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Lee SY, Jeung JU, Mo Y. Allelic combinations of Hd1, Hd16, and Ghd7 exhibit pleiotropic effects on agronomic traits in rice. G3 (Bethesda) 2024; 14:jkad300. [PMID: 38168849 PMCID: PMC10917519 DOI: 10.1093/g3journal/jkad300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Revised: 12/24/2023] [Accepted: 12/27/2023] [Indexed: 01/05/2024]
Abstract
Heading date is a critical agronomic trait that significantly affects grain yield and quality in rice. As early heading is typically associated with reduced yield due to shorter growth duration, it is essential to harness optimum heading date genes and their allelic combinations to promote heading while minimizing yield penalties. In this study, we identified quantitative trait loci (QTLs) for heading date and other major agronomic traits in a recombinant inbred line (RIL) population derived from a cross between Koshihikari and Baegilmi. Analyses on 3 major QTLs for heading date and their underlying genes (Hd1, Hd16, and Ghd7) revealed their pleiotropic effects on culm length, panicle length, and head rice percentage. Additionally, Ghd7 exhibited pleiotropic effects on panicle number and grain size. Among 8 different types of allelic combinations of the 3 heading date genes, RILs carrying a single nonfunctional hd16 or ghd7 under the functional background of the other 2 genes (Hd1hd16Ghd7 and Hd1Hd16ghd7) showed potential for maintaining yield and quality-related traits while accelerating heading. These results provide valuable insights for fine-tuning heading dates in rice breeding programs.
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Affiliation(s)
- Seung Young Lee
- Department of Crop Science and Biotechnology, Jeonbuk National University, Jeonju 54896, Republic of Korea
- National Institute of Crop Science, Rural Development Administration, Wanju 55365, Republic of Korea
| | - Ji-Ung Jeung
- National Institute of Crop Science, Rural Development Administration, Wanju 55365, Republic of Korea
| | - Youngjun Mo
- Department of Crop Science and Biotechnology, Jeonbuk National University, Jeonju 54896, Republic of Korea
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Mo Y, Lee CM, Park HM, Ha SK, Kim MJ, Kwak J, Lee HS, Lee JH, Jeung JU. Hd1 Allele Types and Their Associations with Major Agronomic Traits in Korean Rice Cultivars. Plants (Basel) 2021; 10:plants10112408. [PMID: 34834770 PMCID: PMC8619422 DOI: 10.3390/plants10112408] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 11/03/2021] [Accepted: 11/05/2021] [Indexed: 06/13/2023]
Abstract
Optimizing flowering time in crop plants is critical for maximizing yield and quality under target environments. While there is a wide range of heading date variation in Korean rice cultivars, the underlying gene mechanisms are unclear. Here, we sequenced the protein coding regions of Hd1, the major rice heading date gene, from 293 Korean rice cultivars and investigated the associations between Hd1 allele types and major agronomic traits under four different environments. There were four functional Hd1 and five nonfunctional hd1 alleles distributed among the 293 Korean rice cultivars. The effects of the Hd1 allele types were highly significant for days to heading in all four environments, explaining 51.4-65.8% of the phenotypic variation. On average, cultivars carrying nonfunctional hd1 headed 13.7 days earlier than those carrying functional Hd1. While the Hd1 allele types exhibited highly significant effects on culm length and protein content under all four environments, the differences between cultivars carrying Hd1 and hd1 were minimal. The effects of the Hd1 allele types on amylose content were significant in only one of the four environments. Our results provide useful information for fine-tuning rice heading dates by utilizing different Hd1 alleles in rice breeding programs.
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Affiliation(s)
- Youngjun Mo
- National Institute of Crop Science, Rural Development Administration, Wanju 55365, Korea; (Y.M.); (C.-M.L.); (H.-M.P.); (S.-K.H.); (M.-J.K.); (J.K.); (H.-S.L.); (J.-H.L.)
- Department of Crop Science and Biotechnology, Jeonbuk National University, Jeonju 54896, Korea
| | - Chang-Min Lee
- National Institute of Crop Science, Rural Development Administration, Wanju 55365, Korea; (Y.M.); (C.-M.L.); (H.-M.P.); (S.-K.H.); (M.-J.K.); (J.K.); (H.-S.L.); (J.-H.L.)
- Department of Crop Science and Biotechnology, Jeonbuk National University, Jeonju 54896, Korea
| | - Hyang-Mi Park
- National Institute of Crop Science, Rural Development Administration, Wanju 55365, Korea; (Y.M.); (C.-M.L.); (H.-M.P.); (S.-K.H.); (M.-J.K.); (J.K.); (H.-S.L.); (J.-H.L.)
| | - Su-Kyung Ha
- National Institute of Crop Science, Rural Development Administration, Wanju 55365, Korea; (Y.M.); (C.-M.L.); (H.-M.P.); (S.-K.H.); (M.-J.K.); (J.K.); (H.-S.L.); (J.-H.L.)
| | - Mi-Jung Kim
- National Institute of Crop Science, Rural Development Administration, Wanju 55365, Korea; (Y.M.); (C.-M.L.); (H.-M.P.); (S.-K.H.); (M.-J.K.); (J.K.); (H.-S.L.); (J.-H.L.)
