• Journal of Life Science
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• v.16 no.6
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• pp.949-954
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• 2006

Soybean [Glycine max (L.) Merr.] is an important crop, accounting for 48% of the world market in oil crops. Improvement of the quality and quantity of soybean seed constituents is one of the most important objectives in soybean breeding. Protein content and seed size are important properties to determine the quality of tofu and soy sprouts respectively. The objective of this study was to identify quantitative trait loci (QTLs) that control seed weight, protein and oil content in soybean. The 117 $F_{2:10}$ recombinant inbred lines (RlL) developed from a cross of 'Keunolkong' and 'Shinpaldalkong' were used. Narrow-sense heritability estimates based on a plot mean on seed weight, protein and oil content were 0.8, 0.78 and 0.71, respectively. Four independent QTLs for seed weight were identified from linkage group (LG) F, I and K. Five QTL for protein content were located on LG D1b, E, H, I and L. Oil content was related with six QTLs located on LG D1b, E, G, I, J and N. Protein and oil content have three common QTLs on LG D1b, E and I. Thus, we identified major loci improving soybean seed quality.

• 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 CROP SCIENCE
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• v.42 no.6
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• pp.712-721
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• 1997

The objectives of this study were; (1) to identify and localize QTLs for resistance to soybean cyst nematode(SCN) race 5 on RAPD map, (2) to idntify the magnitude and mode of inheritance for each QTL, and (3) to identify the best combinations of QTLs for resistance to SCN race 5. Based on the univariate regression analysis, we detected 26 markers(22 RAPD and 4 RFLP) which showed significant association(P<0.05) with resistance to SCN race 5. From MAPMAKER /QTL analysis, we identified two regions (LGC-20 and Group 2) for resistance to SCN race 5. The QTL that was localized at 8.0 cM from pK418C on LGC-20 showed a recessive mode of inheritance and the QTL that was localized between W03 and E02$^3$ on Group 2 showed a dominant mode of inheritance. Two pairs of flanking markers (E02$^3$ and W03, pK418C and pK418E$_1$) and one unlinked RAPD marker, G10$^1$ were used for multiple regression analysis. Marker combination which was composed of 4 markers, E02$^3$, G10$^1$, W03, and pK418E$_1$, explained the highest amount of phenotypic variation by SCN (35.2％). Further research for the identification of QTLs for resistance to SCN race 5 to explain larger portion of phenotypic variation is needed.

• Journal of Life Science
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• v.7 no.4
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• pp.358-360
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• 1997

Soybean [Glycine max (L.) Merr.] seed size is a important yield component and is a primary consideration in the development of cultivars for specialty markets. Our objective was to examine the consistency of QTLs for seed size across generations. A 68-plant F$_{2} segregation population derived from a mating between Marcury (small seed) and PI 467.468 (large seed) was evaluated with RAPD markers. In the F$_{2} plant generation (i.e. F$_{3} seed), three markers, OPL09a, OPM)7a, and OPAC12 were significantly (P<0.01) associated with seed size QTLs. In the F$_{2} ; F$_{3} generation (i.e., F$_{4} seed), four markers, OPA092, OPG19, OPL09b, and OPP11 were significantly (P<0.01) associated with seed size QTLs. Just two markers, OPL09a, and OPL09b were significantly (P<0.05) associated with seed size QTLs in both generations. The consistency of QTLs across generations indicates that marker-assisted selection for seed size is possible in a soybean breeding program.

• Asian-Australasian Journal of Animal Sciences
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• v.18 no.12
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• pp.1669-1674
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• 2005

Maximum likelihood methodology was applied to analyze the efficiency and statistical power of interval mapping by using a threshold model. The factors that affect QTL detection efficiency (e.g. QTL effect, heritability and incidence of categories) were simulated in our study. Daughter design with multiple families was applied, and the size of segregating population is 500. The results showed that the threshold model has a great advantage in parameters estimation and power of QTL mapping, and has nice efficiency and accuracy for discrete traits. In addition, the accuracy and power of QTL mapping depended on the effect of putative quantitative trait loci, the value of heritability and incidence directly. With the increase of QTL effect, heritability and incidence of categories, the accuracy and power of QTL mapping improved correspondingly.

• Asian-Australasian Journal of Animal Sciences
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• v.20 no.5
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• pp.669-676
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• 2007

