• Asian-Australasian Journal of Animal Sciences
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• 제17권10호
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• pp.1344-1349
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• 2004

Titin-cap (TCAP), one of the abundant transcripts in skeletal muscles, was nvestigated in this study in cattle because of its role in regulating the proliferation and differentiation of myoblasts by interacting with the myostatin gene. From the 5, and 3, RACE experiments, full-length TCAP coding sequence was identified, comprising 166 amino acids. The amino acid comparison showed high sequence similarities with previously identified human (95.8%) and mouse (95.2%) TCAP genes. The TCAP expression, addressed by northern blot, is limited in muscle tissues as indicated by Valle et al. (1997). The radiation hybrid analysis localized the gene on BTA19, where the comparative human and porcine counterparts are on HSA17 and SSC12. A few muscle-related genetic disorders were mapped on HSA17 and some growth-related QTLs were identified on SSC12. The bovine TCAP gene found in this study opens up new possibilities for the investigation of muscle-related genetic diseases as well as meat yield traits in cattle.

• Molecules and Cells
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• 제23권1호
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• pp.72-79
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• 2007

Demand for low-input sustainable crop cultivation is increasing to meet the need for environment-friendly agriculture. Consequently, developing genotypes with high nutrient use efficiency is one of the major objectives of crop breeding programs. This study was conducted to identify QTLs for traits associated with physiological nitrogen use efficiency (PNUE). A recombinant inbred population (DT-RILs) between Dasanbyeo (a tongil type rice, derived from an indica ${\times}$ japonica cross and similar to indica in its genetic make-up) and TR22183 (a Chinese japonica variety) consisting of 166 $F_8$ lines was developed and used for mapping. A frame map of 1,409 cM containing 113 SSR and 103 STS markers with an average interval of 6.5 cM between adjacent marker loci was constructed using the DT-RILs. The RILs were cultivated in ordinary-N ($N-P_2O_5-K_2O=100-80-80kg/ha$) and low-N ($N-P_2O_5-K_2O=50-80-80kg/ha$) (100 kg/ha) conditions. PNUE was positively correlated with the harvest index and grain yield in both conditions. Twenty single QTLs (S-QTLs) and 58 pairs of epistatic loci (E-QTLs) were identified for the nitrogen concentration of grain, nitrogen concentration of straw, nitrogen content of shoot, harvest index, grain yield, straw yield and PNUE in both conditions. The phenotypic variance explained by these S-QTLs and E-QTLs ranged from 11.1 to 44.3% and from 16.0% to 63.6%, respectively. The total phenotypic variance explained by all the QTLs for each trait ranged from 35.8% to 71.3%, showing that the expression of PNUE and related characters depends signify- cantly upon genetic factors. Both S-QTLs and E-QTLs may be useful for marker-assisted selection (MAS) to develop higher PNUE genotypes.

• 원예과학기술지
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• 제32권4호
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• pp.535-543
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• 2014

Backcross breeding is the method most commonly used to introgress new traits into elite lines. Conventional backcross breeding requires at least 4-5 generations to recover the genomic background of the recurrent parent. Marker-assisted backcrossing (MABC) represents a new breeding approach that can substantially reduce breeding time and cost. For successful MABC, highly polymorphic markers with known positions in each chromosome are essential. Single nucleotide polymorphism (SNP) markers have many advantages over other marker systems for MABC due to their high abundance and amenability to genotyping automation. To facilitate MABC in hot pepper (Capsicum annuum), we utilized expressed sequence tags (ESTs) to develop SNP markers in this study. For SNP identification, we used Bukang $F_1$-hybrid pepper ESTs to prepare a reference sequence through de novo assembly. We performed large-scale transcriptome sequencing of eight accessions using the Illumina Genome Analyzer (IGA) IIx platform by Solexa, which generated small sequence fragments of about 90-100 bp. By aligning each contig to the reference sequence, 58,151 SNPs were identified. After filtering for polymorphism, segregation ratio, and lack of proximity to other SNPS or exon/intron boundaries, a total of 1,910 putative SNPs were chosen and positioned to a pepper linkage map. We further selected 412 SNPs evenly distributed on each chromosome and primers were designed for high throughput SNP assays and tested using a genetic diversity panel of 27 Capsicum accessions. The SNP markers clearly distinguished each accession. These results suggest that the SNP marker set developed in this study will be valuable for MABC, genetic mapping, and comparative genome analysis.