| | - Jieun Kwak
- National Institute of Crop Science, Rural Development Administration, Wanju 55365, Korea; (Y.M.); (C.-M.L.); (H.-M.P.); (S.-K.H.); (M.-J.K.); (J.K.); (H.-S.L.); (J.-H.L.)
| | - Hyun-Sook Lee
- National Institute of Crop Science, Rural Development Administration, Wanju 55365, Korea; (Y.M.); (C.-M.L.); (H.-M.P.); (S.-K.H.); (M.-J.K.); (J.K.); (H.-S.L.); (J.-H.L.)
| | - Jeong-Heui Lee
- National Institute of Crop Science, Rural Development Administration, Wanju 55365, Korea; (Y.M.); (C.-M.L.); (H.-M.P.); (S.-K.H.); (M.-J.K.); (J.K.); (H.-S.L.); (J.-H.L.)
| | - Ji-Ung Jeung
- National Institute of Crop Science, Rural Development Administration, Wanju 55365, Korea; (Y.M.); (C.-M.L.); (H.-M.P.); (S.-K.H.); (M.-J.K.); (J.K.); (H.-S.L.); (J.-H.L.)
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Lee JS, Chebotarov D, McNally KL, Pede V, Setiyono TD, Raquid R, Hyun WJ, Jeung JU, Kohli A, Mo Y. Novel Sources of Pre-Harvest Sprouting Resistance for Japonica Rice Improvement. Plants (Basel) 2021; 10:1709. [PMID: 34451754 PMCID: PMC8401653 DOI: 10.3390/plants10081709] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 08/09/2021] [Accepted: 08/17/2021] [Indexed: 12/04/2022]
Abstract
Pre-harvest sprouting (PHS), induced by unexpected weather events, such as typhoons, at the late seed maturity stage, is becoming a serious threat to rice production, especially in the state of California, USA, Japan, and the Republic of Korea, where japonica varieties (mostly susceptible to PHS) are mainly cultivated. A projected economic loss by severe PHS in these three countries could range between 8-10 billion USD per year during the next 10 years. Here, we present promising rice germplasm with strong resistance to PHS that were selected from a diverse rice panel of accessions held in the International Rice Genebank (IRG) at the International Rice Research Institute (IRRI). To induce PHS, three panicle samples per accession were harvested at 20 and 30 days after flowering (DAF), respectively, and incubated at 100% relative humidity (RH), 30 °C in a growth chamber for 15 days. A genome-wide association (GWA) analysis using a 4.8 million single nucleotide polymorphisms (SNP) marker set was performed to identify loci and candidate genes conferring PHS resistance. Interestingly, two tropical japonica and four temperate japonica accessions showed outstanding PHS resistance as compared to tolerant indica accessions. Two major loci on chromosomes 1 and 4 were associated with PHS resistance. A priori candidate genes interactions with rice gene networks, which are based on the gene ontology (GO), co-expression, and other evidence, suggested that a key resistance mechanism is related to abscisic acid (ABA), gibberellic acid (GA), and auxin mediated signaling pathways.
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Affiliation(s)
- Jae-Sung Lee
- International Rice Research Institute, Los Baños 4031, Philippines; (J.-S.L.); (D.C.); (K.L.M.); (V.P.); (T.D.S.); (R.R.)
| | - Dmytro Chebotarov
- International Rice Research Institute, Los Baños 4031, Philippines; (J.-S.L.); (D.C.); (K.L.M.); (V.P.); (T.D.S.); (R.R.)
| | - Kenneth L. McNally
- International Rice Research Institute, Los Baños 4031, Philippines; (J.-S.L.); (D.C.); (K.L.M.); (V.P.); (T.D.S.); (R.R.)
| | - Valerien Pede
- International Rice Research Institute, Los Baños 4031, Philippines; (J.-S.L.); (D.C.); (K.L.M.); (V.P.); (T.D.S.); (R.R.)
| | - Tri Deri Setiyono
- International Rice Research Institute, Los Baños 4031, Philippines; (J.-S.L.); (D.C.); (K.L.M.); (V.P.); (T.D.S.); (R.R.)
| | - Rency Raquid
- International Rice Research Institute, Los Baños 4031, Philippines; (J.-S.L.); (D.C.); (K.L.M.); (V.P.); (T.D.S.); (R.R.)
| | - Woong-Jo Hyun
- National Institute of Crop Science, Rural Development Administration, Wanju 55365, Korea; (W.-J.H.); (J.-U.J.)
| | - Ji-Ung Jeung
- National Institute of Crop Science, Rural Development Administration, Wanju 55365, Korea; (W.-J.H.); (J.-U.J.)
| | - Ajay Kohli
- International Rice Research Institute, Los Baños 4031, Philippines; (J.-S.L.); (D.C.); (K.L.M.); (V.P.); (T.D.S.); (R.R.)
| | - Youngjun Mo
- National Institute of Crop Science, Rural Development Administration, Wanju 55365, Korea; (W.-J.H.); (J.-U.J.)
