• Genomics & Informatics
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• v.6 no.3
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• pp.130-135
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• 2008

The haplotypes of a 200 kb region in the human chromosome X terminal band (q28) were analyzed using the International HapMap Project Phasell data, which had been collected for three analysis panels (YRI, CEU, and CHB＋JPT). When multiple linkage disequilibrium blocks were encountered for a panel, the neighboring haplotypes that had crossover rate of 5% or more in the panel were combined to generate 'haploid' configurations. This resulted in 8, 7, and 5 'haploid' configurations for the panels of YRI, CEU, and CHB＋JPT, respectively. The multiple sequence alignment of these 'haploids' was used for the calculation of allele-sharing distances and the subsequent principal coordinate analysis. Two 'haploids' in CEU and CHB＋JPT were hypothesized as 'parental' in light of the observations that the successive recombinants of these haploids can model two other haploids in CEU and CHB＋JPT, and that their configurations were consistent with those in YRI. This study demonstrates the utility of haplotype phylogeny in understanding population evolution.

• KOREAN JOURNAL OF CROP SCIENCE
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• v.52 no.1
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• pp.51-54
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• 2007

Soybean has a morphological type with a broadened and flattened stem. Fasciation has been suggested as a new gene for soybean research. SSR marker linked to the $\Large f$ locus that controls fasciation phenotype has not identified within 10 cM. A mapping population consisting of 94 $F_2$ progenies was derived from a cross between wild type Clark (FF) and fasciation mutant C32 (${\Large f}{\Large f}$). The phenotype of $F_2$ individual plants was recorded at R2 and R3 growth stage from field. One-thousand 10-mer oligonucleotide RAPD primers and 29 SSR primers selected from the D1b+W of the soybean molecular linkage map were used. A genetic map was constructed from the segregating 35 RAPD, four SSR markers and one phenotypic(wild type/fasciation) marker. The segregation ratios of 3 : 1 observed in the $F_2$ population and the Chi-square values strongly suggest that the fasciation trait is controlled by a single recessive gene. Satt537 marker was linked to $\Large f$ locus at a distance of 9.6 cM. Assignment of the $\Large f$ locus to linkage group D1b+W and identification of markers can be used as an initial step for fine mapping of the $\Large f$ gene.

• KOREAN JOURNAL OF CROP SCIENCE
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• v.51 no.2
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• pp.169-172
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• 2006

Leaflet number of soybean controlled by Lf2 locus is the important trait in photosynthesis and plant type. The objective of this research was to identity molecular markers linked to the lf2 locus. A total of $115F_2$ plants were derived from a cross between normal three-leaflet type Sinpaldalkong (Lf2Lf2) and seven-leaflet mutant type T255 (lf2lf2). All leaflet counts of parents and $F_2$ individual plants were made in the field on fully expanded leaves on the main stem when terminal growth of the main stem had ceased. One-thousand 10-mer oligonucleotide RAPD primers and 664 SSR primers were used. The segregation ratios of 3 : 1 were observed in the $F_2$ population and the Chi-square values strongly suggested that the seven-leaflet was controlled by a single recessive gene. A genetic map was constructed from the 15 segregating markers (9 RAPDs, 5 SSRs, 1 lf2 locus). OPAD03 and OPAI13 RAPD markers were linked to the lf2 locus that controlled seven-leaflet type at a distance of 20.5 and 23.5 cM, respectively. Molecular markers identified in this study linked with lf2 locus will be helpful to locate lf2 locus on the public soybean molecular linkage map and would be useful for tagging the lf2 locus that controls seven-leaflet trait.

