• Asian-Australasian Journal of Animal Sciences
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• v.14 no.11
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• pp.1505-1510
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• 2001

A method for mapping quantitative trait loci (QTL) was introduced incorporating the information of mixed progeny from complex pedigrees. The method consisted of two steps based on single marker analysis. The first step was to examine the marker-trait association with a mixed model considering common environmental effect and reversed QTL-marker linkage phase. The second step was to estimate QTL effects by a weighted least square analysis. A simulation study indicated that the method incorporating mixed progeny from multiple generations improved the accuracy of QTL detection. The influence of within-genotype variance and recombination rate on QTL analysis was further examined. Detecting a QTL with a large within-genotype variance was more difficult than with a small within-genotype variance. Most of the significant marker-QTL association was detectable when the recombination rate was less than 15%.

• Asian-Australasian Journal of Animal Sciences
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• v.14 no.4
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• pp.587-596
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• 2001

In the last decade, rapid developments in molecular biotechnology and of genomic tools have enabled the creation of dense linkage maps across whole genomes of human, plant and animals. Successful development and implementation of interval mapping methodologies have allowed detection of the quantitative trait loci (QTL) responsible for economically important traits in experimental and commercial livestock populations. The candidate gene approach can be used in any general population with the availability of a large resource of candidate genes from the human or rodent genomes using comparative maps, and the validated candidate genes can be directly applied to commercial breeds. For the QTL detected from primary genome scans, two incipient fine mapping approaches are applied by generating new recombinants over several generations or utilizing historical recombinants with identity-by-descent (IBD) and linkage disequilibrium (LD) mapping. The high resolution definition of QTL position from fine mapping will allow the more efficient implementation of breeding programs such as marker-assisted selection (MAS) or marker-assisted introgression (MAI), and will provide a route toward cloning the QTL.

• 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.

• Animal Bioscience
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• v.35 no.4
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• pp.511-516
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• 2022

Objective: A genomic region associated with a particular phenotype is called quantitative trait loci (QTL). To detect the optimal F₂ population size associated with QTLs in native chicken, we performed a simulation study on F₂ population derived from crosses between two different breeds. Methods: A total of 15 males and 150 females were randomly selected from the last generation of each F₁ population which was composed of different breed to create two different F₂ populations. The progenies produced from these selected individuals were simulated for six more generations. Their marker genotypes were simulated with a density of 50K at three different heritability levels for the traits such as 0.1, 0.3, and 0.5. Our study compared 100, 500, 1,000 reference population (RP) groups to each other with three different heritability levels. And a total of 35 QTLs were used, and their locations were randomly created. Results: With a RP size of 100, no QTL was detected to satisfy Bonferroni value at three different heritability levels. In a RP size of 500, two QTLs were detected when the heritability was 0.5. With a RP size of 1,000, 0.1 heritability was detected only one QTL, and 0.5 heritability detected five QTLs. To sum up, RP size and heritability play a key role in detecting QTLs in a QTL study. The larger RP size and greater heritability value, the higher the probability of detection of QTLs. Conclusion: Our study suggests that the use of a large RP and heritability can improve QTL detection in an F₂ chicken population.

• Asian-Australasian Journal of Animal Sciences
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• v.25 no.11
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• pp.1507-1510
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• 2012

Quantitative trait loci (QTL) associated with fat deposition traits in pigs are important gene positions in a chromosome that influence meat quality of pork. For QTL study, 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 were produced. 80 microsatellite markers covering chromosomes 1 to 10 were selected to genotype the resource population. Intervals between adjacent markers were approximately 19 cM. Linkage analysis was performed using CRIMAP software version 2.4 with a FIXED option to obtain the map distances. For QTL analysis, the public web-based software, QTL express (http://www.qtl.cap.ed.ac.uk) was used. Two significant and two suggestive QTL were identified on SSC 6, 7, and 8 as affecting body fat and IMF traits. For QTL affecting IMF, the most significant association was detected between marker sw71 and sw1881 on SSC 6, and a suggestive QTL was identified between sw268 and sw205 on SSC8. These QTL accounted for 26.58% and 12.31% of the phenotypic variance, respectively. A significant QTL affecting IMF was detected at position 105 cM between markers sw71 and sw1881 on SSC 6.

• 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.

• 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.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.28 no.7
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• pp.926-935
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• 2015

The efficiency of genome-wide association analysis (GWAS) depends on power of detection for quantitative trait loci (QTL) and precision for QTL mapping. In this study, three different strategies for GWAS were applied to detect QTL for carcass quality traits in the Korean cattle, Hanwoo; a linkage disequilibrium single locus regression method (LDRM), a combined linkage and linkage disequilibrium analysis (LDLA) and a $BayesC{\pi}$ approach. The phenotypes of 486 steers were collected for weaning weight (WWT), yearling weight (YWT), carcass weight (CWT), backfat thickness (BFT), longissimus dorsi muscle area, and marbling score (Marb). Also the genotype data for the steers and their sires were scored with the Illumina bovine 50K single nucleotide polymorphism (SNP) chips. For the two former GWAS methods, threshold values were set at false discovery rate <0.01 on a chromosome-wide level, while a cut-off threshold value was set in the latter model, such that the top five windows, each of which comprised 10 adjacent SNPs, were chosen with significant variation for the phenotype. Four major additive QTL from these three methods had high concordance found in 64.1 to 64.9Mb for Bos taurus autosome (BTA) 7 for WWT, 24.3 to 25.4Mb for BTA14 for CWT, 0.5 to 1.5Mb for BTA6 for BFT and 26.3 to 33.4Mb for BTA29 for BFT. Several candidate genes (i.e. glutamate receptor, ionotropic, ampa 1 [GRIA1], family with sequence similarity 110, member B [FAM110B], and thymocyte selection-associated high mobility group box [TOX]) may be identified close to these QTL. Our result suggests that the use of different linkage disequilibrium mapping approaches can provide more reliable chromosome regions to further pinpoint DNA makers or causative genes in these regions.