- Department of Crop Science and Biotechnology, Jeonbuk National University, Jeonju 54896, Korea
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Mo Y, Jeong JM, Ha SK, Kim J, Lee C, Lee GP, Jeung JU. Characterization of QTLs and Candidate Genes for Days to Heading in Rice Recombinant Inbred Lines. Genes (Basel) 2020; 11:E957. [PMID: 32825032 PMCID: PMC7565938 DOI: 10.3390/genes11090957] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 08/17/2020] [Accepted: 08/17/2020] [Indexed: 11/16/2022] Open
Abstract
Understanding the gene mechanisms controlling days to heading (DH) is important in rice breeding for adaption in the target environment. Using a recombinant inbred line population derived from the cross between two japonica rice cultivars, Koshihikari and Baegilmi, we identified three consistent quantitative trait loci (QTLs) for DH for two years, qDH3, qDH6, and qDH7 on chromosomes 3, 6, and 7, respectively. While Baegilmi contributed the allele for early heading at qDH6 and qDH7 with the additive effect of five days each, Koshihikari contributed the allele for early heading at qDH3 with the additive effect of three days. Notably, pyramiding two or more alleles for early heading at these QTLs accelerated heading effectively. Sequencing of Hd16, Hd1, and Ghd7, the previously known heading date genes underlying qDH3, qDH6, and qDH7, respectively, revealed that Baegilmi and Koshihikari carry different alleles at the three genes. Molecular markers were developed to screen the allelic compositions of the three genes among 295 Korean commercial rice cultivars. The results showed that few cultivars carry alleles for early heading at the three genes, highlighting that DH can be further accelerated and fine-tuned in breeding programs by combining the desirable alleles of Hd16, Hd1, and Ghd7.
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Affiliation(s)
- Youngjun Mo
- National Institute of Crop Science, Rural Development Administration, Wanju 55365, Korea; (Y.M.); (J.-M.J.); (S.-K.H.); (J.K.); (C.L.)
| | - Jong-Min Jeong
- National Institute of Crop Science, Rural Development Administration, Wanju 55365, Korea; (Y.M.); (J.-M.J.); (S.-K.H.); (J.K.); (C.L.)
| | - Su-Kyung Ha
- National Institute of Crop Science, Rural Development Administration, Wanju 55365, Korea; (Y.M.); (J.-M.J.); (S.-K.H.); (J.K.); (C.L.)
| | - Jinhee Kim
- National Institute of Crop Science, Rural Development Administration, Wanju 55365, Korea; (Y.M.); (J.-M.J.); (S.-K.H.); (J.K.); (C.L.)
| | - Changmin Lee
- National Institute of Crop Science, Rural Development Administration, Wanju 55365, Korea; (Y.M.); (J.-M.J.); (S.-K.H.); (J.K.); (C.L.)
| | - Gung Pyo Lee
- Department of Integrative Plant Science, Chung-Ang University, Anseong 17546, Korea;
| | - Ji-Ung Jeung
- National Institute of Crop Science, Rural Development Administration, Wanju 55365, Korea; (Y.M.); (J.-M.J.); (S.-K.H.); (J.K.); (C.L.)
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Wang H, Ham TH, Im DE, Lar SM, Jang SG, Lee J, Mo Y, Jeung JU, Kim ST, Kwon SW. A New SNP in Rice Gene Encoding Pyruvate Phosphate Dikinase (PPDK) Associated with Floury Endosperm. Genes (Basel) 2020; 11:genes11040465. [PMID: 32344582 PMCID: PMC7230733 DOI: 10.3390/genes11040465] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 04/16/2020] [Accepted: 04/22/2020] [Indexed: 01/26/2023] Open
Abstract
Rice varieties with suitable flour-making qualities are required to promote the rice processed-food industry and to boost rice consumption. A rice mutation, Namil(SA)-flo1, produces grains with floury endosperm. Overall, grains with low grain hardness, low starch damage, and fine particle size are more suitable for use in flour processing grains with waxy, dull endosperm with normal grain hardness and a high amylose content. In this study, fine mapping found a C to T single nucleotide polymorphism (SNP) in exon 2 of the gene encoding cytosolic pyruvate phosphate dikinase (cyOsPPDK). The SNP resulted in a change of serine to phenylalanine acid at amino acid position 101. The gene was named FLOURY ENDOSPERM 4-5 (FLO4-5). Co-segregation analysis with the developed cleaved amplified polymorphic sequence (CAPS) markers revealed co-segregation between the floury phenotype and the flo4-5. This CAPS marker could be applied directly for marker-assisted selection. Real-time RT-PCR experiments revealed that PPDK was expressed at considerably higher levels in the flo4-5 mutant than in the wild type during the grain filling stage. Plastid ADP-glucose pyrophosphorylase small subunit (AGPS2a and AGPS2b) and soluble starch synthase (SSIIb and SSIIc) also exhibited enhanced expression in the flo4-5 mutant.
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Affiliation(s)
- Heng Wang
- Department of Plant Bioscience, College of Natural Resources and Life Science, Pusan National University, Miryang 50463, Korea; (H.W.); (D.-E.I.); (S.M.L.); (S.-G.J.); (S.T.K.)
