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Variation block-based genomics method for the detection of functional loci
Yul Ho Kim,Hyang Mi Park,Tae-Young Hwang,Ho-Sung Yoon,Dongwoo Lee,Sunghoon Lee 한국육종학회 2014 한국육종학회 심포지엄 Vol.2014 No.07
In contrast with wild species, cultivated crop genomes consist of reshuffled recombination blocks, which occurred by crossing and selection processes. Accordingly, recombination block-based genomics analysis can be an effective approach for screening target loci with agricultural traits. We propose the variation block method, a three-step process for recombination block detection and comparison. The first step is to detect variations by comparing short-read DNA sequences of the cultivar to a reference genome of the target crop. Next, sequence blocks with variation patterns are examined and defined. The boundaries between the variation-containing sequence blocks are regarded as recombination sites. All the assumed recombination sites in the cultivar set are used to split the genomes, and the resulting sequence regions are named as variation blocks. Finally, the genomes are compared using the variation blocks. The variation block method identified recurring recombination blocks accurately and successfully represented block-level diversities in the publicly available genomes of 31 soybeans and 23 rice accessions. The practicality of this approach was demonstrated by the identification of a putative locus determining soybean hilum color. We suggest that the variation block method is an efficient genomics method for recombination block-level comparison of crop genomes. We expect that this method holds the prospect of developing crop genomics by bringing genomics technology to the field of crop breeding.
Kim, Hyang-Yul,Song, Il-Sub,Lee, Seung-Hee The Korean Institute of Electrical and Electronic 2003 Transactions on Electrical and Electronic Material Vol.4 No.1
We have studied the influence of rubbing angles with respect to in-plane field direction on electro-optic characteristics of in-plane switching (IPS) liquid crystal display. The results show that the threshold voltage increases and the operational voltage decreases as the rubbing angle increases. Further, the total response time and also response times associated with grey-to-grey transitions become fast as the rubbing angle decreases.
Hyang Mi Park,Yul Ho Kim,Yong Jae Won,Eok Keun Ahn,Young Jun Mo,Kyoung Ho Kang,Ji Ung Jeung 한국육종학회 2013 한국육종학회 심포지엄 Vol.2013 No.07
NGS costs are decreasing rapidly, and beneficial application of the technology to plant genomics seems inevitable. Trying to interpret the agriculturally important traits like yield is actively in progress all across the globe. However, the current stage of bio-informatic technology as applied to the interpretation of agricultural trait appears not yet at a level of maturity to justify widespread plant genome sequencing for user-friendly molecular breeding. It is necessary to construct dense mutation block (DMB) based molecular breeding system for selecting plants with optimal agricultural performance; as well as for identifying useful quantitative trait loci (QTLs). Firstly, we screened and selected DMBs-specific INDEL markers obtained from SNV density profiles using 42 genome sequences of Korean cultivar and public sequences of 24 japonica rice cultivars. Secondly, we analyzed the genetic similarity between 288 Korean cultivars using 113 DMB-specific INDEL markers, which could differentiate on agarose gel by PCR. And we are going to integrate 360 INDEL markers up to 30 per each chromosome. Finally, we selected 40 founder lines considering the importance of the breeding, the purpose of use, and plant ecotype. To construct rice nested association mapping population we crossed each founder lines with the pollen of Hwayoungbyeo which was most commonly used in korean rice breeding program. F2 seed multiplication and generation iteration are ongoing.
