본 논문은 국제벼연구소(International Rice Research Institute: IRRI)의 분자육종체계의 현황을 살펴보고, 국제적으로 시장중 심의 육종체계로 변화함에 따라, 새로운 분자마커 이용 육종 법이 갖추어야 할 조건에 대해 논하였다. 벼에 있어서 신품종 개량을 위한 분자생물학의 도움을 받는 분자육종법은 재해 및 병충해 저항성과 수량 및 품질 제고에 전반적으로 활용되고 있으며, 관련 계통 및 품종이 속속 개발 되고 있다. 국제벼연구소는 기후변화 및 자원부족에 대응하면 서도 수량과 품질의 저하가 없는 쌀 품종을 개발하기 위해, 분자육종법을 적극 활용하고 있다. 지역적으로 시장구조별로 특화시킨 품종개발프로필(VDP)을 개발하고, 그에 맞는 형질을 발굴하여, 빠르게 우수형질에 도 입하기 위해서 분자표지를 이용한 육종이 활용될 수 있다. 각 형질은 유전적으로 우수하고 분명한 효과를 보이는 것으 로서, 분자마커는 해당 형질에 강하게 연관되어야 유용하다. 성공적인 분자표지육종법을 위해서, 고효율 유전분석법, 생장 촉진 및 세대촉진법, 연관마커 신속 설계 및 분석, 중간계통의 효율적인 표현형 검정법 개발이 필수적이다. 최근에는 차세대유전체분석법 (NGS)의 발달로 저렴하게 계 통의 유전체 분석이 용이해졌고, 이를 위해서 생물정보학과 유 전체학의 도움을 받는 유전체선발법이 개발되었다. 향후 성공적인 대량 신속 계통육성을 위한 분자육종법의 도 입을 위해 필요한 기술과 연구 제목을 제안하면, (1) 경제적 가치평가 기술과 합리적 효과 판정의 적용 (2) 체계적인 기본 식물 관리, (3) 온실 및 농장 전산화, (4) 계통육성시스템과 유전분석시스템의 일체화, (5) 유전분석 비용의 경제화, (6) 대 량 형질 및 유전자 추출 연구, (7) 다형질간 상호작용 연구, (8) 세대촉진법, (9) 육종가를 위한 결정지원소프트웨어 개발, (10) 집단개량 및 집단선발법의 체계화, 그리고 (11) 인위적 변 이 기술과의 접목 등이다. 분자육종법을 이용한 품종개량의 개발이익은 경제사회적으 로 그 효과가 적절히 평가될 때만이 궁극적으로 소비자와 농 민에게 이익을 제공하는 의미를 갖게 될 것이다.

Animal genomics and breeding center works for development of livestock industry through development of breeding technologies based on genomes. Through analysis technology of genomic information with commercialization of DNA chip and development of NGS technique at present, we can select and improve superior breeding stock. DNA chip technique using microarray can analyze millions of SNP genotypes in a short period and we are studying these techniques to make a tool for genomic selection. In the United States, they made a guideline for genomic selection in dairy cattle and this guideline is utilized. In addition Semex company and CRV center use genomic selection for Holstein dairy cattle. Semex says genomic selection reduce two years compared to the existing selection, cost will be shortened 50% and improving speed will be more than 30% accelerated. In Australia, the case of using genomic information has more 10% accuracy than the case of using parent's breeding value without phenotype information. Recently development of NGS technology leads to reduction of analysis costs, increase in analysis data quantity and shorten time of analysis genome. NGS technology is innovative tool in life science. With development of NGS technology, we can expect to increase the efficiency of genomic analysis. Development of NGS technology leads us to expand whole genome study from limited gene study. Human and rodential genome is researched over the past five years, but only recently lots of livestock's genomes like cattle and pig are researched. Also for domestic, studies on livestock genome and genomic information are accomplished but we have a poor infrastructure of genomic analysis. Thus, through the application technology using SNP chip data and NGS, new breeding technology is very important for prior occupation. Animal genomics and breeding center has four strategies and these are divided by application technology. 1. Development of animal breeding and statistical genetics based on genomic information. 2. Development of genomic analysis and application technology through analysis of genetic diversity and structure. 3. Registration of traditional breeds and securing intellectual property rights based on the genome of the unique genetic resources. 4. Development of technologies for improvement of disease resistance and economic traits.

