• Journal of Microbiology and Biotechnology
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• 제16권2호
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• pp.256-263
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• 2006

In the model legume Medicago truncatula, two mutants, sickle and sunn, exhibit morphologically and genetically distinct hypernodulation phenotypes. However, efforts to isolate the single recessive and single semidominant genes for sickle and sunn, respectively, by map-based cloning have so far been unsuccessful, partly due to the absence of clones that enable walks from linked marker positions. To help resolve these difficulties, a new bacterial artificial chromosome (BAC) library was constructed using BamHI-digested genomic fragments. A total of 23,808 clones were collected from ligation mixtures prepared with double-size-selected high-molecular-weight DNA. The average insert size was 116 kb based on an analysis of 88 randomly selected clones using NotI digestion and pulsed-field gel electrophoresis. About 18.5% of the library clones lacked inserts. The frequency of the BAC clones carrying chloroplast or mitochondrial DNA was 0.98% and 0.03%, respectively. The library represented approximately 4.9 haploid M. truncatula genomes. Hybridization of the BAC clone filters with a $C_{0}t-l$ DNA probe revealed that approximately 37% of the clones likely carried repetitive sequence-enriched DNA. An ordered array of pooled BAC DNA was screened by polymerase chain reactions using 13 sequence-characterized molecular markers that belonged to the eight linkage groups. Except for two markers, one to five positive BAC clones were obtained per marker. Accordingly, the sickle- and sunn-linked BAC clones identified herein will be useful for the isolation of these biotechnologically important genes. The new library will also provide clones that fill the gaps between preexisting BAC contigs, facilitating the physical mapping and genome sequencing of M. truncatula.

• Molecules and Cells
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• 제26권3호
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• pp.250-257
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• 2008

Microsatellites or simple sequence repeats (SSR) are widely distributed in eukaryotic genomes and are informative genetic markers. Despite many advantages of SSR markers such as a high degree of allelic polymorphisms, co-dominant inheritance, multi-allelism, and genome-wide coverage in various plant species, they also have shortcomings such as low polymorphic rates between genetically close lines, especially in Capsicum annuum. We developed an alternative technique to SSR by normalizing and alternating anchored primers in random amplified microsatellite polymorphisms (RAMP). This technique, designated reverse random amplified microsatellite polymorphism (rRAMP), allows the detection of nucleotide variation in the 3' region flanking an SSR using normalized anchored and random primer combinations. The reproducibility and frequency of polymorphic loci in rRAMP was vigorously enhanced by translocation of the 5' anchor of repeat sequences to the 3' end position and selective use of moderate arbitrary primers. In our study, the PCR banding pattern of rRAMP was highly dependent on the frequency of repeat motifs and primer combinations with random primers. Linkage analysis showed that rRAMP markers were well scattered on an intra-specific pepper map. Based on these results, we suggest that this technique is useful for studying genetic diversity, molecular fingerprinting, and rapidly constructing molecular maps for diverse plant species.

• Asian-Australasian Journal of Animal Sciences
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• 제21권5호
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• pp.624-627
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• 2008

An enrichment library of GATA-repeats from genomic DNA was constructed in this study to isolate and characterize microsatellite loci in Tsaiya duck (Anas platyrhynchos). Thirty-three microsatellite markers were developed and used to detect polymorphisms in 30 Tsaiya ducks. A total of 177 alleles were observed and all loci except APT022 were polymorphic. The number of alleles ranged from 2 to 9 with an average of 5.5 per microsatellite locus. The observed and expected heterozygosity of these polymorphic markers ranged from 0.07 to 0.93 with an average number of 0.60 and 0.10 to 0.86 with an average number of 0.61, respectively. Among the polymorphic markers, the observed heterozygosities of 23 loci were higher than 0.50 (69.70%). The polymorphism information content (PIC) in the 32 loci ranged from 0.09 to 0.83 with an average of 0.57. Seven of the 33 duck microsatellite loci had orthologs in the chicken genome, but only APT004 had a similar core repeat to chickens. These microsatellite markers will be useful in constructing a genetic linkage map for the duck and a comparative mapping with the chicken can also provide a valuable tool for studies related to biodiversity and population genetics in this duck species.

