• Korean Journal of Breeding Science
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• v.42 no.4
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• pp.390-396
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• 2010

A weedy rice, Ganghwaaengmi 11, shows high level of leaf blast resistance. The chromosomal number and locations of genes conferring the leaf blast resistance were detected by QTL (quantitative trait loci) analysis using SSR markers in the 120 RILs (recombinant inbred lines) derived from the cross between Nagdongbyeo and Ganghwaaengmi 11. Ganghwaaengmi 11 expressed compatibility with 20 of the 45 inoculated blast isolates, in contrast to Nagdongbyeo with 44 compatible isolates. To identify QTLs affecting partial resistance, RILs were assessed in upland blast nursery in three regions and inoculated with selected nine blast isolates. QTLs for resistance to blast isolates were identified on chromosomes 7, 11 and 12. Three QTLs associated with blast resistance in nursery test at three regions were also detected on chromosomes 7, 11 and 12. The QTL commonly detected on chromosome 12 was only increased blast resistance by Ganghwaaengmi 11 allele. This QTL accounted for 60.3~78.6% of the phenotypic variation in the blast nursery test. OSR32 and RM101 markers tightly linked to QTL for blast resistance on chromosome 12 might be useful for marker-assisted selection (MAS) and gene pyramiding to improve the blast resistance of japonica rice.

• Asian-Australasian Journal of Animal Sciences
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• v.18 no.11
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• pp.1542-1547
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• 2005

The Melanocortin-4 Receptor (MC4R) and Insulin-like Growth Factor 2 (IGF2) are two important candidate genes related to fat deposition and carcass traits. MC4R was found on study on human obesity and then was studied as candidate gene affecting food intake and fat deposition traits in mice and pigs. Insulin-like Growth Factor 2 (IGF2) gene plays an important role on tumor cell proliferation and muscle growth. It also affects fat traits and live weight in pigs. In this paper, MC4R and IGF2 were studied as two candidate genes associated with important economic traits such as fat deposition and carcass traits in five different pig populations. Taq I-PCR-RFLP and Bcn I-PCR-RFLP were respectively used to detect the polymorphism of genotypes of MC4R and IGF2 genes. Different MC4R genotype frequencies were observed in four populations. IGF2 genotype frequencies were also different in two populations. The results of association analysis show both MC4R and IGF2 genes were significantly associated with fat deposition and carcass traits in about 300 pigs. This work will add new evidence of MC4R and IGF2 affecting fat deposition and carcass traits in pigs and show that two genes can be used as important candidate genes for marker assistant selection (MAS) of growth and lean meat percentage in pigs.

• Journal of Animal Science and Technology
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• v.49 no.5
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• pp.577-584
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• 2007

Adipocyte-specific secretory factor(ADSF)/resistin, an hormone, is a small cysteine-rich protein secreted from adipose tissue and ADSF/resistin has been implicated in modulating adipogenesis in human and rodents. Although the exact role of ADSF/resistin in bovine has not been identified, it may have directly or indirectly involved in adipocyte differentiation. The objective of this study was to investigate its DNA polymorphism associated with carcass traits in Korean Native Cattle(Hanwoo). To investigate DNA polymorphism in Hanwoo ADSF/resistin gene, blood samples were taken from 295 Hanwoo steers belonging to progeny testing at Hanwoo Improvement Center in Korea. Seven single nucleotide polymorphisms(SNPs) were found in intron regions but not in any other regions including promoter (1.7kb) and 4 exons. The highest frequency among SNPs was C186A(0.16/0.84) following G964A (0.156/0.884). The significant correlation(P<0.05) between the SNPs and economic traits was found on 764Ains associated with marbling but not from any other SNPs determined.  A computer simulation was also conducted to assess the efficiency of marker assisted selection(MAS) versus the conventional breeding scheme.  Results revealed that MAS was more efficient as a breeding tool compared to the conventional. In conclusion, ADSF/Resistin gene is one of candidate genes to evaluate the quality, especially marbling score, in Hanwoo.

• Asian-Australasian Journal of Animal Sciences
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• v.18 no.12
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• pp.1701-1707
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• 2005

This study deals with the characterization of porcine PIK3C3 and association tests with quantitative traits. PIK3C3 belongs to the class 3 PI3Ks that participate in the regulation of hepatic glucose output, glycogen synthase, and antilipolysis in typical insulin target cells such as those in the such as liver, muscle system, and fat. On the analysis of full-length mRNA sequence, the length of the PIK3C3 CDS was recorded as 2,664 bps. As well, nucleotide and amino acid identities between human and pig subjects were 92% and 99%, respectively. Five SNPs were detected over 5 exons. We performed genotyping by using a SNP C2604T on exon24 for 145 F$_2$ animals (from a cross between Korean native boars and Landrace sows) by PCR-RFLP analysis with Hpy8I used to investigate the relationship between growth and fat depot traits. In the total association analysis, which doesn' consider transmission disequilibrium, the SNP showed a significant effect (p<0.05) on body weight and carcass fat at 30 weeks of age as well as a highly significant effect (p<0.01) on back fat. In an additional sib-pair analysis, C allele still showed positive and significant effects (p<0.05) on back fat thickness and carcass fat. Moreover, the effects of C allele on the means of within-family components for carcass fat and back fat were estimated as 2.76 kg and 5.07 mm, respectively. As a result, the SNP of porcine PIK3C3 discovered in this study could be utilized as a possible genetic marker for the selection of pigs that possess low levels of back fat and carcass fat at the slaughter weight.