User friendly molecular breeding platform by analyzing soybean genomes
Yul Ho Kim,Tae-Young Hwang,Hyang Mi Park,Seuk Ki Lee,Man Soo Choi,Kwang Ho Jeong,Min Jung Seo,Hong Tai Yun,Sun Lim Kim,Young-Up Kwon,Ik-Young Choi,Ho-Sung Yoon,Suk-Ha Lee,Jong Bhak,Sunghoon Lee 한국육종학회 2012 한국육종학회 심포지엄 Vol.2012 No.07
Resequencing data is actively used for searching QTL or analyzing genetic diversity in the crops. However, the complexity of genome, caused by genome duplication, limits the utility of genome-wide association studies and linkage analyses to identify genes that regulate agronomically valuable traits. Here, we propose a comparative genomics approach based on core or common variation-based recombination blocks (CRB) using single nucleotide variation (SNV) density information. We found that the soybean genomes are assembled with long and distinct CRBs as large as 10Mb. CRB-based comparative genomics enabled us to accurately identify recombination blocks at the whole-chromosome level. We identified the Ih locus that determines the yellow hilum color in soybeans using CRB-based mapping with representative indel markers. These results suggest that the CRB-based comparison method is a promising platform for molecular breeding and map-based cloning.
High efficient rice transformation method by modifying co-cultivation conditions
Hyang-Mi Park,Yul-Ho Kim,Tae-Young Hwang,Chang In Yang,Ji Ung Jeung,Young Chan Cho,Kyoung Ho Kang,Chung-Kon Kim 한국육종학회 2012 한국육종학회 심포지엄 Vol.2012 No.07
Rice transformation method using A. tumefaciens has already been widely used to generate transgenic plants, the transformation rate is still low in most Korean elite cultivars. We made several modifications of the standard protocol especially in the co-cultivation step to improve the efficiency of the rice transformation. The co-culture medium was modified by the addition of three antioxidant compounds (10.5㎎/ℓ L-cysteine, 1mM sodium thiosulfate, 1mM dithiothreitol) and of Agrobacterium growth-inhibiting agent (5㎎/ℓ silver nitrate). Co-cultivation temperature (23. 5℃ for 1 day, 26.5℃ for 6 days) and duration (7 days) were also changed. The plasmid of pMJC-GB-GUS carrying the GUS reporter gene and the bar gene as the selectable marker was used to evaluate the efficiency of the transformation. After co-cultivation, a high level of GUS gene expression was observed in calli treated with the modified method. It is likely that those newly added compounds helped to minimize the damage due to oxidative bursts during plant cell-Agrobacterium interaction and to prevent necrosis of rice cells. And the transformation rate under the modified method was also remarkably increased approximately 8-fold in Heungnambyeo and 2-fold in Ilmibyeo as compared to the corresponding standard method. Furthermore, we could produce the transgenic plants stably from Ilpumbyeo which is a high-quality rice but its transformation rate is extremely low. Transformation and the copy number of transgenes were confirmed by PCR, bar strip and Southern blot analysis. The improved method would attribute reducing the effort and the time required to produce a large number of transgenic rice plants.
Genomics-assisted breeding platform for designed cultivars
Yul-Ho Kim,Hyang-Mi Park,Tae-Young Hwang,Dongwoo Lee,Sunghoon Lee 한국육종학회 2014 한국육종학회 심포지엄 Vol.2014 No.07
In contrast with wild species, cultivated crop genomes consist of reshuffled recombination blocks, which occurred by crossing and selection processes. Accordingly, recombination block-based genomics analysis can be an effective approach for screening target loci with agricultural traits and for developing designed cultivars. We propose the molecular breeding platform based on the variation block (VB) method, which is a three-step process for recombination block detection and comparison. The first step is to detect variations by comparing the short-read DNA sequences of the cultivar to the reference genome of the target crop. Next, sequence blocks with variation patterns are examined and defined. The boundaries between the variation-containing sequence blocks are regarded as recombination sites. All the assumed recombination sites in the cultivar set are used to split the genomes, and the resulting sequence regions are termed variation blocks. Finally, the genomes are compared using the variation blocks. The variation block method identified recurring recombination blocks accurately and successfully represented block-level diversities in the publicly available genomes of 31 soybeans and 23 rice accessions. The practicality of this approach was demonstrated by the identification of a putative locus determining soybean hilum color. In addition, we identified recombination hot spots of soybean genome in 614 recombinant inbred lines (RILs) using VB-specific indel markers. We expect that this platform facilitate the development of designed cultivars by introducing precise target loci into plant genomes.
