• 농업과학연구
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• 제42권4호
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• pp.397-406
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• 2015

Quantitative traits are mostly controlled by a large number of genes. Some of these genes tend to have a large effect on quantitative traits in cattle and are known as major genes primarily located at quantitative trait loci (QTL). The genetic merit of animals can be estimated by genomic selection, which uses genome-wide SNP panels and statistical methods that capture the effects of large numbers of SNPs simultaneously. In practice, the accuracy of genomic predictions will depend on the size and structure of reference and training population, the effective population size, the density of marker and the genetic architecture of the traits such as number of loci affecting the traits and distribution of their effects. In this review, we focus on the structure of Hanwoo reference and training population in terms of accuracy of genomic prediction and we then discuss of genetic architecture of intramuscular fat(IMF) and marbling score(MS) to estimate genomic breeding value in real small size of reference population.

• Genomics & Informatics
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• 제11권3호
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• pp.135-141
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• 2013

Gene set analysis is a powerful tool for interpreting a genome-wide association study result and is gaining popularity these days. Comparison of the gene sets obtained for a variety of traits measured from a single genetic epidemiology dataset may give insights into the biological mechanisms underlying these traits. Based on the previously published single nucleotide polymorphism (SNP) genotype data on 8,842 individuals enrolled in the Korea Association Resource project, we performed a series of systematic genome-wide association analyses for 49 quantitative traits of basic epidemiological, anthropometric, or blood chemistry parameters. Each analysis result was subjected to subsequent gene set analyses based on Gene Ontology (GO) terms using gene set analysis software, GSA-SNP, identifying a set of GO terms significantly associated to each trait ($p_{corr}$ < 0.05). Pairwise comparison of the traits in terms of the semantic similarity in their GO sets revealed surprising cases where phenotypically uncorrelated traits showed high similarity in terms of biological pathways. For example, the pH level was related to 7 other traits that showed low phenotypic correlations with it. A literature survey implies that these traits may be regulated partly by common pathways that involve neuronal or nerve systems.

• 한국작물학회지
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• 제59권2호
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• pp.109-127
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• 2014

Maize is one of the most important food and feed crops in the world including Southeast Asia. In spite of numberous efforts with conventional breeding, the maize productions remain low and the loss of yields by drought and downy mildew are still severe in Asia. Genetic improvement of maize has been performed with molecular marker and genetic engineering. Because maize is one of the most widely studied crop for its own genome and has tremendous diversity and variant, maize is considered as a forefront crop in development and estimation of molecular markers for agricultural useful trait in genetics and breeding. Using QTL (Quantitative Trait Loci) and MAS (Marker Assisted Breeding), molecular breeders are able to accelerate the development of drought tolerance or downy mildew resistance maize genotype. The present paper overviews QTL/MAS approaches towards improvement of maize production against drought and downy mildew. We also discuss here the trends and importance of molecular marker and mapping population in maize breeding.

• Asian-Australasian Journal of Animal Sciences
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• 제28권11호
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• pp.1525-1531
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• 2015

Using next-generation sequencing, we conducted a genome-wide scan of selective sweeps associated with selection toward genetic improvement in Thoroughbreds. We investigated potential phenotypic consequence of putative candidate loci by candidate gene association mapping for the finishing time in 240 Thoroughbred horses. We found a significant association with the trait for Ral GApase alpha 2 (RALGAP2) that regulates a variety of cellular processes of signal trafficking. Neighboring genes around RALGAP2 included insulinoma-associated 1 (INSM1), pallid (PLDN), and Ras and Rab interactor 2 (RIN2) genes have similar roles in signal trafficking, suggesting that a co-evolving gene cluster located on the chromosome 22 is under strong artificial selection in racehorses.

• 한국작물학회:학술대회논문집
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• 한국작물학회 2017년도 9th Asian Crop Science Association conference
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• pp.103-103
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• 2017

Vigorous root growth at the seedling stage in dry direct-seeded conditions is considered as a critical trait because it is involved in seedling emergence, early vegetative vigour, nutrient uptake as well as drought tolerance. In this study, we performed QTL mapping using the recombinant inbred lines obtained from the cross between Tongil-type Dasan and temperate japonica TR22183 (DT-RILs) to identify QTL underlying early root development. TR22183, which was previously reported to have high nitrogen utility and cold tolerance, showed vigorous root growth at the seedling stage in semi-drought conditions. Root length, fresh weight and dry weight of TR22183 were significantly higher than in Dasan. By QTL analysis with genotyping-by-sequencing method, we identified two QTLs for root fresh weight (RFW) in chromosome 7 and root dry weight (RDW) in chromosome 8, explaining phenotypic variances of 13.5% and 10.6%, respectively. These QTLs would be used to develop rice varieties adapted to direct-seeded cultivating system.

• 한국축산식품학회지
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• 제32권6호
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• pp.776-782
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• 2012

Marbling (intramuscular fat) is the most economically important meat quality trait in Hanwoo (Korean cattle). The endothelial differentiation G-protein coupled receptor 1 (EDG1) gene, involved in blood vessel formation, is located within the genomic region of a quantitative trait locus (QTL) for marbling on bovine chromosome 3. Thus, the EDG1 gene can be considered as a positional and functional candidate gene for meat quality in beef cattle. This study aimed to identify single nucleotide polymorphisms (SNPs) in the EDG1 gene and to evaluate their associations with carcass traits in Hanwoo population. We have sequenced a fragment of 5'-UTR of the EDG1 gene and identified one SNP. Genotyping of the g.166A>G SNP marker was carried out using PCR-RFLP analysis in 309 Hanwoo steers in order to evaluate their association with carcass traits. The g.166A>G SNP marker showed a significant effect on the marbling score. Animals with the GG genotype had higher marbling score compared with AA and AG genotypes (p<0.05). This SNP marker also showed a significant additive effects for the marbling score (p<0.05). These results suggest that the EDG1 gene can be used as a molecular marker for DNA marker-assisted selection in order to increase the levels of the marbling score in Hanwoo.

