• Korean Journal of Breeding Science
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• v.42 no.5
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• pp.470-480
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• 2010

The objectives of this study were to identify QTLs for agronomic traits using introgression lines from a cross between a japonica weedy rice and a Tongil-type rice. A total of 75 introgression lines developed in the Tongil-type rice were characterized. A total of 368 introgressed segments including 285 homozygous and 83 heterozygous loci were detected on 12 chromosomes based on the genotypes of 136 SSR markers. Each of 75 introgression lines contained 0-9 homozygous and 0-8 heterozygous introgressed segments with an average of 5.8 segments per line. A total of 31 quantitative and 2 qualitative loci were identified for 14 agronomic traits and each QTL explained 4.1% to 76.6% of the phenotypic variance. Some QTLs were clustered in a few chromosomal regions. A first cluster was located near RM315 and RM472 on chromosome 1 with QTLs for 1,000 grain weight, culm length, grain width and thickness. Another cluster was detected with four QTLs for 1,000 grain weight, grain length, grain width and grain length/width ratio near the SSR marker RM249 on chromosome 5. Among the 31 QTLs, 9 (28.1%) Hapcheonaengmi3 alleles were beneficial in the Milyang23 background. ILs would be useful to confirm QTLs putatively detected in a primary mapping population for complex traits and serve as a starting point for map-based cloning of the QTLs. Additional backcrosses are being made to purify nearly isogenic lines (NILs) harboring a few favorable Hapcheonaengmi3 alleles in Milyang23 background.

• Journal of Ginseng Research
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• v.35 no.1
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• pp.52-59
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• 2011

Recently, new ginseng cultivars having superior agricultural traits have been developed in Korea. For newly developed plant cultivars, the identification of distinctiveness is very important factors not only in plant cultivar management but also in breeding programs. Thus, eighty-five inter simple sequence repeat (ISSR) primers were applied to detect polymorphisms among six major Korean ginseng cultivars and two foreign ginsengs. A total of 197 polymorphic bands with an average 5.8 polymorphic bands and 2.9 banding patterns per assay unit across six Korean ginseng cultivars and foreign ginsengs from 236 amplified ISSR loci with an average 6.9 loci per assay unit were generated by 34 out of 85 ISSR primers. Three species of Panax ginseng including the Korean ginseng cultivars, P. quinquefolius, and P. notoginseng, could be readily discriminated using most tested primers. UBC-821, UBC-868, and UBC-878 generated polymorphic bands among the six Korean ginseng cultivars, and could distinguish them from foreign ginsengs. Sequence characterized amplified region (SCAR) marker system was introduced in order to increase the reproducibility of the polymorphism. One SCAR marker, PgI821C650, was successfully converted from the randomly amplified polymorphism by UBC-821. It showed the expected dominant polymorphism among ginseng samples. In addition, the specific polymorphism for Sunwon was generated by treating Taq I restriction enzyme to polymerase chain reaction products of PgI821C650. These results will serve as useful DNA markers for identification of Korean ginseng, especially Sunwon cultivar, seed management, and molecular breeding program supplemented with marker-assisted selection.

• Korean Journal of Breeding Science
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• v.43 no.4
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• pp.322-329
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• 2011

Microsatellite markers were utilized to investigate genetic diversity among 70 Korean barley varieties (Hordeum vulgare). Ninety nine microsatellite primer pairs were screened for 9 varieties. Twenty primer pairs showed highly polymorphic. The relationship between markers genotypes and 70 varieties was analyzed. A total of 124 polymorphic amplified fragments were obtained by using 20 microsatellite markers. Two to nine SSR alleles were detected for each locus with an average of 6.2 alleles per locus. Average polymorphism information content (PIC) was 0.734, ranging from 0.498 to 0.882. A total of 124 marker loci were used to calculate Jaccard's distance coefficients for cluster analysis using UPGMA. Clustering group was divided 2 groups corresponding to 2-rowed and 6-rowed barley varieties. The phenogram was discriminated all varieties by markers genotypes. These markers may be used wide range of practical application in variety identification and genetic purity assessment of barley.

