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Map-based cloning of SUI4 gene which controls internode elongation in rice
Hyeonso Ji,Gang-Seob Lee,Doh-Won Yun,Seung-Bum Lee,Seok-Chul Suh,Moo-Young Eun 한국육종학회 2014 한국육종학회 심포지엄 Vol.2014 No.07
Internode elongation is an important agronomic trait in rice that is associated with lodging, yield, and flooding adaptation. We identified a novel rice mutant line showing shortened uppermost internode among the rice Ac/Ds insertional mutant population and named it shortened uppermost internode 4 (sui4). The phenotypes of F1 plants and F2 plants from the cross of sui4 with its original variety, Dongjin, indicated that the SUI4 gene shows incomplete dominance or semidominance. Because the Ds genotypes did not co-segregate with the sui4 phenotypes, we performed mapping of this gene with 273 F2 plants from a cross between sui4 and Milyang23. Primary mapping revealed that the SUI4 locus was located between the S07012 and S07015 markers on rice chromosome 7. Further fine mapping narrowed down the location of SUI4 to the 1.1-Mbp interval of RM1253-S07015. Using re-sequencing data of this mutant along with its original variety, Dongjin, and five other varieties, we found six sui4 specific SNPs occurred within the genic region of five genes in the fine-mapped interval. Among them, one SNP is in exon, while the other five SNPs are in intron. This SNP in exon occurred in the miR172 binding site of a gene encoding AP2 domain transcription factor, which seems to interrupt suppression of this gene activity by miR172. We isolated the genomic region of this gene from sui4 and transformed the wild type variety, Dongjin. The transgenic plants showed remarkably shortened internodes, which indicates that this AP2 domain transcription factor gene is the SUI4 gene.
Selection of salt-tolerant rice mutant lines from Ac/Ds insertional mutant population
Hyeonso Ji,Hakbum Kim,Gang-Seob Lee,Doh-Won Yun,Ung-Han Yoon,Tae-Ho Kim 한국육종학회 2013 한국육종학회 심포지엄 Vol.2013 No.07
In order to find new genetic sources of rice salt tolerance, we did screening with about 10,000 rice mutant lines created by Ac/Ds insertional mutagenesis. First, we raised rice seedlings with media soil on 0.7% NaCl solution and selected 71 putative salt tolerant lines and analyzed their Ds insertion sites. We tested their salt tolerance by growing seedlings on MS medium containing, 0 mM, 150 mM, and 250 mM NaCl. Also, their seedling salt tolerance were evaluated by growing on Yoshida nutritional solution containing 0.6% NaCl. Finally, we selected eight mutant lines showing increased seedling salt tolerance compared with wild type variety, Dongjin, repeatedly. We grow them in rice field and investigated their agronomic traits such as heading time, culm length, panicle length, and panicles per hill. Among them two lines which were named Salt10 and Salt23 and showed favorable agronomic characteristics were crossed with Dongjin for further genetic analysis and mapping the causative gene variation.
Ji, Hyeonso,Kim, Sung-Ryul,Kim, Yul-Ho,Kim, Hakbum,Eun, Moo-Young,Jin, Il-Doo,Cha, Young-Soon,Yun, Doh-Won,Ahn, Byung-Ohg,Lee, Myung Chul,Lee, Gang-Seob,Yoon, Ung-Han,Lee, Jung-Sook,Lee, Yeon-Hee,Suh, Blackwell Publishing Ltd 2010 The Plant journal Vol.61 No.1
<P>Summary</P><P>Although susceptibility to seed shattering causes severe yield loss during cereal crop harvest, it is an adaptive trait for seed dispersal in wild plants. We previously identified a recessive shattering locus, <I>sh-h</I>, from the rice shattering mutant line Hsh that carries an enhanced abscission layer. Here, we further mapped <I>sh-h</I> to a 34-kb region on chromosome 7 by analyzing 240 F<SUB>2</SUB> plants and five F<SUB>3</SUB> lines from the cross between Hsh and Blue&Gundil. Hsh had a point mutation at the 3′ splice site of the seventh intron within LOC_Os07g10690, causing a 15-bp deletion of its mRNA as a result of altered splicing. Two transferred DNA (T-DNA) insertion mutants and one point mutant exhibited the enhanced shattering phenotype, confirming that LOC_Os07g10690 is indeed the <I>sh-h</I> gene. RNA interference (RNAi) transgenic lines with suppressed expression of this gene exhibited greater shattering. This gene, which encodes a protein containing a conserved carboxy-terminal domain (CTD) phosphatase domain, was named <I>Oryza sativa CTD phosphatase-like 1</I> (<I>OsCPL1</I>). Subcellular localization and biochemical analysis revealed that the OsCPL1 protein is a nuclear phosphatase, a common characteristic of metazoan CTD phosphatases involved in cell differentiation. These results demonstrate that OsCPL1 represses differentiation of the abscission layer during panicle development.</P>