• Proceedings of the Korean Society of Crop Science Conference
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• 2017.06a
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• pp.148-148
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• 2017

Soybean is an important economical resource of protein and oil for human and animals. The genetic basis of seed protein and oil content has been separately characterized in soybean. However, the genetic relationship between seed protein and oil content remains to be elucidated. In this study, we used a combined analysis of phenotypic correlation and linkage mapping to dissect the relationship between seed protein and oil content. A $F_{10:11}$ RIL population containing 222 lines, derived from the cross between two Korean soybean cultivars Seadanbaek as female and Neulchan as male parent, were used in this experiment. Soybean seed analyzed were harvested in three different experimental environments. A genetic linkage map was constructed with 180K SoyaSNP Chip and QTLs of both traits were analyzed using the software QTL IciMapping. QTL analyses for seed protein and oil content were conducted by composite interval mapping across a genome wide genetic map. This study detected four major QTL for oil content located in chromosome 10, 13, 15 and 16 that explained 13.2-19.8% of the phenotypic variation. In addition, 3 major QTL for protein content were detected in chromosome 10, 11 and 16 that explained 40.8~53.2% of the phenotypic variation. A major QTLs was found to be associated with both seed protein and oil content. A major QTL were mapped to soybean chromosomes 16, which were designated qHPO16. These loci have not been previously reported. Our results reveal a signi cant genetic relationship between seed protein and oil fi content traits. The markers linked closely to these major QTLs may be used for selection of soybean varieties with improved seed protein and oil content.

• Horticultural Science & Technology
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• v.32 no.4
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• pp.535-543
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• 2014

Backcross breeding is the method most commonly used to introgress new traits into elite lines. Conventional backcross breeding requires at least 4-5 generations to recover the genomic background of the recurrent parent. Marker-assisted backcrossing (MABC) represents a new breeding approach that can substantially reduce breeding time and cost. For successful MABC, highly polymorphic markers with known positions in each chromosome are essential. Single nucleotide polymorphism (SNP) markers have many advantages over other marker systems for MABC due to their high abundance and amenability to genotyping automation. To facilitate MABC in hot pepper (Capsicum annuum), we utilized expressed sequence tags (ESTs) to develop SNP markers in this study. For SNP identification, we used Bukang $F_1$-hybrid pepper ESTs to prepare a reference sequence through de novo assembly. We performed large-scale transcriptome sequencing of eight accessions using the Illumina Genome Analyzer (IGA) IIx platform by Solexa, which generated small sequence fragments of about 90-100 bp. By aligning each contig to the reference sequence, 58,151 SNPs were identified. After filtering for polymorphism, segregation ratio, and lack of proximity to other SNPS or exon/intron boundaries, a total of 1,910 putative SNPs were chosen and positioned to a pepper linkage map. We further selected 412 SNPs evenly distributed on each chromosome and primers were designed for high throughput SNP assays and tested using a genetic diversity panel of 27 Capsicum accessions. The SNP markers clearly distinguished each accession. These results suggest that the SNP marker set developed in this study will be valuable for MABC, genetic mapping, and comparative genome analysis.

• Journal of Crop Science and Biotechnology
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• v.11 no.4
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• pp.243-248
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• 2008

The bean bug Riptortus clavatus Thunberg (Heteroptera: Alydidae) is an important pest, causing serious yield loss in soybean. But the information on mechanism of resistance to R. clavatus is limited. The objective of this study was to identify QTLs for R. clavatus resistance using simple sequence repeat (SSR) markers in a soybean population of recombinant inbred lines (RILs) developed from the cross PI 171451 ${\times}$ Hwaeomputkong. A genetic map from this population was constructed with a total of 136 SSR markers covering 1073.9 cM on 20 linkage groups (LGs). With 126 $F_5$ RILs, two independent QTLs for resistance to R. clavatus were mapped on LGs B1 and C2. The amount of phenotypic variation explained by these QTLs ranged from 12 to 16%. PI 171451 showed an escape response to R. clavatus. Under feeding conditions, 14.4% of RILs showed greater resistance to R. clavatus than the resistant parent. The resistance to R. clavatus in soybean from PI 171451 was incomplete and quantitatively inherited and the QTLs for resistance to R. clavatus detected in the RIL population were not significantly affected by epistatic interactions.

• Spatial Information Research
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• v.19 no.6
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• pp.75-86
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• 2011

This paper proposes a modified way to delimit the boundary of Busan metropolitan area and compares the empirical analysis with the existing metropolitan area boundary. More specifically, the present state of the metropolitan transportation network is reflected by service area analysis in our study area. The analysis of the linkage between the central city and its fringes considers various travel behaviors as well as commuting to work and school, based on origin-destination trip information. In addition, more diverse indices are applied to the analysis of urban characteristics, and the land cover map is used as well. Compared with the current Busan metropolitan area boundary, our empirical analysis captures the status quo of the undergoing spatial dynamics such as the newly form ed homogeneous sphere of living in our study area.

