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Jeonghwan Seo,Md. Babul Akter,Yoon Kyung Lee,Hee-Jong Koh 한국육종학회 2014 한국육종학회 심포지엄 Vol.2014 No.07
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.
( Jeonghwan Seo ),( So-myeong Lee ),( Jae-hyuk Han ),( Na-hyun Shin ),( Hee-jong Koh ),( Joong Hyoun Chin ) 한국육종학회 2019 Plant Breeding and Biotechnology Vol.7 No.4
The yield related traits are controlled by multiple quantitative trait loci (QTLs) and influenced by environmental change in rice. We analyzed QTLs for 15 yield related traits using two backcross populations, derived from crosses between IR64 as recurrent parent and Koshihikari as donor parent, through two years. A total of 67 backcross inbred lines (BILs) and 40 chromosome segment substitution lines (CSSLs) were genotyped using 183 SNP markers using a high-throughput genotyping system. Some genomic gaps between markers were identified in two populations. For fifteen traits in this study, 36 major QTLs (mQTLs) for 12 traits and 16 digenic epistatic QTLs (EpQTLs) for culm length were detected in BILs. On the other hand, 17 mQTLs were detected for nine traits in CSSLs. Among them, six mQTLs for grain yield traits were collocated on chromosome 10 in both years. For spikelet fertility, six putative QTLs were detected under high temperature conditions in 2018. The QTLs identified in this study could be used for the development of rice varieties conferring inter-subspecific combinations of yield-related traits.
QTL analysis for eight agronomic characters in two rice (Oryza sativa) populations
Jeonghwan Seo,Sunghan Kim,Gileung Lee,Sheryl Sierra,Hee-Jong Koh 한국육종학회 2012 한국육종학회 심포지엄 Vol.2012 No.07
The HWC-line of rice showed wide compatibility with both indica and japonica cultivars, tall culm length, long and slender grain shape. For QTL analysis, two F2 populations were derived from the crosses between the HWC-line and each of two Korean variety, Dasanbyeo (Korean Tongil-type cultivar) and Hwacheongbyeo (temperate japonica cultivar), respectively. A total of 190 F2 plants were evaluated in each of two F2 populations. Eight agronomic characters were measured for QTL analysis in F2 populations and parents. Two molecular linkage maps were constructed. In the F2 population from cross between HWC-line / Dasanbyeo (HD) cross, 93 STS markers and 13 SSR markers were mapped on 12 chromosomes, covering a total length of 1942.6 cM, with an average distance of 18.33cM between adjacent markers. In the F2 population from HWC-line / Hwacheongbyeo (HH) cross, 28 STS markers, 29 SSR markers and 1 FNP marker were mapped on 11 chromosomes, spanning a total length of 925.53cM, with an average distance of 15.96cM between adjacent markers. In the F2 population from HD cross, 16 M-QTLs and 1 E-QTL were detected for culm length, spikelets per panicle, spikelet fertility, grain length, grain width, grain shape and 100 grains weight. 7 QTLs of spikelet fertility, grain length, grain width and grain shape were newly identified in this study. In the F2 population from HH cross, 15 M-QTLs were detected for culm length, panicle length, spikelet fertility, grain length, grain width, grain shape and 100 grains weight. 6 QTLs of culm length, grain length, grain width and grain shape were newly identified in this study. The QTLs identified in this study would provide basic information on putative functional genes related agronomic characters and facilitate breed new rice cultivar.
Jeonghwan Seo,Huang Xing,Su Jang,Sunghan Kim,Hee-Jong Koh 한국육종학회 2013 한국육종학회 심포지엄 Vol.2013 No.07
Hybrid sterility is a critical barrier of inter-subspecific crosses in rice. However, hybrid sterility can be overcome by wide compatibility variety. The HWC-line of rice had slender grain shape, tall culm length, wide compatibility with both indica and japonica cultivars. For QTL analysis of HWC-line, two F2 populations were derived from the crosses between the HWC-line and each of two Korean variety, Dasan (Korean Tongil-type cultivar) and Hwacheong (temperate japonica cultivar). In the cross between HWC-line/Dasan (HD), 93 STS markers and 13 SSR markers were mapped on 12 chromosomes. In the population from HWC-line/Hwacheong (HH) cross, 28 STS markers, 29 SSR markers and 1 FNP marker were mapped on 11 chromosomes. Eight agronomic characters were evaluated for QTL analysis in two F2 populations and parents. The F2 population from HD cross revealed 21 M-QTLs and 3 E-QTL for culm length, spikelet per panicle, spikelet fertility, grain length, grain width, grain shape and 100 grains weight. 8 QTLs of culm length, grain length, grain width and grain shape were newly detected in this study. In the F2 population from HH cross, 17 M-QTLs were detected for culm length, panicle length, spikelet fertility, grain length, grain width, grain shape and 100 grains weight. 6 QTLs of culm length, grain length, grain width and grain shape were newly found in this study. These QTLs will be able to provide basic information on putative functional genes related with agronomic characters and promote breeding new rice cultivar. HWC-line could be used as bridge for inter-subspecies crosses and in hybrid breeding.