• Mycobiology
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• v.47 no.2
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• pp.200-206
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• 2019

Allelic differences in A and B mating-type loci are a prerequisite for the progression of mating in the genus Pleurotus eryngii; thus, the crossing is hampered by this biological barrier in inbreeding. Molecular markers linked to mating types of P. eryngii KNR2312 were investigated with randomly amplified polymorphic DNA to enhance crossing efficiency. An A4-linked sequence was identified and used to find the adjacent genomic region with the entire motif of the A locus from a contig sequenced by PacBio. The sequence-characterized amplified region marker $7-2_{299}$ distinguished A4 mating-type monokaryons from KNR2312 and other strains. A BLAST search of flanked sequences revealed that the A4 locus had a general feature consisting of the putative HD1 and HD2 genes. Both putative HD transcription factors contain a homeodomain sequence and a nuclear localization sequence; however, valid dimerization motifs were found only in the HD1 protein. The ACAAT motif, which was reported to have relevance to sex determination, was found in the intergenic region. The SCAR marker could be applicable in the classification of mating types in the P. eryngii breeding program, and the A4 locus could be the basis for a multi-allele detection marker.

• Asian-Australasian Journal of Animal Sciences
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• v.18 no.11
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• pp.1524-1528
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• 2005

Molecular genetic markers were used to detect chromosomal regions which contain economically important traits such as growth, carcass, and meat quality traits in pigs. A three generation resource population was constructed from a cross between Korean native boars and Landrace sows. A total of 240 F2 animals from intercross of F1 was produced. Phenotypic data on 17 traits, birth weight, body weights at 3, 5, 12, and 30 weeks of age, teat number, carcass weight, backfat thickness, body fat, backbone number, muscle pH, meat color, drip loss, cooking loss, water holding capacity, shear force, and intramuscular fat content were collected for F2 animals. Animals including grandparents (F0), parents (F1), and offspring (F2) were genotyped for 80 microsatellite markers covering from chromosome 1 to 10. Least squares regression interval mapping was used for quantitative trait loci (QTL) identification. Significance thresholds were determined by permutation tests. A total of 10 QTL were detected at 5% chromosome-wide significance levels for growth traits on SSCs 2, 4, 5, 6, and 8.

• Asian-Australasian Journal of Animal Sciences
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• v.21 no.5
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• pp.617-623
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• 2008

A fine-mapping method exploiting linkage disequilibrium was used to detect quantitative trait loci (QTL) on the X chromosome affecting milk production, body conformation and productivity traits. The pedigree comprised 22 paternal half-sib families of Black-and-White Holstein bulls in the Netherlands in a grand-daughter design for a total of 955 sons. Twenty-five microsatellite markers were genotyped to construct a linkage map on the chromosome X spanning 170 Haldane cM with an average inter-marker distance of 7.1 cM. A covariance matrix including elements about identical-by-descent probabilities between haplotypes regarding QTL allele effects was incorporated into the animal model, and a restricted maximum-likelihood method was applied for the presence of QTL using the LDVCM program. Significance thresholds were obtained by permuting haplotypes to phenotypes and by using a false discovery rate procedure. Seven QTL responsible for conformation types (teat length, rump width, rear leg set, angularity and fore udder attachment), behavior (temperament) and a mixture of production and health (durable prestation) were detected at the suggestive level. Some QTL affecting teat length, rump width, durable prestation and rear leg set had small numbers of haplotype clusters, which may indicate good classification of alleles for causal genes or markers that are tightly associated with the causal mutation. However, higher maker density is required to better refine the QTL position and to better characterize functionally distinct haplotypes which will provide information to find causal genes for the traits.