• Journal of Crop Science and Biotechnology
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• 제11권2호
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• pp.151-156
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• 2008

The objective of this study is to identify main-effect QTLs, epistatic QTLs, and the interactions between QTL and the environment associated with grain appearances of brown rice. A genetic linkage map was created with 172 DNA markers spanning 12 rice chromosomes based on 120 DH lines, which derived from a cross between 'Samgang'(Tongil) and 'Nagdong'(Japonica). One thousandgrain weight, length, width, length-to-width ratio, and thickness were evaluated regarding the DH population. Twenty independent QTLs and fourteen epistatic QTLs were identified in using CIM by two programs, known as WinQTLcart2.5 and QTLMAPPER. The QTLs of qgw9.1 in an interval of RM434-RM242 on chromosome 9 and qgw11.1 at a peak marker of RM287 on chromosome 11 for one thousand-grain weight, qgwi2.2 for grain width at a peak marker of RM450, qlw2.1 for length-to-width ratio flanked by RM492 and RM324, and qgt2.1 for thickness flanked by 2009 and RM492 on chromosome 2 were detected over two years, which can be considered as stable QTLs. The epistatic effect might be an important component for genetic basis of one thousand-grain weight and width. The main-effect QTLs of grain width and length to width ratio were easily influenced by environments.

• 한국작물학회지
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• 제54권2호
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• pp.165-171
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• 2009

The objective of this study was to characterize the main-effect QTLs, epistatic QTLs and QTL-by-environment interactions (QE), which are involved in the control of protein content. A population of 120 doubled haploid (DH) lines derived from a cross between 'Samgang' and 'Nagdong', was planted and determined for protein content over three years. Based on the population and a genetic linkage map of 172 markers, QTL analysis was conducted by WinQTLcart 2.5 and QTLMAPPER. Three main-effect QTLs affecting protein content of brown rice were detected from 2004 to 2006 on chromosomes 1 and 11. The qPC11.2 was repeatedly detected across two years. Seven pairs of epistatic loci were identified on eight chromosomes for protein content and collectively explained 39.15% of phenotype variation. These results suggest that epistatic effects might be an even more important component of the genetic basis for protein content and that the segregation of the DH lines for protein content could be largely explained by a few main-effect QTLs and many epistatic loci.

• Plant Biotechnology Reports
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• 제2권3호
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• pp.191-198
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• 2008

Germplasm characterization and evolutionary process in viable populations are important links between the conservation and utilization of plant genetic resources. Here, an investigation is made, based on molecular and biochemical techniques for assessing and exploiting the genetic variability in germplasm characterization of taro, which would be useful in plant breeding and ex situ conservation of taro plant genetic resources. Geographical differentiation and phylogenetic relationships of Indian taro, Colocasia esculenta (L.) Schott, were analyzed by random amplified polymorphic DNA (RAPD) and isozyme of seven enzyme systems with specific reference to the Muktakeshi accession, which has been to be proved resistant to taro leaf blight caused by P. colocasiae. The significant differentiations in Indian taro cultivars were clearly demonstrated by RAPD and isozyme analysis. RAPD markers showed higher values for genetic differentiation among taro cultivars and lower coefficient of variation than those obtained from isozymes. Genetic differentiation was evident in the taro accessions collected from different regions of India. It appears that when taro cultivation was introduced to a new area, only a small fraction of genetic variability in heterogeneous taro populations was transferred, possibly causing random differentiation among locally adapted taro populations. The selected primers will be useful for future genetic analysis and provide taro breeders with a genetic basis for selection of parents for crop improvement. Polymorphic markers identified in the DNA fingerprinting study will be useful for screening a segregating population, which is being generated in our laboratory aimed at developing a taro genetic linkage map.