This study analyzed the mitochondrial DNA (mtDNA) sequences of the Red-spotted grouper, Epinephelus akaara (Perciformes, Serranidae), and used for construction of molecular phylogeny and for association between maternal haplotypes and phenotypic differences of F1 progeny. This study revealed phylogenetic position of the endangered red-spotted grouper, Epinephelus akaara (Perciformes, Serranidae) based on the nucleotide sequences of complete mt genome. Complete nucleotide sequences were determined from the mt genomes of two individuals of the red-spotted grouper caught in South Korea. The mitochondrial genome had 16,795 base pairs (bp) and 13 protein-coding genes, 2 ribosomal RNAs, 22 transfer RNAs, and a noncoding control region. The two mt genomes were highly homologous (99.71% similarity). The two mt genomes of E. akaara determined in this study were found in Clade I in the phylogenetic tree with those of E. awoara, E. fasciatomaculosus, E. sexfasciatus, E. diacanthus, E. sticus, and E. morio, suggesting that this may be helpful to understand phylogenetic position of Epinephelus species including red-spotted grouper. The genetic structure and phylogenetic relationship were investigated in the red-spotted grouper populations using the sequence polymorphisms of the cytochrome c oxidase subunit I(COI) gene and variable number of tandem repeats (VNTRs) of the control region (CR). A total of forty-one COIhaplotypes were found from 174 COIsequences from East Asia. The Jeju Island population (n=5) had four haplotypes, and the South Sea population (n=105) had twenty-five haplotypes. The Hong Kong population had nineteen haplotypes from fifty-nine COIsequences determined in this study. Among the COIhaplotypes, EAC_03 is commonly found in all populations (Jeju Island and South Sea of Korea, China, Hong Kong and Taiwan). In addition, there were four haplotypes (EAC_12, EAC_14, EAC_28 and EAC_35) also common among the populations tested in this study and collected from NCBI database. However, twenty haplotypes were specific in the Korean populations, and fifteen haplotypes were specific in the China and Hong Kong populations. The neighbor-joining (NJ) trees constructed from the phylogenetic analyses based on the polymorphisms of the COIhaplotypes showed the monophyletic branching pattern within the genus Epinephelus, indicating that the red spotted grouper populations had evolved from common maternal ancestors. Consequently, East Asian red-spotted grouper populations are maternally related at least in part, as well as sharing the same evolutionary history, and still affected by the East Asian ocean current (Kuroshio). From the haplotype analysis for mtDNA CR, we obtained VNTR polymor-phisms in all populations tested. We found five haplotypes for the CR VNTR patterns. The 133-bp repeat units were counted two to five. Using CR VNTR haplotypes, the statistical association was examined between mtDNA haplotypes and growth traits of aquafarming young fishes of the red-spotted grouper. A total of 386 F1 progeny, which were randomly selected from a progeny population produced by artificial insemination in the farm, were genotyped and statistically compared their body length (BL), body weights (BW) and length-weight indexes (LWI) at 11-months after hatching. There haplotypes H03, H04 and H05 were detected for CR in the parents and progeny populations. The significant difference was found in the BL values among three haplotypes (p<0.05). The F1 animals with haplotype H03 had freater level of BL (19.22±2.000 cm) than those of H04 (18.64±1.964 cm) and H05 (18.86±1.512 cm). There were no significant differences in BW and LWI among haplotypes (p<0.05). These results concluded that the maternal lineages affected the growth rates during early developmental stage in the red-spotted grouper. These findings suggested that the mitochondrial background of the fertilized eggs may play an important role in the early development, and the markerassisted selection system for broodstork animals may be helpful in improving performance traits for aquaculture industry as well as for conservation biology of the endangered red-spotted grouper. However, the results from the association analysis between haplotypes and phenotypes of F1 progeny (n=1,093) at 60-days after hatching showed that there were no significant difference (p>0.05). Consequently, the results of this study may be useful information for understanding the evolutionary relation with other species and may be good genetic markers for breeding management in the red-spotted grouper aquaculture system.

