• Korean Journal of Animal Reproduction
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• v.25 no.4
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• pp.295-304
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• 2001

Characterization of quantitative trait loci (QTL) was investigated in the experimental crosses between Berkshire and Yorkshire breed. A total of 525 F$_2$ progenies from 65 matting of F$_1$ Parents were produced. Phenotypic measurements included average daily gain (ADG), average back fat thickness (ABF), and loin eye area (LEA). To identify the presence of QTL for reproductive performance, birth weight (BWT) and body weight at 16 days (16DAY) were included as indirect trait. QTL segregation was deduced using 8 markers assigned to chromosome 2 (SSC2). Quantitative trait locus analyses were performed using interval mapping by regression under line-cross model. Presence of imprinting was tested under the statistical model that separated the expression of paternally and maternally inherited alleles. To set the evidence of QTL presence, significance thresholds were derived by permutation following statistical tests, respectively. Genome scan revealed significant evidence for three quantitative trait loci (QTL) affecting growth and body compositions, of which two were identified to be QTL with imprinting expression mode near the ICF II gene region. For average back fat thickness (ABF), a paternally expressed QTL was found on chromosome 2 (SSC2). A paternally expressed QTL affecting loin eye area (LEA) was found in the region of SSC2 where evidence of imprinted QTL was found for average back fat thickness (ABF). For average daily gain (ADG), QTL expressed with Mendelian mode was found on chromosome 2 (SS2). Also, QTL affecting average daily gain (ADC), was identified to be expressed with Mendelian express mode.

• Journal of Animal Science and Technology
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• v.46 no.4
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• pp.525-536
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• 2004

The objective of this study was to identify the quantitative traits loci(QTL) for meat quality traits in pigs. Three-generation resource population was constructed from a cross between Korean native boars and Landrace sows. The resource population including founders, $F_1$ and $F_2$ was genotyped for 23 microsatellite markers on chromosome 7. The sex average total length of linkage map on chromosome 7 was estimated 154.6 cM. Meat quality traits including meat pH, meat color, drip loss, shear force, heating loss, crude fat, crude protein, crude ash and water content in muscle were collected from $F_2$ animals. For the QTL mapping, we used $F_2$ QTL Analysis Servlet of QTL express for web-based QTL mapping tools(http://qtl.cap.ed.ac.uk/). The QTLs for CIE-a and CIE-b on SSC7 were significantly detected at 1% and 5% chromosome-wide level, respectively.

• 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.

• 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.

• Asian-Australasian Journal of Animal Sciences
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• v.16 no.10
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• pp.1402-1405
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• 2003

The QTL(quantitative traits loci) linkage mapping of Hanwoo (Korean Cattle) chromosome 6 for daily gain and marbling score was performed using 378 individuals from 18 paternal half-sib families in Hanwoo. Hanwoo chromosome 6 were mapped to total length of 394.2 cM between 28 microsatellite loci using 36 microsatellite primers of BTA 6 linkage group. The QTL analysis for daily gain in Hanwoo showed 8 microsatellite loci (BM3026-5.66, EL03-5.58, BM4311-5.29, ILSTS035-4.50, BMS1242-4.37, BM1329-3.67, BM415-3.11, BMS2460-3.03) in larger than LOD score 3.0. Based on the QTL analysis for marbling score, LOD scores of 12 microsatellite loci (BM415-8.88, BM3026-7.15, ILSTS093-5.45, ILSTS035-4.91, EL03-4.69, BMS690-4.52, BM1329-4.43, BMS511-3.74, BMS1242-3.66, BMS518-3.65, BM4311-3.41, BMC4203-3.36) were found larger than 3.0.

• Asian-Australasian Journal of Animal Sciences
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• v.24 no.12
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• pp.1644-1650
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• 2011

This study was conducted to detect quantitative trait loci (QTL) affecting meat quality 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 17 autosomes. The data set was analyzed using least squares Mendelian and parent-of-origin interval-mapping models. Lack-of-fit tests between models were used to characterize the QTL for mode of gene expressions. A total of 10 (32) QTL were detected at the 5% genome (chromosome)-wise level for the analyzed traits. Of the 42 QTL detected, 13 QTL were classified as Mendelian, 10 as paternal, 14 as maternal, and 5 as partial expressed QTL, respectively. Among the QTL detected at 5% genome-wise level, four QTL had Mendelian mode of inheritance on SSCs 5, 10, 12, and 13 for cooking loss, drip loss, crude lipid and crude protein, respectively; two QTL maternal inheritance for pH at 24-h and shear force on SSC11; three QTL paternal inheritance for CIE b and Hunter b on SSC9 and for cooking loss on SSC15; and one QTL partial expression for crude ash on SSC13, respectively. Most of the Mendelian QTL (9 of 13) had a dominant mode of gene action, suggesting potential utilization of heterosis for genetic improvement of meat quality within the cross population via marker-assisted selection.