• Genomics & Informatics
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• 제6권2호
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• pp.91-94
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• 2008

Single nucleotide polymorphisms (SNPs) are the most abundant form of human genetic variation and are a resource for mapping complex genetic traits. A genome is covered by millions of these markers, and researchers are able to compare which SNPs predominate in people who have a certain disease. The International HapMap Project, launched in October, 2002, motivated us to start the Korean HapMap Project in order to support Korean HapMap infrastructure development and to accelerate the finding of genes that affect health, disease, and individual responses to medications and environmental factors. A Korean SNP and haplotype database system was developed through the Korean HapMap Project to provide Korean researchers with useful data-mining information about disease-associated biomarkers for studies on complex diseases, such as diabetes, cancer, and stroke. Also, we have developed a series of software programs for association studies as well as the comparison and analysis of Korean HapMap data with other populations, such as European, Chinese, Japanese, and African populations. The developed software includes HapMapSNPAnalyzer, SNPflank, HWE Test, FESD, D2GSNP, SNP@Domain, KMSD, KFOD, KFRG, and SNP@WEB. We developed a disease-related SNP retrieval system, in which OMIM, GeneCards, and MeSH information were integrated and analyzed for medical research scientists. The kHapMap Browser system that we developed and integrated provides haplotype retrieval and comparative study tools of human ethnicities for comprehensive disease association studies (http://www.khapmap.org). It is expected that researchers may be able to retrieve useful information from the kHapMap Browser to find useful biomarkers and genes in complex disease association studies and use these biomarkers and genes to study and develop new drugs for personalized medicine.

• 생명과학회지
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• 제21권3호
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• pp.468-472
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• 2011

DNA 마커는 유전현상 분석이나 품종육성에 널리 사용되고 있다. 본 연구에서는 내냉성 오이 계통인 'NC76'과 냉해 감수성 계통인 'GY14'로부터 내냉성 연관 마커을 목적으로 기존의 총 995개 SSR 마커의 다형성을 평가하였다. Agarose gel 전기영동법으로 'NC76과 'GY14' 간 PCR증폭 산물의 길이 다형성을 보이는 145개 SSR 마커를 개발하였으며, high resolution melting (HRM) 기술을 사용하여 염기서열 다형성을 보이는 30개의 SSR 마커를 확인하였다. 개발된 175개 SSR 마커 중 20개 마커를 선발하여 'NC76'과 'GY14' 간 $F_2$ 분리 집단에 대한 연관지도를 작성하였으며 그 결과 13개의 마커가 예상했던 연관군에 일치하여 위치됨을 확인할 수 있었다. 따라서 본 연구에서 확인된 175개의 SSR 마커는 향 후 냉해 저항성 연관 마커 개발을 위한 오이 유전자 지도 작성 및 이를 통한 품종 육성에 크게 활용될 수 있을 것으로 기대된다.

• 제어로봇시스템학회논문지
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• 제8권2호
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• pp.126-135
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• 2002

The study is concerned with an approach to the design of new architectures of fuzzy neural networks and the discussion of comprehensive design methodology supporting their development. We propose an Adaptive Fuzzy Polynomial Neural Networks(APFNN) based on Fuzzy Neural Networks(FNN) and Self-organizing Networks(SON) for model identification of complex and nonlinear systems. The proposed AFPNN is generated from the mutually combined structure of both FNN and SON. The one and the other are considered as the premise and the consequence part of AFPNN, respectively. As the premise structure of AFPNN, FNN uses both the simplified fuzzy inference and error back-propagation teaming rule. The parameters of FNN are refined(optimized) using genetic algorithms(GAs). As the consequence structure of AFPNN, SON is realized by a polynomial type of mapping(linear, quadratic and modified quadratic) between input and output variables. In this study, we introduce two kinds of AFPNN architectures, namely the basic and the modified one. The basic and the modified architectures depend on the number of input variables and the order of polynomial in each layer of consequence structure. Owing to the specific features of two combined architectures, it is possible to consider the nonlinear characteristics of process system and to obtain the better output performance with superb predictive ability. The availability and feasibility of the AFPNN are discussed and illustrated with the aid of two representative numerical examples. The results show that the proposed AFPNN can produce the model with higher accuracy and predictive ability than any other method presented previously.