• Journal of Crop Science and Biotechnology
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• 제10권4호
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• pp.243-248
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• 2007

Rice is a facultative short-day plant that flowers in response to reduced day lengths. This study was conducted to identify quantitative trait loci(QTL) for the early heading date(EHD) using H143 line showing extreme EHD compared to other regular cultivars in rice. The japonica H143 was crossed with a japonica cultivar 'Dongjinbyeo' as well as a tongil cultivar 'Milyang23' to measure the inheritance mode of EHD and identify major QTL conferring EHD, respectively. Pooling test revealed that segregation distortion occurred on chromosome 7 and subsequent linkage map was constructed using 10 SSR markers. QTL analysis using Q-gene 3.06 revealed that the EHD trait in H143 was largely controlled by two major QTL, EH7-1 and EH7-2, accounting for more than 40% of genetic variation that were closely related to the previously reported QTL, Hd4 and Hd2, respectively. This result suggests that these two QTL markers may be a useful source for the control of heading date in rice breeding programs.

• Asian-Australasian Journal of Animal Sciences
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• 제20권9호
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• pp.1327-1333
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• 2007

Lactose synthase catalyses the formation of lactose which is the major osmole of bovine milk and regulates the milk volume. Alpha-lactalbumin (${\alpha}$-LA) is involved in the synthesis of lactose synthase in the mammary gland. Therefore ${\alpha}$-LA is regarded as a plausible candidate gene for the milk yield trait. To determine whether ${\alpha}$-LA is associated with milk performance traits, 1,028 Chinese Holstein cows were used to detect polymorphisms in the ${\alpha}$-LA by means of single-strand conformation polymorphism (SSCP). Two nucleotide transitions were identified in the 5'flanking region and intron 3 of ${\alpha}$-LA. Associations of such polymorphisms with five milk performance traits were analyzed using a general linear model procedure. No significant associations were observed between these polymorphisms and the five milk performance traits (p>0.05). RH mapping placed ${\alpha}$-LA on BTA5q21, linked most closely to markers U63110, CC537786 and L10347 (LOD>8.3), which is far distant from the region of the quantitative trait locus (QTL) on bovine chromosome 5 for variation in the milk yield trait. In summary, based on our findings, we eliminated these SNPs from having an effect on milk performance traits.

• Asian-Australasian Journal of Animal Sciences
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• 제25권5호
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• pp.613-620
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• 2012

Marbling from intramuscular fat is an important trait of meat quality and has an economic benefit for the beef industry. Quantitative trait loci (QTL) fine mapping was performed to identify the marbling trait in 266 Hanwoo steers using a 10K single nucleotide polymorphism panel with the combined linkage and linkage disequilibrium method. As a result, we found nine putative QTL regions for marbling: three on BTA6, two on BTA17, two on BTA22, and two on BTA29. We detected candidate genes for marbling within 1 cM of either side of the putative QTL regions. Additionally, to understand the functions of these candidate genes at the molecular level, we conducted a functional categorization using gene ontology and pathway analyses for those genes involved in lipid metabolism or fat deposition. In these putative QTL regions, we found 95 candidate genes for marbling. Using these candidate genes, we found five genes that had a direct interaction with the candidate genes. We also found SCARB1 as a putative candidate gene for marbling that involves fat deposition related to cholesterol transport.

• Asian-Australasian Journal of Animal Sciences
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• 제24권2호
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• pp.162-172
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• 2011

In this paper, simulation was used to determine accuracies of genomic breeding values for polygenic traits associated with many thousands of markers obtained from high density genome scans. The statistical approach was based upon stochastically simulating a pedigree with a specified base population and a specified set of population parameters including the effective and noneffective marker distances and generation time. For this population, marker and quantitative trait locus (QTL) genotypes were generated using either a single linkage group or multiple linkage group model. Single nucleotide polymorphism (SNP) was simulated for an entire bovine genome (except for the sex chromosome, n = 29) including linkage and recombination. Individuals drawn from the simulated population with specified marker and QTL genotypes were randomly mated to establish appropriate levels of linkage disequilibrium for ten generations. Phenotype and genomic SNP data sets were obtained from individuals starting after two generations. Genetic prediction was accomplished by statistically modeling the genomic relationship matrix and standard BLUP methods. The effect of the number of linkage groups was also investigated to determine its influence on the accuracy of breeding values for genomic selection. When using high density scan data (0.08 cM marker distance), accuracies of breeding values on juveniles were obtained of 0.60 and 0.82, for a low heritable trait (0.10) and high heritable trait (0.50), respectively, in the single linkage group model. Estimates of 0.38 and 0.60 were obtained for the same cases in the multiple linkage group models. Unexpectedly, use of BLUP regression methods across many chromosomes was found to give rise to reduced accuracy in breeding value determination. The reasons for this remain a target for further research, but the role of Mendelian sampling may play a fundamental role in producing this effect.