• Asian-Australasian Journal of Animal Sciences
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• v.16 no.3
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• pp.320-324
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• 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.

• KOREAN JOURNAL OF CROP SCIENCE
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• v.44 no.2
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• pp.166-170
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• 1999

The identification of quantitative trait loci (QTL) has the potential to enhance the efficiency of im- proving food processing traits of soybean. In this study, 92 restriction fragment length polymorphism (RFLP) loci and two morphological markers (W$_1$ and T) were used to identify QTL associated with food processing traits of soybean for sprout in 83 F$_2$-derived lines from a cross of ＇Pureun＇ x ＇Jinpum 2＇. The genetic map consisted of 76 loci which covered about 760 cM and converged into 20 linkage groups. Eighteen markers remained unlinked. Phenotypic data were collected for hypocotyl length, abnormal seedling rate, and sprout yield seven days after seed germination at 2$0^{\circ}C$. Based on the single-factor analysis of variance, eight independent markers were associated with hypocotyl length. Four of seven markers associated with abnormal seedling rate were identified as independent. Seven loci were associated with sprout yield. For three different traits, much of genetic variation was explained by the identified QTL in this population. Several RFLP markers in linkage group (LG) Bl were detected as being associated with three traits, providing a genetic explanation for the biological correlation of sprout yield with hypocotyl length (r=OA07＊＊＊) and with abnormal seedling rate (r=-406＊＊＊).

• Asian-Australasian Journal of Animal Sciences
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• v.27 no.10
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• pp.1406-1410
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• 2014

Age at first calving is an important trait for achieving earlier reproductive performance. To detect quantitative trait loci (QTL) for reproductive traits, a genome wide association study was conducted on the 96 Hanwoo cows that were born between 2008 and 2010 from 13 sires in a local farm (Juk-Am Hanwoo farm, Suncheon, Korea) and genotyped with the Illumina 50K bovine single nucleotide polymorphism (SNP) chips. Phenotypes were regressed on additive and dominance effects for each SNP using a simple linear regression model after the effects of birth-year-month and polygenes were considered. A forward regression procedure was applied to determine the best set of SNPs for age at first calving. A total of 15 QTL were detected at the comparison-wise 0.001 level. Two QTL with strong statistical evidence were found at 128.9 Mb and 111.1 Mb on bovine chromosomes (BTA) 2 and 7, respectively, each of which accounted for 22% of the phenotypic variance. Also, five significant SNPs were detected on BTAs 10, 16, 20, 26, and 29. Multiple QTL were found on BTAs 1, 2, 7, and 14. The significant QTLs may be applied via marker assisted selection to increase rate of genetic gain for the trait, after validation tests in other Hanwoo cow populations.

• Asian-Australasian Journal of Animal Sciences
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• v.15 no.2
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• pp.303-308
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• 2002

Genetic markers engendered by genome projects drew enormous interest in quantitative genetics, but knowledge on genetic architecture of complex traits is limited. Complexities in genetics will not allow us to easily clarify relationship between genotypes and phenotypes for quantitative traits. Quantitative genetics guides an important way in facing such challenges. It is our exciting task to find genes that affect complex traits. In this paper, landmark research and future prospects are discussed on genetic parameter estimation and quantitative trait locus (QTL) mapping as major subjects of interest.

• 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.20 no.3
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• pp.453-460
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• 2007

An overview of developments important in the future of animal breeding is discussed. Examples from the application of quantitative genetic principles to selection in chickens and mice are given. Lessons to be learned from these species are that selection for production traits in livestock must also consider selection for reproduction and other fitness-related traits and inbreeding should be minimized. Short-term selection benefits of best linear unbiased predictor methodology must be weighed against long-term risks of increased rate of inbreeding. Different options have been developed to minimize inbreeding rates while maximizing selection response. Development of molecular genetic methods to search for quantitative trait loci provides the opportunity for incorporating marker-assisted selection and introgression as new tools for increasing efficiency of genetic improvement. Theoretical and computer simulation studies indicate that these methods hold great promise once genotyping costs are reduced to make the technology economically feasible. Cloning and transgenesis are not likely to contribute significantly to genetic improvement of livestock production in the near future.

• Genomics & Informatics
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• v.13 no.2
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• pp.40-44
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• 2015

DNA microarray and next-generation sequencing provide data that can be used for the genetic analysis of multiple quantitative traits such as gene expression levels, transcription factor binding profiles, and epigenetic signatures. In particular, chromatin opening is tightly coupled with gene transcription. To understand how these two processes are genetically regulated and associated with each other, we examined the changes of chromatin accessibility and gene expression in response to genetic variation by means of quantitative trait loci mapping. Regulatory patterns commonly observed in yeast and human across different technical platforms and experimental designs suggest a higher genetic complexity of transcription regulation in contrast to a more robust genetic architecture of chromatin regulation.