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Tae-Ho Ham
- Department of Applied Bioscience, Konkuk University, Seoul 05029, Korea; (T.-H.H.); (J.L.)
| | - Da-Eun Im
- Department of Plant Bioscience, College of Natural Resources and Life Science, Pusan National University, Miryang 50463, Korea; (H.W.); (D.-E.I.); (S.M.L.); (S.-G.J.); (S.T.K.)
| | - San Mar Lar
- Department of Plant Bioscience, College of Natural Resources and Life Science, Pusan National University, Miryang 50463, Korea; (H.W.); (D.-E.I.); (S.M.L.); (S.-G.J.); (S.T.K.)
| | - Seong-Gyu Jang
- Department of Plant Bioscience, College of Natural Resources and Life Science, Pusan National University, Miryang 50463, Korea; (H.W.); (D.-E.I.); (S.M.L.); (S.-G.J.); (S.T.K.)
| | - Joohyun Lee
- Department of Applied Bioscience, Konkuk University, Seoul 05029, Korea; (T.-H.H.); (J.L.)
| | - Youngjun Mo
- National Institute of Crop Science, Rural Development Administration, Jeonju 54874, Korea; (Y.M.); (J.-U.J.)
| | - Ji-Ung Jeung
- National Institute of Crop Science, Rural Development Administration, Jeonju 54874, Korea; (Y.M.); (J.-U.J.)
| | - Sun Tae Kim
- Department of Plant Bioscience, College of Natural Resources and Life Science, Pusan National University, Miryang 50463, Korea; (H.W.); (D.-E.I.); (S.M.L.); (S.-G.J.); (S.T.K.)
| | - Soon-Wook Kwon
- Department of Plant Bioscience, College of Natural Resources and Life Science, Pusan National University, Miryang 50463, Korea; (H.W.); (D.-E.I.); (S.M.L.); (S.-G.J.); (S.T.K.)
- Correspondence: ; Tel.: +82-55-350-5506
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Wang H, Mo YJ, Im DE, Jang SG, Ham TH, Lee J, Jeung JU, Kwon SW. A new SNP in cyOsPPDK gene is associated with floury endosperm in Suweon 542. Mol Genet Genomics 2018; 293:1151-1158. [PMID: 29744589 DOI: 10.1007/s00438-018-1446-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 05/06/2018] [Indexed: 10/16/2022]
Abstract
Pyruvate orthophosphate dikinase (PPDK) is a component of glycolysis to mediate endosperm energy charge by adjusting the ratio of ATP to ADP and AMP that proposed to balance the flow of carbon into starch, protein, fatty acid and amino acid biosynthesis. However, these were inconsistent with the first report of a T-DNA insertional knockout mutant of the rice PPDK gene (flo4) showed that rice with inactivated PPDK gene failed to produce a opaque seeds. Therefore, the PPDK might have multifaceted functions in grain filling stage, which in some ways might depend on the direction of the reversible catalysis. Suweon 542 is a rice (Oryza sativa L.) mutant developed from Oryza sativa ssp. japonica cv. Namil. Suweon 542 has a milky-white floury endosperm suitable for dry filling, with low starch damage, low grain hardness, and fine flour particle size. The mutant locus on chromosome 5 controls the floury endosperm phenotype of Suweon 542. Fine mapping of this locus is required for efficient breeding of rice germplasm suitable for dry milling. In this study, whole genome of Suweon 542 and Milyang 23 were re-sequenced using Illumina HiSeq 2500. Co-segregation analysis of F3:4 family populations derived from Suweon 542/Milyang 23 was performed using eight CAPS markers and phenotypic evaluation of the endosperm. The target region was mapped to a 33 kb region and identified to encode cytosolic pyruvate orthophosphate dikinase protein (cyOsPPDK). A G→A SNP in exon 8 of cyOsPPDK resulting in a missense mutation from Gly to Asp at amino acid position 404 was responsible for the floury endosperm of Suweon 542. qRT-PCR experiments revealed that FLO4-4 was expressed to a considerably higher level in Suweon 542 than in Namil during the grain filling stage. Overall, fine mapping of FLO4-4 and candidate gene analysis provided further insight into the floury endosperm of rice, and reveal a novel SNP in cyOsPPDK gene can affect the floury endosperm phenotype through active PPDK gene during grain filling stage.
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Affiliation(s)
- Heng Wang
- Department of Plant Bioscience, College of Natural Resources and Life Science, Pusan National University, Miryang, 50463, Republic of Korea
| | - Young-Jun Mo
- National Institute of Crop Science, Rural Development Administration, Jeonju, 54874, Republic of Korea.,Department of Plant Sciences, University of California, Davis, USA
| | - Da-Eun Im
- Department of Plant Bioscience, College of Natural Resources and Life Science, Pusan National University, Miryang, 50463, Republic of Korea
| | - Seong-Gyu Jang
- Department of Plant Bioscience, College of Natural Resources and Life Science, Pusan National University, Miryang, 50463, Republic of Korea
| | - Tae-Ho Ham
- Department of Agricultural Science, Korea National Open University, Seoul, 03087, Republic of Korea.,Department of Applied Bioscience, Konkuk University, Seoul, 05029, Republic of Korea
| | - Joohyun Lee
- Department of Applied Bioscience, Konkuk University, Seoul, 05029, Republic of Korea
| | - Ji-Ung Jeung
- National Institute of Crop Science, Rural Development Administration, Jeonju, 54874, Republic of Korea
| | - Soon-Wook Kwon
- Department of Plant Bioscience, College of Natural Resources and Life Science, Pusan National University, Miryang, 50463, Republic of Korea.