• Proceedings of the Korean Society of Crop Science Conference
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• 2022.10a
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• pp.282-282
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• 2022

Arsenic (As) is a toxic heavy metal that affects the major rice-growing regions of the world and can cause cancer in humans. Rice paddy fields in South Asia are mostly dependent on arsenic-contaminated water sources due to which rice takes up the arsenic from the soil through roots and accumulates it in plant different parts. Here, we present a quantitative trait locus (QTL) mapping study to find out candidate genes conferring As toxicity tolerance in rice (Oryza sativa L.) at the seedling stage. Three weeks old, 120 double haploid CNDH lines derived from a cross between the Indica variety Cheongcheong and the Japonica variety Nagdong and their parental lines were used by treating with 25 μM As. After 2 weeks ofAs stress, 5 traits such as; shoot length (SL), root length (RL), shoot fresh weight (SFW), root fresh weight (RFW), and chlorophyll contents (CHC) were measured. A linkage map of 12 rice chromosomes was constructed from genotypic data DH lines using 778 SSR markers. The linkage map covered a total genetic distance of 2121.7 cM of the rice genome with an average interval of 10.6 cM between markers. A total of seventeen QTLs (LOD>2) were mapped on chromosomes 1, 2, 3, 6, 7, 8, 9, 11, and 12 using composite interval mapping with trait-increasing alleles coming from both parents. Five QTLs for SL, Two QTLs for RL, Five QTLs for SHL, Three QTLs for RFW, and Two QTLs for CHC were detected. The QTLs related to CHC were selected for forther study.

• Journal of Animal Science and Technology
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• v.45 no.6
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• pp.939-948
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• 2003

The objective of this study was to identify the quantitative traits loci(QTL) for economically important traits such as growth, carcass and meat quality on pig chromosome 6. A three generation resource population was constructed from cross between Korean native boars and Landrace sows. A total of 240 F$_2$ animals were produced using intercross between 10 boars and 31 sows of F$_1$ animals. Phenotypic data including body weight at 3 weeks, backfat thickness, muscle pH, shear force and crude protein level were collected from F$_2$ animals. Animals including grandparents(F$_0$), parents(F$_1$) and offspring(F$_2$) were genotyped for 29 microsatellite markers and PCR-RFLP marker on chromosome 6. The linkage analysis was performed using CRI-MAP software version 2.4(Green et al., 1990) with FIXED option to obtain the map distances. The total length of SSC6 linkage map estimated in this study was 169.3cM. The average distance between adjacent markers was 6.05cM. For mapping of QTL, we used F$_2$ QTL Analysis Servlet of QTL express, a web-based QTL mapping tool(http://qtl.cap.ed.ac.uk). Five QTLs were detected at 5% chromosome-wide level for body weight of 3 weeks of age, shear force, meat pH at 24 hours after slaughtering, backfat thickness and crude protein level on SSC6.

• Genomics & Informatics
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• v.5 no.4
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• pp.152-160
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• 2007

Most common diseases are caused by multiple genetic and environmental factors. Among the genetic factors, single nucleotide polymorphisms (SNPs) are common DNA sequence variations in individuals and can serve as important genetic markers. Recently, investigations of gene-based and whole genome-based SNPs have been applied to association studies for marker discovery. However, SNPs are so population-specific that the association needs to be verified. Fifty-five genes and 384 SNPs were selected based on association with disease. Genotypes of 337 SNPs in candidate genes were determined using Illumina Sentrix Array Matrix (SAM) chips by an allele-specific extension method in 364 unrelated Korean individuals. Allelic frequencies of SNPs were compared with those of other populations obtained from the International HapMap database. Minor allele frequencies, linkage disequilibrium blocks, tagSNPs, and haplotypes of functional candidate SNPs in 55 genetic disease-associated genes were provided. Our data may provide useful information for the selection of genetic markers for gene-based genetic disease-association studies of the Korean population.