• Journal of Crop Science and Biotechnology
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• 제11권2호
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• pp.91-100
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• 2008

Melting curve analysis of fluorescently labeled DNA fragments is used extensively for genotyping single nucleotide polymorphism(SNP). Here, we evaluated a SNP genotyping method by melting curve analysis with the two probe chemistries in a 384-well plate format on a Roche LightCycler 480. The HybProbe chemistry is based on the fluorescence resonance energy transfer(FRET) and the SimpleProbe chemistry uses a terminal self-quenching fluorophore. We evaluated FRET HybProbes and SimpleProbes for two SNP sites closely linked to two quantitative trait loci(QTL) for southern root-knot nematode resistance. These probes were used to genotype the two parents and 94 $F_2$ plants from the cross of PI 96354$\times$Bossier. The SNP genotypes of all samples determined by the LightCycler software agreed with previously determined SSR genotypes and the SNP genotypes determined on a Luminex 100 flow cytometry instrument. Multiplexed HybProbes for the two SNPs showed a 98.4% success rate and 100% concordance between repeats two of the same 96 DNA samples. Also, we developed a HybProbe assay for the Rcs3 gene conditioning broad resistance to the frogeye leaf spot(FLS) disease. The LightCycler 480 provides rapid PCR on 384-well plate and allows simultaneous amplification and analysis in approximately 2 hours without any additional steps after amplification. This allowed for a reduction of the potential contamination of PCR products, simplicity, and enablement of a streamlined workflow. The melting curve analysis on the LightCycler 480 provided high-throughput and rapid SNP genotyping and appears highly effective for marker-assisted selection in soybean.

• Journal of Plant Biotechnology
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• 제42권4호
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• pp.312-325
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• 2015

본 논문에서는 장미과 과수의 유전체 연구의 모델작물인 복숭아 유전체 연구에 대한 동향을 파악해서 국내 복숭아 유전체 연구 방향을 설정하고자 하였다. 분자육종을 위한 기반 연구인 유전자지도는 다양한 교배집단에서 작성되었고, 현재 차세대 염기서열분석을 통해 얻은 대량의 single nucleotide polymorphism 마커를 이용하여 고밀도화시키고 있다. 과실형질, 개화기, 병 저항성 등 질적형질과 양적형질에 관한 분자마커와 양적형질유전자좌가 동정되었고, 이중 과육의 용질성과 핵의 점리 형질에 대한 분자마커를 이용한 조기선발(marker assisted selection)의 활용성은 매우 높다. 애기장대, 포플라, 사과, 딸기 등 다른 작물과의 비교유전체, 복숭아의 성숙 및 발달, 플라보노이드 합성, 수확 후 저장기간에 발현하는 유전자 등에 대한 전사체, 과실 성숙기간에 발현되는 병 저항성 단백질 등에 대한 단백질체 연구도 보고되었다. 현재 차세대 염기서열 분석을 통해 대량 분자마커의 개발, 핵심 유전자원의 구축, 집단의 유전형 분석이 빠르게 진행되고 있다. 이를 통해 농업적으로 유용한 형질에 대해 더 정확한 양적형질 유전자좌 분석과 유용유전자의 개발이 가능하게 되고, 효율적인 분자육종의 기초기반을 구축할 수 있을 것으로 기대한다.

• Genomics & Informatics
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• 제7권3호
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• pp.152-158
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• 2009

Although the genetic basis for bone mineral density (BMD) has been studied by many groups so far, genes responsible for this complex trait has not been completely revealed. In order to localize quantitative trait loci (QTLs) for BMD variation in Asian population, the study was designed using a group of Mongolian population, a genetically closed population with a homogeneous lifestyle. BMD was measured at the left and right wrists and ankles using DEXA in 1,082 participants from 142 families. Genotyping of 13 polymorphic microsatellite markers on chromosome 13 (average spacing 8-9 cM) and two-point and multipoint linkage analysis were performed. In two-point linkage analysis, we identified two markers, D13S175 (6.03 cM) and D13S265 (68.73 cM) that had LOD scores greater than 1 for left ankle (LOD=2.09, LOD=1.49, respectively). We also found a marker D13S175 (6.03 cM) with a high LOD for left wrist (LOD=1.49) and the markers D13S265 (68.73 cM) and D13S217 (17.21 cM) for the right wrist (LOD= 1.82, LOD= 1.62, respectively). Among these significant marker regions, only two regions at 17 cM (13p11) and 65 cM (13q21) for the right wrist overlapped with major QTLs reported in following multipoint linkage analysis (LOD= 1.7549, LOD=1.4462, respectively). This study provides the possible evidence of the presence of QTLs affecting right wrist BMD in Mongolian populations on 13p11 and 13q21. Modest evidence was also found for genes affecting left ankle and left wrist BMD on 13p13.