• 한국자원식물학회:학술대회논문집
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• 한국자원식물학회 2022년도 추계학술대회
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• pp.23-23
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• 2022

Rapeseed (Brassica napus L.) is one of the most valuable oilseed crop in the world. It is widely used in various industries, such as food, animal feed, energy and chemical industries. In order to improve the industrial requirements for rapeseed, useful agronomic characteristics (higher yields and disease resistance etc.) and modified oil traits (fatty acid composition and fat content) are important in rapeseed. However, Korea has limiting genetic resources of novel traits in rapeseed. In this research, novel rapeseed mutant genotypes by mutation breeding was developed. The mutant lines were generated by the treatment of the seeds of the original cultivar 'Tamra' with 700 Gy of gamma-ray (⁶⁰Co). Mutants showing varied in flowering time, crude fat content, seed yield and fatty acid content that exhibited stable inheritance of the mutated characteristics from M₅ to M₇ generations were selected. We investigated genetic variation using SNPs identified from GBS analysis in rapeseed mutant lines derived from the gamma-ray, and interactions between the major agronomic and the oil traits. Significantly associated SNP loci were explored along with candidate genes using SNPs obtained by GBS analysis. As a results of association mapping, a total of 322 SNPs were significantly associated with agronomic traits (155 SNPs) and oil traits (167 SNPs). A total of 70 genes were annotated from agronomic characteristics SNPs; among them 7 genes significantly enriched in developmental process, and a total of 70 genes were annotated from crude fat content and fatty acid compositions SNPs; among them, 11genes were significantly enriched in biosynthetic process. These results could be used for the selection of rapeseed cultivar with enhanced qualities and potential economic benefits.

• Journal of Plant Biotechnology
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• 제45권3호
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• pp.242-249
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• 2018

본 연구는 국내 육종 회사에서 개발된 수박(Citrullus lanatus L.) 우량 육성계통 20종을 대상으로 Genotyping-by-sequencing(GBS) 분석을 통해 품종식별, 순도검정, 그리고 마커이용여교잡(Marker-assisted backcross, MABC)용 SNP 세트를 개발하고자 수행되었다. GBS 분석 결과 총 1,100,000천개 raw read 중 77%가 수박 유전체에 mapping되었으며 평균 mapping region은 약 4,000 Kb로 2.3%의 genome coverage를 보였다. Filtering을 통해 평균 depth 31.57의 SNP 총 2,670개를 얻었으며, 20개 계통에 대한 이들의 Polymorphic information content(PIC) 값의 범위는 0.1 ~ 0.38 였다. 이 중 PIC 값이0.3이상이며 각 염색체 별로 5개씩 균등히 분포된 SNP 총 55개를 최종 선발하였다. 사용된 20개 계통의 유연관계분석을 위해 선발된 55개 SNP를 기반으로 한 주성분 분석(Principle component analysis, PCA) 결과 주성분 1 (52%)과 주성분 2 (11%)를 기준으로 4개의 그룹으로 분류 되었으며 각 계통 간 유전자형에 따른 뚜렷한 식별이 가능하였다. 계층적 군집화(Hierarchical clustering) 분석에서도PCA에서와 유사한 분류양상을 관찰할 수 있었다. 따라서 본 연구에서 개발된 SNP 세트는 적용 가능성이 검증된 20개 계통뿐 만 아니라 향후 다양한 수박 육종소재 및 품종에 대한 품종식별, F1 순도검정 및 MABC에 활용될 수 있으리라 기대된다.

• 한국작물학회:학술대회논문집
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• 한국작물학회 2017년도 9th Asian Crop Science Association conference
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• pp.92-92
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• 2017