• Asian-Australasian Journal of Animal Sciences
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• v.28 no.10
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• pp.1394-1406
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• 2015

The AT motif-binding factor (ATBF1) not only interacts with protein inhibitor of activated signal transducer and activator of transcription 3 (STAT3) (PIAS3) to suppress STAT3 signaling regulating embryo early development and cell differentiation, but is required for early activation of the pituitary specific transcription factor 1 (Pit1) gene (also known as POU1F1) critically affecting mammalian growth and development. The goal of this study was to detect novel nucleotide variations and haplotypes structure of the ATBF1 gene, as well as to test their associations with growth-related traits in goats. Herein, a total of seven novel single nucleotide polymorphisms (SNPs) (SNP 1-7) within this gene were found in two well-known Chinese native goat breeds. Haplotypes structure analysis demonstrated that there were four haplotypes in Hainan black goat while seventeen haplotypes in Xinong Saanen dairy goat, and both breeds only shared one haplotype (hap1). Association testing revealed that the SNP2, SNP5, SNP6, and SNP7 loci were also found to significantly associate with growth-related traits in goats, respectively. Moreover, one diplotype in Xinong Saanen dairy goats significantly linked to growth related traits. These preliminary findings not only would extend the spectrum of genetic variations of the goat ATBF1 gene, but also would contribute to implementing marker-assisted selection in genetics and breeding in goats.

• Korean Journal of Ichthyology
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• v.27 no.1
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• pp.10-15
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• 2015

Giant grouper (Epinephelus lanceolatus) is a endangered species considered as a vulnerable grade-organism in the International Union for Conservation of Nature (IUCN) red list. As a fundamental baseline study for establishing a giant grouper broodstock management system, the efficiency for parentage analysis was evaluated by using microsatellite makers previously available in this species. The eight microsatellites generated a total 52 alleles from 32 individuals, the mean expected heterozygosity was 0.663, and mean inbreeding coefficient was 0.011, consequently suggesting that the present broodstock has retained the high level of genetic diversity. However, our analysis also recommended the collection of more broodfish for more stable brood line, since the estimated value of the effective population size was proven to be 35. The average probability of identity was $6.85{\times}10^{-11}$. NE-2P and NE-PP of paternity non-exclusion probabilities were 0.00835 and 0.00027, respectively. As the result of principle coordinate analysis, the genotype of broodstock was not overlapped, suggesting that the management system of giant grouper based on eight selected microsatellite markers might be effective, although further validation with extended number of broodfish might also be needed in future. Data of present study could be a useful basis to avoid the unwanted selection of broodfish that possess close genetic relationship with current broodstock, and consequently to establish effective broodstock management system allowing the production of progeny with high genetic diversity.

• Journal of Embryo Transfer
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• v.31 no.3
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• pp.281-285
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• 2016

Cluster-of-differentiation antigen 9 (CD9) gene expressed in the male germ line stem cells is crucial for sperm-egg fusion, and was therefore selected as a candidate gene to investigate Duroc boar semen motility and kinematic characteristics. This study was performed to investigatetheir association with semen motility and kinematic characteristics. DNA samples from 96 Duroc pigs with records of sperm motility and kinematic characteristics [Total motile spermatozoa (MOT, $82.27{\pm}5.58$), Curvilinear velocity(VCL, $68.37{\pm}14.58$), Straight-line velocity(VSL, $29.06{\pm}6.58$), the ratio between VSL and VCL(LIN, $47.36{\pm}8.42$), Amplitude of Lateral Head displacement(ALH, $2.88{\pm}0.70$)] were used in present study. A single nucleotide polymorphism (g.358A>T) in intron 6 was associated with MOT, VCL, VAP and ALH in Duroc population (p<0.05). Therefore, we suggest that the porcine CD9 may be used as a molecular marker for Duroc boar semen quality, although its functional effect was not clear yet. These results will improve the understanding of the functions of the CD9 in spermatogenesis within the reproductive tracts, and will shed light on CD9 as a candidate gene in the selection of good sperm quality boars.