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Mo YJ, Jeung JU, Shin WC, Kim KY, Ye C, Redoña ED, Kim BK. Effects of allelic variations in starch synthesis-related genes on grain quality traits of Korean nonglutinous rice varieties under different temperature conditions. Breed Sci 2014; 64:164-75. [PMID: 24987303 PMCID: PMC4065324 DOI: 10.1270/jsbbs.64.164] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2013] [Accepted: 03/12/2014] [Indexed: 05/07/2023]
Abstract
Influences of allelic variations in starch synthesis-related genes (SSRGs) on rice grain quality were examined. A total of 187 nonglutinous Korean rice varieties, consisting of 170 Japonica and 17 Tongil-type varieties, were grown in the field and in two greenhouse conditions. The percentages of head rice and chalky grains, amylose content, alkali digestion value, and rapid visco-analysis characteristics were evaluated in the three different environments. Among the 10 previously reported SSRG markers used in this study, seven were polymorphic, and four of those showed subspecies-specific allele distributions. Six out of the seven polymorphic SSRG markers were significantly associated with at least one grain quality trait (R (2) > 0.1) across the three different environments. However, the association level and significance were markedly lower when the analysis was repeated using only the 170 Japonica varieties. Similarly, the significant associations between SSRG allelic variations and changes in grain quality traits under increased temperature were largely attributable to the biased allele frequency between the two subpopulations. Our results suggest that within Korean Japonica varieties, these 10 major SSRG loci have been highly fixed during breeding history and variations in grain quality traits might be influenced by other genetic factors.
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Affiliation(s)
- Young-Jun Mo
- National Institute of Crop Science, Rural Development Administration,
Suwon 441-857,
Republic of Korea
| | - Ji-Ung Jeung
- National Institute of Crop Science, Rural Development Administration,
Suwon 441-857,
Republic of Korea
| | - Woon-Chul Shin
- National Institute of Crop Science, Rural Development Administration,
Suwon 441-857,
Republic of Korea
| | - Ki-Young Kim
- National Institute of Crop Science, Rural Development Administration,
Suwon 441-857,
Republic of Korea
| | - Changrong Ye
- Plant Breeding, Genetics, and Biotechnology Division, International Rice Research Institute,
DAPO Box 7777, Metro Manila,
Philippines
| | - Edilberto D. Redoña
- Plant Breeding, Genetics, and Biotechnology Division, International Rice Research Institute,
DAPO Box 7777, Metro Manila,
Philippines
| | - Bo-Kyeong Kim
- National Institute of Crop Science, Rural Development Administration,
Suwon 441-857,
Republic of Korea
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Mo YJ, Jeung JU, Shin YS, Park CS, Kang KH, Kim BK. Agronomic and genetic analysis of Suweon 542, a rice floury mutant line suitable for dry milling. Rice (N Y) 2013; 6:37. [PMID: 24321450 PMCID: PMC4883716 DOI: 10.1186/1939-8433-6-37] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2013] [Accepted: 12/05/2013] [Indexed: 05/07/2023]
Abstract
BACKGROUND Producing rice flour of good quality by dry milling is necessary to reduce milling costs and promote the processed rice food industry. This study was conducted to evaluate the dry milling properties of Suweon 542, a floury endosperm mutant, and identify the chromosomal region responsible for the floury endosperm characteristics. RESULTS Compared with the wild type, after dry milling process, the grain hardness of Suweon 542 was significantly lower because of its round and loosely packed starch granules. Also, the flour of Suweon 542 had significantly smaller particles and less damaged starch than Namil and other rice cultivars and its particle size distribution was similar to a commercial wheat cultivar. Considering that the yield loss of Suweon 542 due to its floury endosperm was largely compensated for by an increased number of spikelets per panicle, Suweon 542 has potential value as a raw material for rice flour production. Association analysis using 70 genome-wide SSR markers and 94 F2 plants derived from Suweon 542/Milyang 23 showed that markers on chromosome 5 explained a large portion of the variation in floury grains percentage (FGP). Further analysis with an increased number of SSR markers revealed that the floury endosperm of Suweon 542 was directed by a major recessive locus, flo7(t), located in the 19.33-19.86 Mbp region of chromosome 5, with RM18639 explaining 92.2% of FGP variation in the F2 population. CONCLUSIONS The floury endosperm of Suweon 542 is suitable for dry milling, with a small flour particle size and low damaged starch content. Further physical mapping of flo7(t), the floury endosperm locus of Suweon 542, would facilitate efficient breeding of rice cultivars with proper dry milling adaptability that can be used in the processed rice food industry.