Bakanae disease is one of the most serious and oldest problems of rice production, which was first described in 1828 in Japan. This disease has also been identified in Asia, Africa, North America, and Italy. Germinating rice seeds in seed boxes for mechanical transplantation has caused many problems associated with diseases, including bakanae disease. Bakanae disease has become a serious problem in the breeding of hybrid rice, which involves the increased use of raising plants in seed beds. The indica rice variety Shingwang was selected as resistant donor to bakanae disease. One hundred sixty nine NILs, YR28297 ($BC_6F_4$) generated by five backcrosses of Shingwang with the genetic background of susceptible japonica variety, Ilpum were used for QTL analysis. Rice bakanae disease pathogen, CF283, was mainly used in this study and inoculation and evaluation of bakanae disease was performed with the method of the large-scale screening method developed by Kim et al. (2014). SSR markers evenly distributed in the entire rice chromosomes were selected from the Gramene database (http://www.gramene.org), and the polymorphic markers were used for frame mapping of a $BC_5F_5$ resistant line. Here, we developed 168 near-isogenic rice lines (NILs, $BC_6F_4$) to locate a QTL for resistance against bakanae disease. The lines were derived from a cross between Shingwang, a highly resistant variety (indica), and Ilpum, a highly susceptible variety (japonica). The 24 markers representing the Shingwang allele in a bakanae disease-resistant NIL, YR24982-9-1 (parental line of the $BC_6F_4$ NILs), were located on chromosome 1, 2, 7, 8, 10, 11, and 12. Single marker analysis using an SSR marker, RM9, showed that a major QTL was located on chromosome 1. The QTL explained 65 % of the total phenotype variation in $BC_6F_4$ NILs. The major QTL designated qBK1 was mapped in 91 kb region between InDel15 and InDel21. The identification of qBK1 and the closely linked SSR marker, InDel18, could be useful for improving rice bakanae disease resistance in marker-assisted breeding.

• Journal of Plant Biotechnology
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• 제39권1호
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• pp.33-48
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• 2012

작물의 구조와 기능을 이해하려는 과학적 탐구심과 이를 작물 육종에 적용하려는 실험적 노력의 일환으로 다양한 작물에서 유전자 지도가 개발되었다. 특히, 배추과 작물의 경우 모델식물인 애기장대의 유전체 정보가 공개된 이후 다양한 정보 (염기서열 정보, 유전자 구조 및 기능정보 등)의 이용이 가능해져 유전자 지도 작성이 가속화 되었으며 이는 최근 $B.$ $rapa$ A genome (배추)유전체 해독이라는 결과를 가져왔다. 배추과 작물의 유전자 지도 작성에 있어서 초기에는 RFLP 마커들이 사용되었으나 이후 분자마커, 즉, RAPD, AFLP, SSR 등과 같이 비교적 사용이 간단하고 시간적 제약이 없는 PCR 마커의 형태로 점차 바뀌었다. 배추과 작물의 경제적, 학문적 가치가 고려되어 $B.$ $rapa$ (배추)를 표준재료로 A genome 유전체 염기서열 해독이라는 목표로 다국적 유전체 프로젝트가 결성되었고 2011년 국내연구진이 주도적으로 참여한 국제 컨소시엄 (BrGSPC, $B.$ $rapa$ Genome Sequencing Project Consortium)에 의해 배추 (10개 염색체)의 유전자 영역(gene space), 약 98% (83.8 Mb)의 염기서열이 해독되어 발표되었다. 유전체 해독 과정에서 축적된 염기서열 정보는 대량의 SSR, SNP, IBP 마커의 개발을 가능하게 하였고 이들 마커는 $B.$ $rapa$ A genome 유전자 지도와 물리 지도 작성에 이용되어 이후 배추과 작물연구 전반에 널리 적용되고 있다. 대량의 분자마커 개발은 유전자 지도 작성을 가속화하여 더욱 정밀한 유전자 지도를 가능하게 하였고 공통의 분자마커 정보는 애기장대와 배추과 작물 간 비교유전체 연구를 통해 농업적 우수 형질의 클로닝, 마커도움선발 (MAS)등의 방법으로 분자육종의 기반을 제공하고 있다. 뿐만 아니라. 최근 등장한 NGS 유전체 해독 기술로 생산된 대량의 정보는 분자육종 실현 가능성을 높여 분자육종 실용화에 박차를 가하는 계기가 되고 있다. 본 논문에서는 $B.$ $rapa$에서 분자마커를 이용한 유전자 지도 개발의 과정과 농업적 유용형질 탐색을 위한 양적 형질 유전자좌 (QTLs)의 연구 현황에 대하여 알아보고 유전체연구에서 유전자 지도의 중요성과 육종에의 응용에 대하여 서술하였다. 또한 다양한 유전체 정보와 오믹스 정보를 국내 배추과 분자육종에 효율적으로 활용하여 분자육종 실용화를 가능하게 하기 위해 사용자가 쉽게 사용할 수 있는 데이터베이스를 구축함으로서 연구자와 육종가 간의 간격을 좁히고 원활한 정보교환의 필요성을 제기하였다.