly hampered by the reproductive, genetic, and genomic properties of chrysanthemum such as self-incompatibility, inbreeding depression, allohexaploid, heterozygosity, and gigantic genome size. Nevertheless, several genetic studies have constructed genetic linkage maps and identified molecular markers linked to important traits of flower, leaf, and plant architecture. With progress in sequencing technology, chrysanthemum transcriptome has been sequenced to construct reference gene set and identify genes responsible for developments or induced by biotic or abiotic stresses. Recently, a genome sequencing project has been launched on a diploid wild Chrysanthemum species. The massive sequencing information would serve as fundamental resources for molecular breeding of chrysanthemum. In this review, we summarized the current status of molecular genetics and genomics in chrysanthemum and briefly discussed future prospects.