• Asian-Australasian Journal of Animal Sciences
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• v.26 no.11
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• pp.1536-1544
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• 2013

A least squares regression interval mapping model was derived to detect quantitative trait loci (QTL) with a unique mode of genomic imprinting, polar overdominance (POD), under a breed cross design model in outbred mammals. Tests to differentiate POD QTL from Mendelian, paternal or maternal expression QTL were also developed. To evaluate the power of the POD models and to determine the ability to differentiate POD from non-POD QTL, phenotypic data, marker data and a biallelic QTL were simulated on 512 F2 offspring. When tests for Mendelian versus parent-of-origin expression were performed, most POD QTL were classified as partially imprinted QTL. The application of the series of POD tests showed that more than 90% and 80% of medium and small POD QTL were declared as POD type. However, when breed-origin alleles were segregating in the grand parental breeds, the proportion of declared POD QTL decreased, which was more pronounced in a mating design with a small number of parents ($F_0$ and $F_1$). Non-POD QTL, i.e. with Mendelian or parent-of-origin expression (complete imprinting) inheritance, were well classified (>90%) as non-POD QTL, except for QTL with small effects and paternal or maternal expression in the design with a small number of parents, for which spurious POD QTL were declared.

• Korean Journal of Veterinary Research
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• v.41 no.3
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• pp.401-406
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• 2001

These studies were carried out to survey the genetic contamination of six inbred mice (A, BALB/c, C3H, C57BL/6, CBA and KK) produced and supplied from the conventional breeding unit for improving the quality of mice as experimental animal. We examined alleles of five loci (Akp-1, Car-2, Hbb, Es-1 and Trf) by the use of biochemical markers with celluose acetate electrophoresis. As the results of test, BALB/c, A, C3H, C57BL/6, CBA and KK showed standard alleles in Akp-1, Car-2 and Hbb. But Es-1 of A and C57BL/6 and Trf of A, C3H, C57BL/6 and CBA did allelic divergence in loci. These results suggest that the colonies of A, C3H, C57BL/6 and CBA were genetically contaminated. Therefore, we recommend to eliminate the genetically contaminated mice thoroughly, to check on genetic monitoring regularly and to consider a counterpaln for improving the quality control as soon as possible.

• Journal of Plant Biotechnology
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• v.47 no.2
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• pp.124-130
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• 2020

The sweet potato (Ipomoea batatas [L.] Lam.) is the sixth-most important crop in the world following rice, wheat, potato, maize, and cassava. Four varieties ('Beniharuka', 'Annobeni', 'Pungwonmi', 'Hogammi') and their Japanese cultivars are broadly distributed in South Korea. In the Korean marketplace, sweet potatoes are classified by color and shape, not by variety, making it necessary to differentiate varieties for uniform production and consumption. In this study, molecular markers were developed to distinguish the four varieties of sweet potato using SNPs and genotyping-by-sequencing (GBS) analysis via a tetra-primer amplification refractory mutation system (ARMS)-PCR. The results revealed that three variety-specific fragments (164 bp and 241 bp of SNP 04-27457768 and 292 bp of SNP 03-16195623) were amplified in the 'Beniharuka', 'Pungwonmi', and 'Annobeni' sweet potato varieties. There were instances where some varieties produced three bands within the gel electrophoresis, indicating heterozygosity at the given SNPs loci. DNA sequencing analysis also confirmed the results of electrophoresis at the SNPs loci. Overall, these molecular markers would provide a useful, rapid, and, simple evaluation method for the Korean sweet potato marketplace, where the mixing of varieties is a serious issue.

• Korean Journal of Agricultural Science
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• v.42 no.4
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• pp.397-406
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• 2015

Quantitative traits are mostly controlled by a large number of genes. Some of these genes tend to have a large effect on quantitative traits in cattle and are known as major genes primarily located at quantitative trait loci (QTL). The genetic merit of animals can be estimated by genomic selection, which uses genome-wide SNP panels and statistical methods that capture the effects of large numbers of SNPs simultaneously. In practice, the accuracy of genomic predictions will depend on the size and structure of reference and training population, the effective population size, the density of marker and the genetic architecture of the traits such as number of loci affecting the traits and distribution of their effects. In this review, we focus on the structure of Hanwoo reference and training population in terms of accuracy of genomic prediction and we then discuss of genetic architecture of intramuscular fat(IMF) and marbling score(MS) to estimate genomic breeding value in real small size of reference population.