• 한국균학회소식:학술대회논문집
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• 한국균학회 2015년도 춘계학술대회 및 임시총회
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• pp.42-42
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• 2015

Plasmodiophora brassicae, the causal agent of clubroot disease, does the most serious damage to the Brassica crops. The limited control approaches make that the identification of clubroot resistance (CR) is more important for developing CR cultivars of the Brassica crops. So far, 8 CR loci were mapped. However, the variation of P. brassicae leads to the rapid erosion of its resistance. To identify novel CR genes, we employed three mapping population, derived from crosses between Chinese cabbage and turnip inbred lines ($59-1{\times}ECD04$ and $BJN3-1{\times}Siloga$) or between Chinese cabbage inbred lines ($BJN3-1{\times}85-I-II$), to perform QTL analysis. Totally, 8 CR loci were indentified and showed race-specific resistance. Physical mapping of these 8 loci suggested that 4 were located previously mapped position, indicating they might be the same allele or different alleles of the same genes. Other 4 loci were found to be novel. Further, CR near isogenic line carrying each CR locus was developed based on the marker assisted selection. Verification of these CR loci was underway. Identification of these novel CR genes would facilitate to breed broad-spectrum and durable CR cultivars of B. rapa by pyramiding strategies.

• 한국작물학회:학술대회논문집
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• 한국작물학회 2017년도 9th Asian Crop Science Association conference
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• pp.13-13
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• 2017

By the progress of genome sequencing, infrastructures for marker-assisted breeding (MAB) of rice came to be established. Fine mapping and gene isolation have been conducted using the breeding materials derived from natural variations and artificial mutants. Such genetic analysis by the genome-wide dense markers provided us the knowledge about the many genes controlling important traits. We identified several genes or quantitative trait loci (QTL) for heading date, blast resistance, eating quality, high-temperature stress tolerance, and so on. NILs of each gene controlling heading date contribute to elongate the rice harvest period. Determination of precise gene location of blast resistance gene pi21, allowed us to overcome linkage drag, co-introduction of undesirable eating quality. We could also breed the first practical rice cultivar in Japan with a brown planthopper resistance gene bph11 in the genetic back-ground of an elite cultivar. Discovery of major and minor QTLs for good eating quality allowed us to fine-tune of eating quality according to the rice planting area or usage of rice grain. Many rice cultivars have bred efficiently by MAB for several traits, or by marker-assisted backcross breeding through chromosome segment substitution lines (CSSLs) using genetically diverse accessions. We are also systematically supporting the crop breeding of other sectors by MAB or by providing resources such as CSSLs. It is possible to pyramid many genes for important traits by using MAB, but is still difficult to improve the yielding ability. We are performing a Genomic Selection (GS) for improvement of rice biomass and grain yield. We are also trying to apply the genome editing technology for high yield rice breeding.

• 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.

• 한국작물학회:학술대회논문집
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• 한국작물학회 2017년도 9th Asian Crop Science Association conference
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• pp.95-95
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• 2017

Lodging is a serious issue in rice production, because it drastically decreases the biomass production and grain yield. Since the Green Revolution, the lodging resistance has been increased by lowering the moment of above-ground parts due to the short culm by the semi-dwarf gene sd1. However, it has been pointed out that sd1 alone has suppressive effects for biomass production and yield. To increase rice yield, the long-culm and large panicle type varieties with a superior lodging resistance need to be developed. To improve the lodging resistance and yield of these type varieties, it would be effective to identify novel alleles for these traits underlying natural variations in rice and to pyramid these alleles to a single rice variety. In order to perform this strategy, we have developed new rice lines derived from crosses among varieties with superior alleles. At first, TULT-gh-5-5 was selected from a cross between strong culm and high biomass variety Leaf Star and high-yielding variety Takanari, and TUAT-32HB was selected from a cross between high-yielding variety Akenohoshi and Takanari. Then, we developed the super thick-culm and super grain-bearing line, LTAT-29 derived from a cross between TULT-gh-5-5 and TUAT-32HB. In the current study, to identify the QTLs and genes relating to the strong culm and the high yield of LTAT-29, we performed QTL analysis using SNPs markers with $F_2$ population derived from a cross between LTAT-29 and Takanari. LTAT-29 has never lodged throughout the growth period despite it had long culms and heavy panicles. LTAT-29 had a larger outer diameter of the culm and twice the size of the section modulus than Takanari. As a result, the bending moment at breaking of LTAT-29 was significantly larger than that of Takanari. Brown rice yield of LTAT-29 was $9.2t\;ha^{-1}$ about 10% higher than that of Takanari due to the larger number of spikelets per panicle. LTAT-29 had a greater number of secondary branches per panicle. In the $F_2$ population between LTAT-29 and Takanari, we found continuous frequency distributions in the section modulus and the spikelet number per panicle. Two QTLs increased the section modulus by the alleles of LTAT-29 were detected on Chr.1L and Chr.2L. One QTL increased the spikelet number per panicle of Takanari by the allele of LTAT-29 was detected on Chr.1L, and two QTLs increased the number of secondary branches per panicle by the alleles of LTAT-29 were detected on Chr.1L and Chr.4L. It was found that the alleles of these QTLs were the japonica type originated from Leaf Star or Akenohoshi. The novel QTLs for the traits related to super thick-culm and super grain-bearing and their combinations could be utilized for improving the lodging resistance and yield in rice varieties.