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Affiliation(s)
- Young-Jun Mo
- />National Institute of Crop Science, Rural Development Administration, Suwon, 441-857 Republic of Korea
| | - Ji-Ung Jeung
- />National Institute of Crop Science, Rural Development Administration, Suwon, 441-857 Republic of Korea
| | - Young-Seop Shin
- />National Institute of Crop Science, Rural Development Administration, Suwon, 441-857 Republic of Korea
| | - Chul Soo Park
- />Department of Crop Science and Biotechnology, Chonbuk National University, Jeonju, 561-756 Republic of Korea
| | - Kyung-Ho Kang
- />National Institute of Crop Science, Rural Development Administration, Suwon, 441-857 Republic of Korea
| | - Bo-Kyeong Kim
- />National Institute of Crop Science, Rural Development Administration, Suwon, 441-857 Republic of Korea
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Suh JP, Jeung JU, Noh TH, Cho YC, Park SH, Park HS, Shin MS, Kim CK, Jena KK. Development of breeding lines with three pyramided resistance genes that confer broad-spectrum bacterial blight resistance and their molecular analysis in rice. Rice (N Y) 2013; 6:5. [PMID: 24280417 PMCID: PMC4883717 DOI: 10.1186/1939-8433-6-5] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2012] [Accepted: 02/05/2013] [Indexed: 05/04/2023]
Abstract
BACKGROUND The development of resistant cultivars has been the most effective and economical strategy to control bacterial leaf blight (BB) disease of rice caused by Xanthomonas oryzae pv. oryzae (Xoo). Molecular markers have made it possible to identify and pyramid valuable genes of agronomic importance in resistance rice breeding. In this study, three resistance genes (Xa4 + xa5 + Xa21) were transferred from an indica donor (IRBB57), using a marker-assisted backcrossing (MAB) breeding strategy, into a BB-susceptible elite japonica rice cultivar, Mangeumbyeo, which is high yielding with good grain quality. RESULTS Our analysis led to the development of three elite advanced backcross breeding lines (ABL) with three resistance genes by foreground and phenotypic selection in a japonica genetic background without linkage drag. The background genome recovery of the ABL expressed more than 92.1% using genome-wide SSR marker analysis. The pathogenicity assays of three resistance-gene-derived ABL were conducted under glasshouse conditions with the 18 isolates of Xoo prevalent in Korea. The ABL exhibited very small lesion lengths, indicating a hypersensitive reaction to all 18 isolates of Xoo, with agronomic and grain quality traits similar to those of the recurrent parent. Pyramiding the resistance genes Xa4, xa5 and Xa21 provided a higher resistance to Xoo than the introduction of the individual resistance genes. Additionally, the combination of two dominant and one recessive BB resistance gene did not express any negative effect on agronomic traits in the ABL. CONCLUSIONS The strategy of simultaneous foreground and phenotypic selection to introduce multiple R genes is very useful to reduce the cost and the time required for the isolation of desirable recombinants with target resistance genes in rice. The resistance-gene-derived ABL have practical breeding value without a yield penalty by providing broad-spectrum resistance against most of the existing isolates of BB in South Korea and will have a high impact on the yield stability and sustainability of rice productivity.
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Affiliation(s)
- Jung-Pil Suh
- />National Institute of Crop Science, RDA, Suwon, 441-857 Republic of Korea
| | - Ji-Ung Jeung
- />National Institute of Crop Science, RDA, Suwon, 441-857 Republic of Korea
| | - Tae-Hwan Noh
- />National Institute of Crop Science, RDA, Suwon, 441-857 Republic of Korea
| | - Young-Chan Cho
- />National Institute of Crop Science, RDA, Suwon, 441-857 Republic of Korea
| | - So-Hyun Park
- />National Institute of Crop Science, RDA, Suwon, 441-857 Republic of Korea
| | - Hyun-Su Park
- />National Institute of Crop Science, RDA, Suwon, 441-857 Republic of Korea
| | - Mun-Sik Shin
- />National Institute of Crop Science, RDA, Suwon, 441-857 Republic of Korea
| | - Chung-Kon Kim
- />National Institute of Crop Science, RDA, Suwon, 441-857 Republic of Korea
| | - Kshirod K Jena
- />Plant Breeding, Genetics, and Biotechnology Division, International Rice Research Institute, DAPO, Box 7777, Metro Manila, Philippines
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10
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Kang CS, Jeung JU, Baik BK, Park CS. Effects of Allelic Variations inWx-1, Glu-D1, Glu-B3, andPinb-D1Loci on Flour Characteristics and White Salted Noodle-Making Quality of Wheat Flour. Cereal Chem 2012. [DOI: 10.1094/cchem-03-12-0034-r] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Chon-Sik Kang
- National Institute of Crop Science, Rural Development Administration, Suwon 441-857, Korea
| | - Ji-Ung Jeung
- National Institute of Crop Science, Rural Development Administration, Suwon 441-857, Korea
| | - Byung-Kee Baik
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99164-6420
| | - Chul Soo Park
- Department of Crop Science and Biotechnology, Chonbuk National University, Jeon-ju 561-756, Korea
- Corresponding author. Phone: +82-63-270-2533. Fax: +82-63-270-2640. E-mail:
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11
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Suh JP, Jeung JU, Lee JI, Choi YH, Yea JD, Virk PS, Mackill DJ, Jena KK. Identification and analysis of QTLs controlling cold tolerance at the reproductive stage and validation of effective QTLs in cold-tolerant genotypes of rice (Oryza sativa L.). Theor Appl Genet 2010; 120:985-95. [PMID: 20012263 DOI: 10.1007/s00122-009-1226-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2009] [Accepted: 11/18/2009] [Indexed: 05/03/2023]
Abstract
Low temperature or cold stress is one of the major constraints of rice production and productivity in temperate rice-growing countries and high-altitude areas in the tropics. Even though low temperature affects the rice plant in all stages of growth, the percent seed set is damaged severely by cold and this reduces the yield potential of cultivars significantly. In this study, a new source of cold-tolerant line, IR66160-121-4-4-2, was used as a donor parent with a cold-sensitive cultivar, Geumobyeo, to produce 153 F(8) recombinant inbred lines (RILs) for quantitative trait locus (QTL) analysis. QTL analysis with 175 polymorphic simple sequence repeat (SSR) markers and composite interval mapping identified three main-effect QTLs (qPSST-3, qPSST-7, and qPSST-9) on chromosomes 3, 7, and 9. The SSR markers RM569, RM1377, and RM24545 were linked to the identified QTLs for cold tolerance with respect to percent seed set using cold-water (18-19 degrees C) irrigation in the field and controlled air temperature (17 degrees C) in the greenhouse. The total phenotypic variation for cold tolerance contributed by the three QTLs was 27.4%. RILs with high percent seed set under cold stress were validated with linked DNA markers and by haplotype analysis that revealed the contribution of progenitor genomes from the tropical japonica cultivar Jimbrug (Javanica) and temperate japonica cultivar Shen-Nung89-366. Three QTLs contributed by the cold-tolerant parent were identified which showed additive effect on percent seed set under cold treatment. This study demonstrated the utility of a new phenotyping method as well as the identification of SSR markers associated with QTLs for selection of cold-tolerant genotypes to improve temperate rice production.