• Proceedings of the Korean Society of Developmental Biology Conference
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• 2003.10a
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• pp.101-101
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• 2003

Main strategy for a treatment of Parkinson's disease (PD), due to a progressive degeneration of dopaminergic neurons, is a pharmaceutical supplement of dopamine derivatives or ceil replacement therapy. Both of these protocols have pros and cons; former exhibiting a dramatic relief but causing a severe side effects on long-term prescription and latter also having a proven effectiveness but having availability and ethical problems Embryonic stem (ES) cells have several characteristics suitable for this purpose. To investigate a possibility of using ES cells as a carrier of therapeutic gene(s), human ES (hES, MB03) cells were transfected with cDNAs coding for tyrosine hydroxylase (TH) in pcDNA3.1 (+) and the transfectants were selected using neomycin (250 $\mu /ml$). Expression of TH being confirmed, two of the positive clone (MBTH2 & 8) were second transfected with GTP cyclohydrolase 1 (GTPCH 1) in pcDNA3.1 (+)-hyg followed by selection with hygromycin-B (150 $\mu /ml$) and RT-PCR confirmation. By immune-cytochemistry, these genetically modified but undifferentiated dual drug-resistant cells were found to express few of the neuronal markers, such as NF200, $\beta$-tubulin, and MAP2 as well as astroglial marker GFAP. This results suggest that over-production of BH4 by ectopically expressed GTPCH I may be involved in the induction of those markers. Transplantation of the cells into striatum of 6-OHDA- denervated PD animal model relieved symptomatic rotational behaviors of the animals. Immunohistochemical analyses showed the presence of human cells within the striatum of the recipients. These results suggest a possibility of using hES cells as a carrier of therapeutic gene(s).

• Asian-Australasian Journal of Animal Sciences
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• v.23 no.4
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• pp.417-424
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• 2010

The purpose of this study was to detect significant SNPs for carcass quality traits using DNA chips of high SNP density in Hanwoo populations. Carcass data of two hundred and eighty nine steers sired by 30 Korean proven sires were collected from two regions; the Hanwoo Improvement Center of National Agricultural Cooperative Federation in Seosan, Chungnam province and the commercial farms in Gyeongbuk province. The steers in Seosan were born between spring and fall of 2006 and those in Gyeonbuk between falls of 2004 and 2005. The former steers were slaughtered at approximately 24 months, while the latter steers were fed six months longer before slaughter. Among the 55,074 SNPs in the Illumina bovine 50K chip, a total of 32,756 available SNPs were selected for whole genome association study. After adjusting for the effects of sire, region and slaughter age, phenotypes were regressed on each SNP using a simple linear regression model. For the significance threshold, 0.1% point-wise p value from F distribution was used for each SNP test. Among the significant SNPs for a trait, the best set of SNP markers were selected using a stepwise regression procedure, and inclusion and exclusion of each SNP out of the model was determined at the p<0.001 level. A total of 118 SNPs were detected; 15, 20, 22, 28, 20, and 13 SNPs for final weight before slaughter, carcass weight, backfat thickness, weight index, longissimus dorsi muscle area, and marbling score, respectively. Among the significant SNPs, the best set of 44 SNPs was determined by stepwise regression procedures with 7, 9, 6, 9, 7, and 6 SNPs for the respective traits. Each set of SNPs per trait explained 20-40% of phenotypic variance. The number of detected SNPs per trait was not great in whole genome association tests, suggesting additional phenotype and genotype data are required to get more power to detect the trait-related SNPs with high accuracy for estimation of the SNP effect. These SNP markers could be applied to commercial Hanwoo populations via marker-assisted selection to verify the SNP effects and to improve genetic potentials in successive generations of the Hanwoo populations.

• Asian-Australasian Journal of Animal Sciences
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• v.33 no.5
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• pp.704-711
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• 2020

Objective: Muscle fiber types, numbers and area are crucial aspects associated with meat production and quality. However, there are few studies of pig muscle fibre traits in terms of the detection power, false discovery rate and confidence interval precision of whole-genome quantitative trait loci (QTL). We had previously performed genome scanning for muscle fibre traits using 183 microsatellites and detected 8 significant QTLs in a White Duroc×Erhualian F₂ population. The confidence intervals of these QTLs ranged between 11 and 127 centimorgan (cM), which contained hundreds of genes and hampered the identification of QTLs. A whole-genome sequence imputation of the population was used for fine mapping in this study. Methods: A whole-genome sequences association study was performed in the F₂ population. Genotyping was performed for 1,020 individuals (19 F₀, 68 F₁, and 933 F₂). The whole-genome variants were imputed and 21,624,800 single nucleotide polymorphisms (SNPs) were identified and examined for associations to 11 longissimus dorsi muscle fiber traits. Results: A total of 3,201 significant SNPs comprising 7 novel QTLs showing associations with the relative area of fiber type I (I_RA), the fiber number per square centimeter (FN) and the total fiber number (TFN). Moreover, one QTL on pig chromosome 14 was found to affect both FN and TFN. Furthermore, four plausible candidate genes associated with FN (kinase non-catalytic C-lobe domain containing [KNDC1]), TFN (KNDC1), and I_RA (solute carrier family 36 member 4, contactin associated protein like 5, and glutamate metabotropic receptor 8) were identified. Conclusion: An efficient and powerful imputation-based association approach was utilized to identify genes potentially associated with muscle fiber traits. These identified genes and SNPs could be explored to improve meat production and quality via marker-assisted selection in pigs.