Radish is one of the most widely consumed vegetable crops in Korea. Root is the major part of radish supplied to the market, thus the size, shape, and quality of radish roots are main targets of breeding programs. Despite of the importance of this crop, the molecular breeding of radish is still in the rudimentary stage. In Golden Seed Project, we aim to establish the molecular breeding program of radish using genome-wide approaches. To this end, we selected inbred lines that have distinctive root traits such as yield, shape, disease resistance, and texture. Single nucleotide variation (SNV) among these lines will be identified based on the low coverage genome sequencing data. These SNVs can be used for finding genomic regions associated with root traits from segregating mapping populations which are also in the middle of development. Korean radish roots are harvested after being grown for only nine weeks. During that period, root biomass reaches to more than two kilograms. While investigating the root growth of radish inbred lines, we found that cytokinin contributes as a key growth regulator that promotes radial growth of radish roots. A difference in growth rates of two distinctive inbred lines was explained by the difference in response to cytokinin. Genes responsive to cytokinin are highly enriched in the cambium, the meristematic cell population that drives radial growth. For comprehensive understanding of genes that affect yields of radish roots, we turned to developing a tissue specific transcriptome data using laser capture microdissection. We expect that the compendium of genomics-based data will help establishing molecular breeding of radish at a fast track.

Marker assisted selection (MAS) for disease resistance is widely applied in practical tomato breeding program both in public and private sectors. Due to the commercial value and the importance as a model crop system, tomato has taken the lead in MAS among the other horticultural crops. A wide range of disease resistance genes were identified and the mechanism of the resistances has been explored in tomatoes. In the case of disease resistance Tomato yellow leaf curl virus (TYLCV) is one of the major threats for tomato production worldwide, and several resistance sources for TYLCV resistance have been identified among wild tomato species. Ty1/3 resistance gene has been recently identified as a DFDGD-class RNA dependent RNA polymerase (RDR). Late blight (LB) in tomato is caused by Phythophthora infestans, and several resistances sources have been applied in the practical breeding program. Ph3 resistance, a LB resistance against a wide-range of P. infestans isolates, has been reported as a gene coding a CC-NBS-LRR gene on chromosome 9. In this study, we developed reliable and comprehensive molecular markers based on the single nucleotide polymorphisms (SNPs) or insertion/deletion (InDel) directly responsible for the resistance phenotype. These functional molecular markers are expected to enhance the effectivity and accuracy of MAS for disease resistance in tomato breeding programs.

Molecular markers, such as PCR-based and SNP-based markers, are extremely useful for plant genetics and crop breeding. Marker-assisted selection (MAS) has been widely applied in plant breeding to improve crop yield, quality, and tolerance to biotic and abiotic stresses. To develop gene-based (or -specific) molecular markers, three different approaches have been used in Brassica species: Known-gene-based, RNA seq/Exon-based and RNA seq/Intron-based molecular marker development for several years. Using these techniques, molecular markers have been developed to identify flowering time, anthocyanin accumuation and abiotic stresses in B. rapa and B. oleracea. Markers were distributed in exons as well as introns, and coding sequences and untranslated regions (UTRs). All markers developed have been transformed into SNP marker after HRM confirmation. I will discuss efficiency, accuracy, and potential problems and contribution of these markers for Brassica breeding.

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.

The goals of this research project are to identify the genes controlling plant architecture through the establishment of foundation for molecular breeding and to develop new rice varieties with useful characters associated with high yield leading to its commercialization. The research subjects of this project are as follows: improvement of plant architecture including tiller angle and number associated to harvest-index, construction of genetic and QTL map related to plant architecture and isolation of target genes, development of molecular markers with high efficiency, and further study for the mechanisms of recombination event and reproductive barrier occurring from cross between subspecies, development of new elite rice varieties with high yield and its commercialization. The isolated genes and products of this research project will be patented and molecular markers for those genes will be applied to breeding procedure. The breeding materials produced as outcomes will be provided to other breeders for further breeding programs. The developed varieties will be patented and registered to the national list of varieties, and will be distributed to our agricultural industries for the increase of its competitiveness and farmer’s income. The patents for genes, molecular markers, and varieties will be licensed out to uphold the agricultural biotechnology industries.