This study was conducted to detect quantitative trait loci (QTL) affecting growth and body composition in an $F_2$ reference population of Korean native pig and Landrace crossbreds. The three-generation mapping population was generated with 411 progeny from 38 $F_2$ full-sib families, and 133 genetic markers were used to produce a sex-average map of the 18 autosomes. The data set was analyzed using least squares Mendelian and parent-of-origin interval-mapping models. Lack-of-fit tests between the models were used to characterize QTL for mode of expressions. A total of 8 (39) QTL were detected at the 5% genome (chromosome)-wise level for the 17 analyzed traits. Of the 47 QTL detected, 21 QTL were classified as Mendelian expressed, 13 QTL as paternally expressed, 6 QTL as maternally expressed, and 7 QTL as partially expressed. Of the detected QTL at 5% genome-wise level, two QTL had Mendelian mode of inheritance on SSC6 and SSC9 for backfat thickness and bone weight, respectively, two QTL were maternally expressed for leather weight and front leg weight on SSC6 and SSC12, respectively, one QTL was paternally expressed for birth weight on SSC4, and three QTL were partially expressed for hot carcass weight and rear leg weight on SSC6, and bone weight on SSC13. Many of the Mendelian QTL had a dominant (complete or overdominant) mode of gene action, and only a few of the QTL were primarily additive, which reflects that heterosis for growth is appreciable in a cross between Korean native pig and Landrace. Our results indicate that alternate breed alleles of growth and body composition QTL are segregating between the two breeds, which could be utilized for genetic improvement of growth via marker-assisted selection.

• Journal of Life Science
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• v.31 no.6
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• pp.568-573
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• 2021

This study identified genomic factors associated with endoplasmic reticulum protein (ERp)29 gene expression in a genome-wide association study (GWAS) of genetic variants, including single-nucleotide polymorphisms (SNPs). In total, 373 European genes from the 1000 Genomes Project were analyzed. SNPs with an allelic frequency of less than or more than 5% were removed, resulting in 5,913,563 SNPs including in the analysis. The following expression quantitative trait loci (eQTL) from the long noncoding RNA LOC105372577 were strongly associated with ERp29 expression: rs6138266 (p<4.172e10), rs62193420 (p<1.173e10), and rs6138267 (p<2.041e10). These were strongly expressed in the testis and in the brain. The three eQTL were identified through a transcriptome-wide association study (TWAS) and showed a significant association with ERp29 and osteosarcoma amplified 9 (OS9) expression. Upstream sequences of rs6138266 were recognized by ChIP-seq data, while HaploReg was used to demonstrate how its regulatory DNA binds upstream of transcription factor 1 (USF1). There were no changes in the expression of OS9 or USF1 following ER stress.

• Asian-Australasian Journal of Animal Sciences
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• v.25 no.1
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• pp.17-21
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• 2012

The purpose of this study was to improve mapping power and resolution for the QTL influencing carcass quality in Hanwoo, which was previously detected on the bovine chromosome (BTA) 6. A sample of 427 steers were chosen, which were the progeny from 45 Korean proven sires in the Hanwoo Improvement Center, Seosan, Korea. The samples were genotyped with the set of 2,535 SNPs on BTA6 that were imbedded in the Illumina bovine 50 k chip. A linkage disequilibrium variance component mapping (LDVCM) method, which exploited both linkage between sires and their steers and population-wide linkage disequilibrium, was applied to detect QTL for four carcass quality traits. Fifteen QTL were detected at 0.1% comparison-wise level, for which five, three, five, and two QTL were associated with carcass weight (CWT), backfat thickness (BFT), longissimus dorsi muscle area (LMA), and marbling score (Marb), respectively. The number of QTL was greater compared with our previous results, in which twelve QTL for carcass quality were detected on the BTA6 in the same population by applying other linkage disequilibrium mapping approaches. One QTL for LMA was detected on the distal region (110,285,672 to 110,633,096 bp) with the most significant evidence for linkage (p< $10^{-5}$). Another QTL that was detected on the proximal region (33,596,515 to 33,897,434 bp) was pleiotrophic, i.e. influencing CWT, BFT, and LMA. Our results suggest that the LDVCM is a good alternative method for QTL fine-mapping in detection and characterization of QTL.

• Plant Resources
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• v.3 no.3
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• pp.184-193
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• 2000

Soybean [Glycine max (L.) Merr.] seed weight is a important trait in cultivar development. Objective of this study was to identify and confirm quantitative trait loci (QTLs) for seed weight variation in the F2 and F2:3 generations. QTLs for seed weight were identified in F2 and F2:3 generations using interval mapping (MapMaker/QTL) and single-factor analysis of variance (ANOVA). In the F2 plant generation (i.e., F3 seed), three markers, OPL9a, OPM7a, and OPAC12 were significantly (P<0.01) associated with seed weight QTLs. In the F2:3 plant row generation (i.e., F4 seed), five markers, OPA9a, OPG19, OPL9b, OPP11, and Sat_085 were significantly (P<0.01) associated with seed weight QTLs. Two markers, OPL9a and OPL9b were significantly (P<0.05) associated with seed weight QTLs in both generations. Two QTLs on USDA soybean linkage group C1 and R were identified in both F2 and F2:3 generations using interval mapping. The linkage group C1 QTL explained 16% of the variation in seed weight in both generations, and the linkage group R QTL explained 39% and 41% of the variation for F2 and F2:3 generation, respectively. The linkage group C2 QTL identified in F2:3 generation explained 14.9% of variation. Linkage groups C1, C2 and R had previously been identified as harbouring seed size QTLs. The consistency of QTLs across generations and populations indicates that marker-assisted selection is possible in a soybean breeding program.

• Proceedings of the Korean Society of Crop Science Conference
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• 2021.04a
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• pp.119-119
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• 2021