• Asian-Australasian Journal of Animal Sciences
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• v.17 no.10
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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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• v.23 no.1
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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.

• Horticultural Science & Technology
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• v.32 no.4
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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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• v.6 no.2
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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.

• Journal of Life Science
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• v.21 no.3
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• pp.468-472
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• 2011

DNA marker is a powerful tool for plant genetics and breeding. In this study, 995 SSR markers were employed with chilling resistant cucumber, known as 'NC76', and chilling susceptible cucumber, known as 'GY14'. Using 2% agarose gel electrophoresis, 145 SSR markers were identified as length variation markers between 'NC76' and 'GY14'. The SSR markers that showed no length polymorphism were then screened using high resolution melting analysis technique and additional 30 polymorphic SSR markers were identified. As a preliminary evaluation for mapping, 20 markers among these 175 markers were employed to a $F_2$ population of 'NC76' x 'GY14' cross. Linkage analysis revealed 13 markers that joined into six linkage groups and seven markers that remained unlinked. This result indicates that these 175 markers could be used for construction of a genetic map using a cross between 'NC76' and 'GY14' for further investigation in developing markers related to resistance to chilling in cucumbers.

• Journal of Institute of Control, Robotics and Systems
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• v.8 no.2
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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.

• Proceedings of the Plant Resources Society of Korea Conference
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• 2022.09a
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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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• v.45 no.3
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• pp.242-249
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• 2018

This study was conducted to develop an SNP set that can be useful for marker-assisted breeding (MAB) in watermelon (Citrullus. lanatus L) using Genotyping-by-sequencing (GBS) analysis of 20 commercial elite watermelon inbreds. The result of GBS showed that 77% of approximately 1.1 billion raw reads were mapped on the watermelon genome with an average mapping region of about 4,000 Kb, which indicated genome coverage of 2.3%. After the filtering process, a total of 2,670 SNPs with an average depth of 31.57 and the PIC (Polymorphic Information Content) value of 0.1~0.38 for 20 elite inbreds were obtained. Among those SNPs, 55 SNPs (5 SNPs per chromosome that are equally distributed on each chromosome) were selected. For the understanding genetic relationship of 20 elite inbreds, PCA (Principal Component Analysis) was carried out with 55 SNPs, which resulted in the classification of inbreds into 4 groups based on PC1 (52%) and PC2 (11%), thus causing differentiation between the inbreds. A similar classification pattern for PCA was observed from hierarchical clustering analysis. The SNP set developed in this study has the potential for application to cultivar identification, F1 seed purity test, and marker-assisted backcross (MABC) not only for 20 elite inbreds but also for diverse resources for watermelon breeding.

• Proceedings of the Korean Society of Crop Science Conference
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• 2017.06a
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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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• v.39 no.1
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• pp.33-48
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• 2012

As a scientific curiosity to understand the structure and the function of crops and experimental efforts to apply it to plant breeding, genetic maps have been constructed in various crops. Especially, in the case of Brassica crop, genetic mapping has been accelerated since genetic information of model plant $Arabidopsis$ was available. As a result, the whole $B.$ $rapa$ genome (A genome) sequencing has recently been done. The genome sequences offer opportunities to develop molecular markers for genetic analysis in $Brassica$ crops. RFLP markers are widely used as the basis for genetic map construction, but detection system is inefficiency. The technical efficiency and analysis speed of the PCR-based markers become more preferable for many form of $Brassica$ genome study. The massive sequence informative markers such as SSR, SNP and InDels are also available to increase the density of markers for high-resolution genetic analysis. The high density maps are invaluable resources for QTLs analysis, marker assisted selection (MAS), map-based cloning and comparative analysis within $Brassica$ as well as related crop species. Additionally, the advents of new technology, next-generation technique, have served as a momentum for molecular breeding. Here we summarize genetic and genomic resources and suggest their applications for the molecular breeding in $Brassica$ crop.