• 한국자원식물학회:학술대회논문집
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• 한국자원식물학회 2020년도 춘계학술대회
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• pp.49-49
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• 2020

Bacterial leaf blight (BLB), caused by X. oryzae pv. oryzae(Xoo), is one of the most destructive diseases of rice due to its high epidemic potential. Understanding BLB resistance at a genetic level is important to further improve the rice breeding that provides one of the best approaches to control BLB disease. In the present investigation, a total of 10,000 accessions of rice germplasm were tested to resistance degree of four Korean isolated races (K1, K2, K3 and K3a) of Xoo by bioassay and a diverse 268 accessions was selected to the genome-wide association study (GWAS) using high quality 34,724 SNPs to identify the associated with resistance loci. LOC_Os04g53160 of chromosome 4 was significantly associated with K1 race resistant. LOC_Os11g46230 and LOC_Os11g47150 of chromosome 11 were highly associated with K2 and K3 races as 23.7 and 27.4 of -log(P) value, but K3a resistant loci was weakly associated at LOC_Os03g55270 of chromosome 3. The results of the GWAS validate known gene of BLB resistant and identified novel loci of R genes that provide useful targets for further investigation to help the breeding system and identified gene and QTL provide valuable sources for further functional characterization.

• Asian-Australasian Journal of Animal Sciences
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• 제20권2호
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• pp.172-177
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• 2007

Thyroid hormones play an important role in regulating metabolism and can affect homeostasis of fat depots. The gene encoding thyroglobulin (TG), producing the precursor for thyroid hormones, has been proposed as a positional and functional candidate gene for a QTL with an effect on fat deposition. The SNP occurs in the 5' promoter region of the TG gene and is widely used in marker assisted selection (MAS) programs to improve the predictability of marbling level and eating quality in beef cattle. In this study, we identified three SNPs at the 5' promoter region of the TG gene in Korean cattle. Of the three SNPs identified in TG gene, the C257T and A335G were previously unreported new SNPs. The sequence data were submitted to GenBank (GenBank accession number: AY615525). The previously reported C422T SNP showed three genotypes, CC, CT and TT, by digestion with the restriction enzyme MflI using the PCR-RFLP method. A new allelic variant corresponding to the C${\rightarrow}$T and A${\rightarrow}$G mutations at positions 257 and 335, respectively, could be detected by the SSCP analysis. The gene-specific SNP marker association analysis indicated that the C422T SNP marker was significantly associated (p<0.05) with marbling score. Animals with the CC and CT genotypes had higher marbling score than those with the TT genotype. Results from this study suggest that TG gene-specific SNP may be a useful marker for meat quality traits in future MAS programs in Korean cattle.

• Asian-Australasian Journal of Animal Sciences
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• 제20권10호
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• pp.1473-1477
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• 2007

Four-and-a-half LIM-only protein 3 (FHL3) is a member of the LIM protein superfamily and can participate in mediating protein-protein interaction by binding one another through their LIM domains. In this study, the 5'- and 3'- cDNA ends were characterized by RACE (Rapid Amplification of the cDNA Ends) methodology in combination with in silico cloning based on the partial cDNA sequence obtained. Bioinformatics analysis showed FHL3 protein contained four LIM domains and four LIM zinc-binding domains. In silico mapping assigned this gene to the gene cluster MTF1-INPP5B-SF3A3-FHL3-CGI-94 on pig chromosome 6 where several QTL affecting intramuscular fat and eye muscle area had previously been identified. Transcription of the FHL3 gene was detected in spleen, liver, kidney, small intestine, skeletal muscle, fat and stomach, with the greatest expression in skeletal muscle. The A/G polymorphism in exon II was significantly associated with birth weight, average daily gain before weaning, drip loss rate, water holding capacity and intramuscular fat in a Landrace-derived pig population. Together, the present study provided the useful information for further studies to determine the roles of FHL3 gene in the regulation of skeletal muscle cell growth and differentiation in pigs.