Capsinoids, low-pungent compounds, have the same biological effects as capsaicinoids such as anticancer and anti-obesity. A precursor of capsinoids, vanillyl alcohol, is known to be produced by mutations in the putative-aminotransferase (pAMT) gene. In the previous study, ‘SNU11-001’ (Capsicum chinense) containing high levels of capsinoids was identified in germplasm collections of Capsicum. This collection has a unique mutation in the pAMT gene that can cause dysfunction of this gene. In order to develop pepper varieties containing high capsinoids contents, marker-assisted foreground and background selections were performed during backcross breeding. Compared to the conventional backcrossing, marker-assisted backcrossing (MABC) is extremely useful for recovery of a recurrent parent’s genetic background. For foreground selection, plants carrying the pAMT/pamt genotype were selected from a BC1F1 and BC2F1 populations using SCAR markers derived from the unique pAMT mutation of ‘SNU11-001’. To obtain background selection markers, a total of 412 single nucleotide polymorphism (SNP) markers was screened on ‘Shinghong’ parental lines and ‘SNU11-001’ to obtain polymorphic SNP markers. Of the 412 SNP markers, 144 and 204 polymorphic SNP markers evenly distributed in pepper genome were finally selected. BC1F1 and BC2F1 plants carrying the pAMT/pamt genotype were subjected to background selection using the selected marker sets. Multiple genotype analysis was done using a high-throughput genotyping system (EP1TM, Fluidigm®, USA). As a result, one BC1F1 plant 84% similar to the recurrent parent and several BC2F1 plants more than 96% recovery rate of the recurrent parent were selected. Genetic backgrounds of the selected BC2F1 plants were evaluated by the genotype-by-sequencing (GBS) method in order to confirm the background selection results using the SNP marker set. GBS results showed that recovery rate and positions of introgressed segments were well matched between two methods demonstrating MABC can be successfully done with a couple hundred SNP markers.

본 연구과제의 목적은 1) 양질 다수성 콩 기술 이전, 2) 양질 다수성 콩 품종 출원, 3) 고밀도 유전자지도 작성을 통한 다수성관련 QTL 동정 및 다수성 형질 연관 마커 개발, 4) 콩 품종 판별 마커 개발, 5) 기능성 콩 가공식품 개발이다. 이를 위해 당해연도는 양질 다수성 콩 품종 육성을 위한 생산력 검정 및 지역적응성 검정을 실시하고 초다수성 우량 계통 육성을 위해 1단계 사업에서 선발된 우량 계통들을 지속적으로 세대진전하고자 한다. 특히 다수성관련 형질연관 QTL 동정을 위해 길육69 x SS0404-T5-76 RIL 집단(400계통)을 육성하였고 이 집단을 이용한 고밀도 유전자지도 작성하고자 한다. 먼저 모부본 염기서열 변이 탐색 및 RIL들의 다수성 형질 표현형을 조사할 것이다. 한편, 품종보호 및 종자순도 관리에 있어서 중요한 분자 마커 개발을 위해 주요품종들에 대한 SSR 마커 분석을 실시하였다. 당해연도에는 1단계 사업에서 개발된 ‘CJ행복한1호’ 콩 품종 육성을 위한 채종포를 제주도와 괴산 등지에 조성하며 두부 장류용 우량 계통 SS408-T5-99 에 대한 제품 생산 가능성 분석하고 장류발효과정 중 아이소플라본의 성분 변화를 분석할 것이다.