Toward mapping of genes conferring broad spectrum resistance to rice brown planthopper
Hyeonso Ji,Eokkeun Ahn,Seung-Bum Lee,Seok-Chul Suh 한국육종학회 2015 한국육종학회 심포지엄 Vol.2015 No.07
Brown planthopper (BPH) is a phloem sap-sucking insect pest of rice, which causes severe yield loss annually. Gayabyeo, a Tongil type rice variety, is known to have broad spectrum resistance to BPH. Before, it was estimated that Gayabyeo has at least two BPH resistance genes. We started a research for mapping resistance genes of Gayabyeo. We did a cross between Taebaekbyeo, a BPH susceptible Tongil type rice variety, and Gayabyeo, We grew F1 plants in winter season of 2014-2015, and planted F2 population in this year. About 100 DNA markers (SSR and InDel markers) showing polymorphism between Gayabyeo and Tabaekbyeo were selected. In addition, we are going to do resequencing Gayabyeo and Taebaekbyeo using Illumina Hiseq2000 to find much more DNA polymorphisms between the two varieties and develop new markers for mapping. The BPH response data will be acquired using F3 plants from the cross between Gayabyeo and Taebaekbyeo next year. In a while, crosses between Gayabyeo and high quality japonica rice varieties are being carried out to introduce BPH resistance genes of Gayabyeo into japonica high quality rice varieties. We expect to develop new DNA markers for BPH resistance genes of Gayabyeo through mapping and produce several japonica high quality rice lines harboring those genes at the end of this project.
Fine-Mapping of a Major Quantitative Trait Locus q2ID1 for Rice Stem Diameter
( Ye-ji Lee ),( Yeisoo Yu ),( Hyeonso Ji ),( Gang-sub Lee ),( Nam-in Hyung ),( Keunpyo Lee ),( Tae-ho Kim ) 한국육종학회 2021 Plant Breeding and Biotechnology Vol.9 No.4
Rice culm is an important trait for determining rice lodging yield, and stem diameter has been suggested as a yield-related trait; however, studies for the genetic basis of its phenotypic variation are still required. In this study, we used 160 recombination inbred lines derived from a cross of two different rice varieties [‘Milyang23’ (Tongil rice) and ‘Giho’ (japonica)] for quantitative trait locus (QTL) mapping with nine stem traits. The analysis showed that QTLs for the diameters of the first, second, third and fourth internode traits were independently separated in the top of chromosome 1, whereas four lengths of internodes were estimated as being related to the semidwarf1 (sd1) gene. A major-effect QTL (q2ID1) was identified that the overlapped region of our previous mapping with a large genomic region. Therefore, we performed high-resolution genetic mapping for fine-mapping of q2ID1 to a ~140 kb region between Ind1_1 and Ind1_2 of genetic markers, with candidate genes predicted using a reference genome. We ultimately identified nine of the 15 candidate genes with specific gene functions and analyzed the sequence variations between two parents. These results offer valuable gene and/or genetic information on stem diameter to improve lodging resistance and yield.
NGS 기반 밀양23호/기호벼 재조합자식 유전집단(MGRIL)을 이용한 CAPS 마커 개발 및 줄기 굵기 형질 관련 QTL 분석
이예지(Ye-Ji Lee),변은주(Eun-Ju Byeon),배선화(Seon-Hwa Bae),지현소(Hyeonso Ji),이강섭(Gang-Seob Lee),윤웅한(Ung-Han Yoon),김태호(Tae-Ho Kim) 한국육종학회 2016 한국육종학회지 Vol.48 No.3
The rice recombinant inbred lines derived from Milyang23 and Gihobyeo cross were used in genetic mapping and QTL analysis studies. In this study, we developed a new 101 CAPS markers based on the SNPs in the whole genome region between these varieties. As a result, the total genetic distance and average distances were 1,696.97 cM and 3.64 cM, respectively. In comparison to the distance of the previous genetic map constructed based on 365 DNA markers, the new genetic map was found to have a decreased distance. The map was applied for the detection of QTLs on all seven traits relevant to diameter of stem internode, length of culms, length of panicles and the number of panicles including the correlation analysis between each trait. The QTLs results were similar to the report in previous studies, whereas the distance between the markers was narrowed and accuracy increased with the addition of 101 CAPS markers. A total of 9 new QTLs were detected for stem internode traits. Among them, qI1D-6 had higher LOD of 5.1 and phenotype variation of 50.92%. In this experiment, a molecular map was constructed with CAPS markers using next generation sequencing showing high accuracy for markers and QTLs. In the future, developing more accurate QTL information on stem internode diameters with various agriculturally important traits will be possible for further rice breeding.