• Asian-Australasian Journal of Animal Sciences
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• 제28권9호
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• pp.1235-1243
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• 2015

The goat Capra hircus is one of several economically important livestock in China. Advances in molecular genetics have led to the identification of several single nucleotide variation markers associated with genes affecting economic traits. Validation of single nucleotide variations in a whole-transcriptome sequencing is critical for understanding the information of molecular genetics. In this paper, we aim to develop a large amount of convinced single nucleotide polymorphisms (SNPs) for Cashmere goat through transcriptome sequencing. In this study, the transcriptomes of Cashmere goat skin at four stages were measured using RNA-sequencing and 90% to 92% unique-mapped-reads were obtained from total-mapped-reads. A total of 56,231 putative SNPs distributed among 10,057 genes were identified. The average minor allele frequency of total SNPs was 18%. GO and KEGG pathway analysis were conducted to analyze the genes containing SNPs. Our follow up biological validation revealed that 64% of SNPs were true SNPs. Our results show that RNA-sequencing is a fast and efficient method for identification of a large number of SNPs. This work provides significant genetic resources for further research on Cashmere goats, especially for the high density linkage map construction and genome-wide association studies.

• 한국콘텐츠학회:학술대회논문집
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• 한국콘텐츠학회 2007년도 추계 종합학술대회 논문집
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• pp.17-21
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• 2007

최근 위성영상이 도시계획 및 관리에 필요한 정보를 획득하는 수단으로 큰 각광을 받고 있지만 도시계획 분야에서는 위성영상이 현황을 설명하는 보조 자료나 지도를 대신하는 베이스맵으로만 이용되고 있는 실정이다. 본 연구는 도시정비사업의 정비예정구역 지정을 위해 사용되는 각종 지표를 표현할 수 있는 세부측정항목을 추출해 내고, 이렇게 설정된 세부지표 측정을 위해 위성영상과 GIS를 활용하였다. 위성영상과 GIS를 연계하면, 도시정비사업의 정비예정구역 지정을 위한 각종 지표들을 정량적으로 파악 할 수 있을 뿐만 아니라 정비예정구역의 지표특성을 기초로 하여 정비유형을 결정하는데 기여할 수 있을 것이다.

• 한국환경복원기술학회지
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• 제21권2호
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• pp.53-64
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• 2018

This study aims to quantitatively evaluate the conservation priorities of unexecuted urban parks in Seoul both from an ecological and public perspective. To this end, two methodologies, ecological network analysis based on graph and circuit theory and accessibility analysis, were employed in order to assess ecological connectivity of and public accessibility to unexecuted parks, respectively. This study applied linkage-mapping methods (shortest path and current flow betweenness centrality) of connectivity analysis to an integrated map of landscape permeability. The population-weighted accessibility to unexecuted parks was measured based on a negative exponential distance decay function. As a result, for both ecological connectivity and accessibility, Gwanaksan, Suraksan, and Bulamsan urban natural parks are found to be the most important (rank 1-3) to be conserved. For these sites, inner park areas with conservation priorities for connectivity and accessibility were identified. The findings of the study can be used for giving conservation priority to the unexecuted urban parks in terms of long-term sustainable urban planning.

• 한국컴퓨터산업학회논문지
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• 제9권3호
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• pp.121-128
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• 2008

본 논문에서는 TPEG와 GIS를 이용한 위치기반 교통정보 서비스 시스템을 제안하여 구현한다. 위치기반 서비스를 제공하기 위하여 측정기술과 위치서버, 응용서비스기술, DB와의 연동기술 등을 사용한다, TPEG-RTM 메시지는 위치정보 및 도로교통 메시지를 포함하고 있다. 각 메시지에 포함되는 위치정보는 도로의 특정지점, 구간 또는 지역범위 등으로 나타난다. 따라서, 본 논문을 구현함에 있어서 TPEG 수신기를 사용한 데이터 수신이 불가능하므로 임의의 DB를 생성하고 이를 읽어들이는 방식을 사용한다. TPEG 메시지와 수신한 WGS84 좌표의 매칭 테스트를 위해서 지도상에 TPEG 이벤트 발생시점을 표시하고 차량이 이벤트 발생시점으로 다가가는 예제를 가지고 검증한다.