• Asian-Australasian Journal of Animal Sciences
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• v.32 no.12
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• pp.1826-1835
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• 2019

Objective: Testicular growth and development are strongly influenced by androgen. Although both testis weight and plasma testosterone level are inherited traits, the interrelationship between them is not fully established. Males of DDD/Sgn (DDD) mice are known to have extremely heavy testes and very high plasma testosterone level among inbred mouse strains. We dissected the genetic basis of testis weight and analyzed the potential influence of plasma testosterone level in DDD mice. Methods: Quantitative trait loci (QTL) mapping of testis weight was performed with or without considering the influence of plasma testosterone level in reciprocal $F_2$ intercross populations between DDD and C57BL/6J (B6) mice, thereby assessing the influence of testosterone on the effect of testis weight QTL. Candidate genes for testis weight QTL were investigated by next-generation sequencing analysis. Results: Four significant QTL were identified on chromosomes 1, 8, 14, and 17. The DDDderived allele was associated with increased testis weight. The $F_2$ mice were then divided into two groups according to the plasma testosterone level ($F_2$ mice with relatively "low" and "high" testosterone levels), and QTL scans were again performed. Although QTL on chromosome 1 was shared in both $F_2$ mice, QTL on chromosomes 8 and 17 were identified specifically in $F_2$ mice with relatively high testosterone levels. By whole-exome sequencing analysis, we identified one DDD-specific missense mutation Pro29Ser in alpha tubulin acetyltransferase 1 (Atat1). Conclusion: Most of the testis weight QTL expressed stronger phenotypic effect when they were placed on circumstance with high testosterone level. High testosterone influenced the QTL by enhancing the effect of DDD-derived allele and diminishing the effects of B6-derived allele. Since Pro29Ser was not identified in other inbred mouse strains, and since Pro29 in Atat1 has been strongly conserved among mammalian species, Atat1 is a plausible candidate for testis weight QTL on chromosome 17.

• 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.

• Journal of Crop Science and Biotechnology
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• v.11 no.1
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• pp.7-12
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• 2008

Quantitative trait loci, a genetic concept for explaining the inheritance of non-Mendelian traits in 1940s, have been realized as particular fragments of chromosome even unique genes in most crops in 21st century. However, only very a small portion of QTL has been screened out by geneticists comparing to a great number of genes underneath the quantitative traits. These identified QTL even have been seldom used into breeding program because crop breeders may not find the QTL in their breeding populations in their field station. Several key points will be proposed to meet the challenges of QTL analysis today: a fine mapping population and the related reference genetic map, QTL evaluation in multiple environments, recognizing real QTL with small genetic effect, map integration.

• Asian-Australasian Journal of Animal Sciences
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• v.18 no.12
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• pp.1675-1683
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• 2005

In the process of crossbreeding, the linkage disequilibria between the quantitative trait loci (QTL) and their linked markers were reduced gradually with increasing generations. To study the potential of QTL mapping using the crossbred population, we presented a mixed effect model that treated the mean allelic value of the different founder populations as the fixed effect and the allelic deviation from the population mean as random effect. It was assumed that there were fifty QTLs having effect on the trait variation, the population mean and variance were divided to each QTL in founder generation in our model. Only the additive effect was considered in this model for simulation. Six schemes (S1-S6) of crossbreeding were studied. The selection index was used to evaluate the synthetic breeding value of two traits of the individual in the scheme of S2, S4 and S6, and the individuals with high selection index were chosen as the parents of the next generation. Random selection was used in the scheme of S1, S3 and S5. In this study, we premised a QTL explained 40% of the genetic variance was located in a region of 20 cM by the linkage analysis previously. The log likelihood ratio (log LR) was calculated to determine the presence of a QTL at the particular chromosomal position in each of the generations from the fourth to twentieth. The profiles of log LR and the number of the highest log LR located in the region of 5, 10 and 20 cM were compared between different generations and schemes. The profiles and the correct number reduced gradually with the generations increasing in the schemes of S2, S4 and S6, but both of them increased in the schemes of S1, S3 and S5. From the results, we concluded that the crossbreeding population undergoing random selection was suitable for improving the resolution of QTL mapping. Even experiencing index selection, there was still enough variation existing within the crossbred population before the fourteenth generation that could be used to refine the location of QTL in the chromosome region.