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Affiliation(s)
- J P Suh
- IRRI-Korea Office, National Institute of Crop Science, RDA, 209 Seodun-Dong, Suwon, 441-857, Republic of Korea
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12
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Bang KH, Lee JW, Kim YC, Kim DH, Lee EH, Jeung JU. Construction of Genomic DNA Library of Korean Ginseng (Panax ginseng C. A. MEYER) and Development of Sequence-Tagged Sites. Biol Pharm Bull 2010; 33:1579-88. [DOI: 10.1248/bpb.33.1579] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Kyong-Hwan Bang
- Ginseng Research Division, National Institute of Horticultural & Herbal Science, Korean Rural Development Administration (RDA)
| | - Jei-Wan Lee
- Ginseng Research Division, National Institute of Horticultural & Herbal Science, Korean Rural Development Administration (RDA)
| | - Young-Chang Kim
- Ginseng Research Division, National Institute of Horticultural & Herbal Science, Korean Rural Development Administration (RDA)
| | - Dong-Hwi Kim
- Ginseng Research Division, National Institute of Horticultural & Herbal Science, Korean Rural Development Administration (RDA)
| | - Eung-Ho Lee
- Ginseng Research Division, National Institute of Horticultural & Herbal Science, Korean Rural Development Administration (RDA)
| | - Ji-Ung Jeung
- Rice Research Division, National Institute of Crop Science, Korean Rural Development Administration (RDA)
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13
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Rahman ML, Jiang W, Chu SH, Qiao Y, Ham TH, Woo MO, Lee J, Khanam MS, Chin JH, Jeung JU, Brar DS, Jena KK, Koh HJ. High-resolution mapping of two rice brown planthopper resistance genes, Bph20(t) and Bph21(t), originating from Oryza minuta. Theor Appl Genet 2009; 119:1237-46. [PMID: 19669727 DOI: 10.1007/s00122-009-1125-z] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2008] [Accepted: 07/21/2009] [Indexed: 05/18/2023]
Abstract
Brown planthopper (BPH) is one of the most destructive insect pests of rice. Wild species of rice are a valuable source of resistance genes for developing resistant cultivars. A molecular marker-based genetic analysis of BPH resistance was conducted using an F(2) population derived from a cross between an introgression line, 'IR71033-121-15', from Oryza minuta (Accession number 101141) and a susceptible Korean japonica variety, 'Junambyeo'. Resistance to BPH (biotype 1) was evaluated using 190 F(3) families. Two major quantitative trait loci (QTLs) and two significant digenic epistatic interactions between marker intervals were identified for BPH resistance. One QTL was mapped to 193.4-kb region located on the short arm of chromosome 4, and the other QTL was mapped to a 194.0-kb region on the long arm of chromosome 12. The two QTLs additively increased the resistance to BPH. Markers co-segregating with the two resistance QTLs were developed at each locus. Comparing the physical map positions of the two QTLs with previously reported BPH resistance genes, we conclude that these major QTLs are new BPH resistance loci and have designated them as Bph20(t) on chromosome 4 and Bph21(t) on chromosome 12. This is the first report of BPH resistance genes from the wild species O. minuta. These two new genes and markers reported here will be useful to rice breeding programs interested in new sources of BPH resistance.