서정환(JeongHwan Seo),김장원(Jangwon Gim),정동원(Dongwon Jeong) 한국정보기술학회 2019 Proceedings of KIIT Conference Vol.2019 No.6
이 논문에서는 최적 항로 탐색 지원을 위한 자율운항선박 모형을 제안한다. 4차 산업혁명의 발달과 함께 인공지능 기반의 자율운항선박(Maritime Autonomous Surface Ship, MASS)에 대한 연구가 활발하게 진행되고 있다. 그러나 소형 선박이 전체 선박 사고의 약 70%를 차지함에도 불구하고 높은 비용으로 인해 시스템 도입에 어려움을 겪고 있다. 따라서 이 논문에서는 소형 선박을 위한 자율운항선박 모형을 제안한다. This paper propose an maritime autonomous surface ship model for optimum route prediction based on machine learning. With the development of the 4th industrial revolution, studies on artificial intelligence based autonomous navigation ship (MASS) have been actively carried out. However, despite the fact that small ships account for about 70% of all ship accidents, it is difficult to introduce the system due to high cost. Therefore, this paper proposes maritime autonomous surface ship models for small ships.
서정환(Jeonghwan Seo),장홍지아(Hongjia Zhang),이아림(Ah-Rim Lee),이원도(Wondo Lee),조유현(Yoo-Hyun Cho),권순욱(Soon-Wook Kwon),이주현(Joohyun Lee) 한국육종학회 2021 한국육종학회지 Vol.53 No.4
Root development at the seedling stage is an important trait for the early growth of rice. In this study, the root length and weightof 211 Korean landrace rice at the seedling stage were evaluated, and the average root length and weight were 6.94 cm and 48.18 mg, respectively. Principal component analysis (PCA) of 211 accessions based on 70,849 SNPs presented three subgroups. Two quantitative trait loci (QTLs)associated with root length were detected on chromosomes 3 and 6 using genome-wide association study (GWAS). Four haplotypes wereidentified using associated SNPs for the two root length QTLs. The average root length of Hap2 and Hap 3 was 7.32 cm and 6.56 cm,respectively, and were significantly different. Gene expression analysis in the candidate regions of QTLs for root length at the seedling stageshowed that several genes were expressed in the root. QTLs associated with root length at the seedling stage identified in this study maybe applied to improve the root length trait and detect candidate genes.
Backki Kim,Dong-Gwan Kim,Gileung Lee,Jeonghwan Seo,Ik-Young Choi,Beom-Soon Choi,Tae-Jin Yang,Kwang soo Kim,Joohyun Lee,Joong Hyoun Chin,Hee-Jong Koh 한국육종학회 2014 한국육종학회 심포지엄 Vol.2014 No.07
Tongil (IR667-98-1-2) rice, developed in 1972, is a high-yielding rice variety derived from a three-way cross between indica and japonica. Tongil contributed to staple food self-sufficiency of Korea, an achievement that was termed the ‘Korean Green Revolution’. In this study, we analyzed the nucleotide-level genome structure of Tongil rice and compared it to those of the parental varieties. A total of 17.3 billion Illumina Hiseq reads, 47× genome coverage, were generated from Tongil rice. Three parental accessions, two indica and one japonica types, of Tongil rice were also sequenced for approximately 30x genome coverage. A total of 2,149,991 SNPs were detected between Tongil and Nipponbare; the average SNP frequency of Tongil was 5.77 per kb. Genome composition based on the SNP data by comparing with the three parental genome sequences on sliding window of Nipponbare genome sequence revealed that 91.8% of the Tongil genome originated from the indica parents and 7.9% from the japonica parent, different from the theoretical expectation in a three-way cross, i.e., 75% indica and 25% japonica parental origins on average. Copy number of SSR motifs, ORF gene distribution throughout the whole genome, gene ontology (GO) annotation, yield-related QTLs or gene locations, and polymorphic transposon insertions were also comparatively analyzed between Tongil and parents using sequence-based tools. The results indicated that each genetic factor was transferred from parents into Tongil in proportion to the whole-genome composition. The Tongil rice is the first successful superior cultivar derived from indica × japonica hybridization in Korea. Defining of genome structure demonstrates that the Tongil genome is composed mostly of the indica genome with a small proportion of japonica genome introgression. 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.