• Asian-Australasian Journal of Animal Sciences
• /
• v.14 no.4
• /
• pp.587-596
• /
• 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
• /
• v.18 no.12
• /
• pp.1669-1674
• /
• 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
• /
• v.14 no.11
• /
• pp.1505-1510
• /
• 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
• /
• v.16 no.3
• /
• pp.320-324
• /
• 2003

The objective of this study was to localize QTL affecting meat quality in a pig family of three generations. All animals were genotyped for twenty-four microsatellites on SSC3 (Sus scrofa chromosome 3), SSC4 and SSC7. One hundred and forty $F_2$ offsprings were scored for eleven meat quality traits. Least square regression interval mapping revealed quantitative trait loci (QTL) effect for meat pH (m. Semipinalis Capitis, SC) on SSC4 and SSC7; for moisture (m. Longissimus Dorsi, LD) on SSC3. Furthermore, there was suggestive evidence for a QTL on SSC4 affecting intramuscular fat (IMF) content that nearly approached the chromosomewise (p=0.05) significance threshold.

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

• Korean Journal of Animal Reproduction
• /
• v.25 no.4
• /
• pp.295-304
• /
• 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
• /
• v.32 no.12
• /
• pp.1826-1835
• /
• 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.

• Journal of the Korean Data and Information Science Society
• /
• v.13 no.2
• /
• pp.97-104
• /
• 2002

K-Means modelling has been tried for finding major DNA marker of ILST035 microsatellite loci in Hanwoo Chromosome 6 linkage map. Major DNA markers are obtained from the ILST035 microsatellite through quantitative trait loci(QTL) and data mining modelling.

• Asian-Australasian Journal of Animal Sciences
• /
• v.15 no.7
• /
• pp.932-937
• /
• 2002

A partial genome scan using porcine microsatellites was carried out to detect quantitative trait loci (QTL) for backfat thickness (BFT) in a pig reference population. This population carried QTL on chromosomes 1, 13 and 18. The QTL on chromosome 1 was located between marker loci S0113 and SW1301. The QTL corresponded to very low density lipoprotein receptor gene (VLDLR) in location and in biological effects, suggesting that VLDLR might be a candidate gene. The QTL found on chromosome 13 was found between marker loci SWR1941 and SW864, but significance for the marker-trait association was inconsistent by using data with different generations. The QTL on chromosome 18 was discovered between markers S0062 and S0117, and it was in proximity of the regions where IGFBP3 and GHRHR were located. The porcine obese gene might be also a candidate gene for the QTL on chromosome 18. In order to understand genetic architecture of BFT better, fine mapping and positional comparative candidate gene analyses are necessary.

• Asian-Australasian Journal of Animal Sciences
• /
• v.28 no.7
• /
• pp.926-935
• /
• 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.