A variant block-based comparative genomics method for the detection of functional loci in soybeans
Yul Ho Kim,Tae-Young Hwang,Hyang Mi Park,Seuk Ki Lee,Man Soo Choi,Seung woo Hwang,Kwang Ho Jeong,Min Jung Seo,Hong Tai Yun,Sun Lim Kim,Young-Up Kwon,Ho-Sung Yoon,Suk-Ha Lee,JongBhak,Sunghoon Lee 한국육종학회 2013 한국육종학회 심포지엄 Vol.2013 No.07
Although much effort has been made to find agronomically important loci in the soybean plant, extensive linkage disequilibrium and genome duplication have limited efficient genome-wide linkage analyses that can identify important regulatory genes. In this respect, recombination block-based analysis of cultivated plant genomes is a potential critical step for molecular breeding and target locus screening. We propose a new three-step method of detecting recombination blocks and comparative genomics of bred cultivars. It utilizes typical reshuffling features of their genomes, which have been generated by the recombination processes of breeding ancestral genomes. To begin with, mutations were detected by comparing genomes to a reference genome. Next, sequence blocks were examined for likenesses and difference with respect to the reference genome. The boundaries between the blocks were taken as recombination sites. All recombination sites found in the cultivar set were used to split the genomes, and the resulting sequence fragments were named as core recombination blocks (CRBs). Finally, the genomes were compared at the CRB level, instead of at the sequence level. In the genomes of the five Korean soybean cultivars used, the CRB-based comparative genomics method produced long and distinct CRBs that are as large as 22.9 Mb. We also demonstrated efficiency in detecting functionally useful target loci by using indel markers, each of which represents a CRB. We further showed that the CRB method is generally applicable to both monocot and dicot crops, by analyzing publicly available genomes of 31 soybeans and 23 rice accessions.
Hyang-Yul Kim,Yong-Je Jeon,Jeoung-Yeon Hwang,Jae-Hyung Kim,Dae-Shik Seo 한국물리학회 2002 Current Applied Physics Vol.2 No.3
In this research,the image-sticking property in the in-plane switching (IPS)-liquid crystal display (LCD) with residual DC voltagehysteresis method in the IPS-LCDs was measured. It was found that the VHR increased with increasing specic resistivity of uorineLCs. The residual DC voltage decreased with increasing concentration of cyano LCs and decreasing with increasing specic re-sistivity of uorine LCs. Consequently,the residual DC voltage can be decreased by high polarity of cyano LC.. 2002 Elsevier Science B.V. All rights reserved.
Soybean molecular breeding platform based on variation blocks
Yul-Ho Kim,Hyang-Mi Park,Sunghoon Lee,Yu-Young Lee,Su Jeong Kim,Whang-Bae Sohn,Su-Young Hong,Jeong-Hwan Nam,Kibum Kweon,Jin-Cheol Jeong 한국육종학회 2015 한국육종학회 심포지엄 Vol.2015 No.07
Much effort has been expended to find agronomically important QTLs for improving soybean yield. However, the complexity of genome, such as genome duplication, limits the utility of genome-wide association studies and linkage analyses to identify genes controlling yield traits. We propose the variation block method, a three-step process for recombination block detection and comparison. The first step is to detect variations by comparing short-read DNA sequences of the cultivar to a reference genome of the target crop. Next, sequence blocks with variation patterns are examined and defined. The boundaries between the variation-containing sequence blocks are regarded as recombination sites. All the assumed recombination sites in the cultivar set are used to split the genomes, and the resulting sequence regions are named as variation blocks. The practicality of this approach was demonstrated by the identification of a putative locus determining soybean hilum color and known genes such as flower color gene. We suggest that the variation block method is an efficient genomics method for recombination block-level comparison of crop genomes. We expect that this method holds the prospect of developing crop genomics by bringing genomics technology to the field of crop breeding.