• Asian-Australasian Journal of Animal Sciences
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• v.22 no.10
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• pp.1359-1365
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• 2009

We performed a genome-wide linkage and quantitative trait locus (QTL) analysis to confirm the existence of QTL affecting Rous Sarcoma Virus (RSV) induced tumor regression, and to estimate their effects on phenotypic variance in an F2 resource population. The F2 population comprised 158 chickens obtained by crossing tumor regressive White Leghorn (WL) and tumor progressive Rhode Island Red (RIR) lines was measured for tumor formation after RSV inoculation. Forty-three tumor progressive and 28 tumor regressive chickens were then used for genome-wide linkage and QTL analysis using a total of 186 microsatellite markers. Microsatellite markers were mapped on 20 autosomal chromosomes. A significant QTL was detected with marker LEI0258 located within the MHC B region on chromosome 16. This QTL had the highest F ratio (9.8) and accounted for 20.1% of the phenotypic variation. Suggestive QTL were also detected on chromosomes 4, 7 and 10. The QTL on chromosome 4 were detected at the 1% chromosome-wide level explaining 17.5% of the phenotypic variation, and the QTLs on chromosome 7 and 10 were detected at the 5% chromosome-wide level and explained 11.1% and 10.5% of the phenotypic variation, respectively. These results indicate that the QTLs in the non-MHC regions play a significant role in RSV-induced tumor regression. The present study constitutes one of the first preliminary reports in domestic chickens for QTLs affecting RSV-induced tumor regression outside the MHC region.

• Molecules and Cells
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• v.37 no.2
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• pp.149-160
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• 2014

Plant breeders have focused on improving plant architecture as an effective means to increase crop yield. Here, we identify the main-effect quantitative trait loci (QTLs) for plant shape-related traits in rice (Oryza sativa) and find candidate genes by applying whole genome re-sequencing of two parental cultivars using next-generation sequencing. To identify QTLs influencing plant shape, we analyzed six traits: plant height, tiller number, panicle diameter, panicle length, flag leaf length, and flag leaf width. We performed QTL analysis with 178 $F_7$ recombinant inbred lines (RILs) from a cross of japonica rice line 'SNU-SG1' and indica rice line 'Milyang23'. Using 131 molecular markers, including 28 insertion/deletion markers, we identified 11 main- and 16 minor-effect QTLs for the six traits with a threshold LOD value > 2.8. Our sequence analysis identified fifty-four candidate genes for the main-effect QTLs. By further comparison of coding sequences and meta-expression profiles between japonica and indica rice varieties, we finally chose 15 strong candidate genes for the 11 main-effect QTLs. Our study shows that the whole-genome sequence data substantially enhanced the efficiency of polymorphic marker development for QTL fine-mapping and the identification of possible candidate genes. This yields useful genetic resources for breeding high-yielding rice cultivars with improved plant architecture.

• Asian-Australasian Journal of Animal Sciences
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• v.21 no.2
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• pp.155-160
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• 2008

Several studies have reported quantitative trait loci (QTL) for meat quality on porcine chromosome 2 (http://www.animalgenome.org/QTLdb/pig.html). For application of the molecular genetic information to the pig industry through marker-assisted selection, single nucleotide polymorphism (SNP) markers were analyzed by comparative re-sequencing of polymerase chain reaction (PCR) products of 13 candidate genes with DNA from commercial pig breeds such as Berkshire, Yorkshire, Landrace, Duroc and Korean Native pig. A total of 34 SNPs were identified in 15 PCR products producing an average of one SNP in every 253 bp. PCR restriction fragment length polymorphism (RFLP) assays were developed for 11 SNPs and used to investigate allele frequencies in five commercial pig breeds in Korea. Eight of the SNPs appear to be fixed in at least one of the five pig breeds, which indicates that different selection among pig breeds might be applied to these SNPs. Polymorphisms detected in the PTH, CSF2 and FOLR genes were chosen to genotype a Berkshire-Yorkshire pig breed reference family for linkage and association analyses. Using linkage analysis, PTH and CSF2 loci were mapped to pig chromosome 2, while FOLR was mapped to pig chromosome 9. Association analyses between SNPs in the PTH, CSF2 and FOLR suggested that the CSF2 MboII polymorphism was significantly associated with several pork quality traits in the Berkshire and Yorkshire crossed F2 pigs. Our current findings provide useful SNP marker information to fine map QTL regions on pig chromosome 2 and to clarify the relevance of SNP and quantitative traits in commercial pig populations.