Capsinoids, low-pungent compounds, have the same biological effects as capsaicinoids such as anticancer and anti-obesity. A precursor of capsinoids, vanillyl alcohol, is known to be produced by mutations in the p-aminotransferase (p-AMT) gene. In the previous study, SNU11-001 (C. chinense) containing high levels of capsinoids was found in germplasm collections of Seoul National University. We found that this collection has a unique mutation in the p-AMT gene. In order to develop a cultivar containing high capsinoids contents, marker-assisted foreground and background selection were performed in this study. Backcrossing is an effective breeding method for introducing useful traits to an elite cultivar. Compared to conventional backcrossing, marker-assisted backcrossing (MABC) is extremely useful for recovery of a recurrent parent’s genetic background. To obtain background selection markers, a total of 412 single nucleotide polymorphism (SNP) markers was screened to obtain polymorphic SNP markers between ‘Takanotsume (C. annuum)’ and ‘SNU11-001’. Of the 412 SNP markers, 96 polymorphic SNP markers evenly distributed in pepper genome were finally selected. Plants carrying the pAmt/pamt genotype were selected from a BC1F1 population using SCAR markers derived from the unique p-AMT mutation of SNU11-001. BC1F1 plants carrying the pAmt/pamt genotype were subjected to background selection. Multiple genotype analysis was done using Fluidigm platform (BioMark). Once we obtain plants carrying most similar genetic background to recurrent parent, capsinoids contents will be measured and another round of MABC be done to obtain plants containing high levels of capsinoids.

Single nucleotide polymorphisms (SNPs) are the most abundant variation in plant genomes. As DNA markers, SNPs are rapidly replacing simple sequence repeats (SSRs) and sequence tagged sites (STSs) markers, because SNPs are more abundant, stable, easy to automation, efficient, and increasingly cost-effective. We developed a 96-plex indica/japonica SNP genotyping set for genetic analysis and molecular breeding in rice using Fluidigm platform. Informative SNPs for indica/japonica populations were selected from 1536 Illumina SNPs and 44K Affymetrix SNP chip data of Rice Diversity and our resequencing data sets. Selected SNPs were evenly distributed across 12 chromosomes and average physical distance between adjacent SNP markers was 4.38Mb. We conducted genetic diversity analysis of 49 Bangladesh germplasm and check varieties to test a 96-plex indica/japonica SNP genotyping set we developed. High-throughput Fluidigm SNP genotyping system will serve a more efficient and valuable tool for genetic diversity analysis, DNA fingerprinting, quantitative trait locus (QTL) mapping and background selection for crosses between indica and japonica in rice. This work was supported by a grant from the Next-Generation BioGreen 21 Program (Plant Molecular Breeding Center No. PJ008125), Rural Development Administration, Republic of Korea.

Capsinoids, low-pungent compounds, have the same biological effects as capsaicinoids such as anticancer and anti-obesity. A precursor of capsinoids, vanillyl alcohol, is known to be produced by mutations in the p-aminotransferase (p-AMT) gene. In the previous study, SNU11-001 (C. chinense) containing high levels of capsinoids was found in germplasm collections of Seoul National University. We found that this collection has a unique mutation in the p-AMT gene. In order to develop a cultivar containing high capsinoids contents, marker-assisted foreground and background selection were performed in this study. Backcrossing is an effective breeding method for introducing useful traits to an elite cultivar. Compared to conventional backcrossing, marker-assisted backcrossing (MABC) is extremely useful for recovery of a recurrent parent’s genetic background. To obtain background selection markers, a total of 412 single nucleotide polymorphism (SNP) markers was screened to obtain polymorphic SNP markers between ‘Takanotsume (C. annuum)’ and ‘SNU11-001’. Of the 412 SNP markers, 96 polymorphic SNP markers evenly distributed in pepper genome were finally selected. Plants carrying the pAmt/pamt genotype were selected from a BC1F1 population using SCAR markers derived from the unique p-AMT mutation of SNU11-001. BC1F1 plants carrying the pAmt/pamt genotype were subjected to background selection. Multiple genotype analysis was done using Fluidigm platform (BioMark). Once we obtain plants carrying most similar genetic background to recurrent parent, capsinoids contents will be measured and another round of MABC be done to obtain plants containing high levels of capsinoids