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Affiliation(s)
- Md Lutfor Rahman
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Korea
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14
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Kwon SW, Cho YC, Kim YG, Suh JP, Jeung JU, Roh JH, Lee SK, Jeon JS, Yang SJ, Lee YT. Development of near-isogenic Japonica rice lines with enhanced resistance to Magnaporthe grisea. Mol Cells 2008; 25:407-16. [PMID: 18443412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023] Open
Abstract
Thirteen near-isogenic lines (NILs) of japonica rice were developed via a backcross method using the recurrent parent Chucheong, which is of good eating quality but is susceptible to Magnaporthe grisea, and three blast resistant japonica donors, Seolak, Daeseong and Bongkwang. The agro-morphological traits of these NILs, such as heading date, culm length, and panicle length, were similar to those of Chucheong. In a genome-wide scan using 158 SSR markers, chromosome segments of Chucheong were identified in most polymorphic regions of the 13 NIL plants, and only a few chromosome segments were found to have been substituted by donor alleles. The genetic similarities of the 13 NILs to the recurrent parent Chucheong averaged 0.961, with a range of 0.932-0.984. Analysis of 13 major blast resistance (R) genes in these lines using specific DNA markers showed that each NIL appeared to contain some combination of the four R genes, Pib, Pii, Pik-m and Pita-2, with the first three genes being present in each line. Screening of nine M. grisea isolates revealed that one NIL M7 was resistant to all nine isolates; the remaining NILs were each resistant to between three and seven isolates, except for NIL M106, which was resistant to only two isolates. In a blast nursery experiment, all the NILs proved to be more resistant than Chucheong. These newly developed NILs have potential as commercial rice varieties because of their increased resistance to M. grisea combined with the desirable agronomic traits of Chucheong. They also provide material for studying the genetic basis of blast resistance.
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Affiliation(s)
- Soon-Wook Kwon
- National Institute of Crop Science, RDA, Suwon 441-857, Korea
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15
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Jeung JU, Kim BR, Cho YC, Han SS, Moon HP, Lee YT, Jena KK. A novel gene, Pi40(t), linked to the DNA markers derived from NBS-LRR motifs confers broad spectrum of blast resistance in rice. Theor Appl Genet 2007; 115:1163-77. [PMID: 17909744 DOI: 10.1007/s00122-007-0642-x] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2007] [Accepted: 08/31/2007] [Indexed: 05/06/2023]
Abstract
Rice blast disease caused by Magnaporthe grisea is a continuous threat to stable rice production worldwide. In a modernized agricultural system, the development of varieties with broad-spectrum and durable resistance to blast disease is essential for increased rice production and sustainability. In this study, a new gene is identified in the introgression line IR65482-4-136-2-2 that has inherited the resistance gene from an EE genome wild Oryza species, O. australiensis (Acc. 100882). Genetic and molecular analysis localized a major resistance gene, Pi40(t), on the short arm of chromosome 6, where four blast resistance genes (Piz, Piz-5, Piz-t, and Pi9) were also identified, flanked by the markers S2539 and RM3330. Through e-Landing, 14 BAC/PAC clones within the 1.81-Mb equivalent virtual contig were identified on Rice Pseudomolecule3. Highly stringent primer sets designed for 6 NBS-LRR motifs located within PAC clone P0649C11 facilitated high-resolution mapping of the new resistance gene, Pi40(t). Following association analysis and detailed haplotyping approaches, a DNA marker, 9871.T7E2b, was identified to be linked to the Pi40(t) gene at the 70 Kb chromosomal region, and differentiated the Pi40(t) gene from the LTH monogenic differential lines possessing genes Piz, Piz-5, Piz-t, and Pi-9. Pi40(t) was validated using the most virulent isolates of Korea as well as the Philippines, suggesting a broad spectrum for the resistance gene. Marker-assisted selection (MAS) and pathotyping of BC progenies having two japonica cultivar genetic backgrounds further supported the potential of the resistance gene in rice breeding. Our study based on new gene identification strategies provides insight into novel genetic resources for blast resistance as well as future studies on cloning and functional analysis of a blast resistance gene useful for rice improvement.
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Affiliation(s)
- J U Jeung
- Plant Breeding, Genetics, and Biotechnology Division, International Rice Research Institute, Los Baños, Laguna, Philippines
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16
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Rahman ML, Chu SH, Choi MS, Qiao YL, Jiang W, Piao R, Khanam S, Cho YI, Jeung JU, Jena K, Koh HJ. Identification of QTLs for some agronomic traits in rice using an introgression line from Oryza minuta. Mol Cells 2007; 24:16-26. [PMID: 17846495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/17/2023] Open
Abstract
Wild progenitor species provide potential gene sources for complex traits such as yield and multiple resistances to biotic and abiotic stresses, and thus are expected to contribute to sustainable food supplies. An introgression line 'IR71033-121-15' was derived from a wild species Oryza minuta (2n = 48, BBCC, Acc No. 101141) at IRRI. Introgression analysis using 530 SSR and STS markers revealed that at least 14 chromosomal segments distributed over 12 chromosomes had been introgressed from O. minuta. An F2:3 population from the cross between IR71033 and Junambyeo (a Korean japonica cultivar) consisting of 146 lines was used for quantitative trait loci (QTL) analysis of 16 agronomic traits. A total of 36 single-locus QTLs (S-QTLs) and 45 digenic epistasis (E-QTLs) were identified. In spite of it's inferiority of O. minuta for most of the traits studied, its alleles contributed positively to 57% of the QTLs. The other QTLs originated from either parent, IR71033 or Junambyeo. QTLs for phenotypically correlated traits were mostly detected on introgressed segments. Fourteen QTLs corresponded to QTLs reported earlier, indicating that these QTLs are stable across genetic backgrounds. Twenty-two QTLs controlling yield and its components had not been detected in previous QTL studies. Of these, thirteen consisted of potentially novel alleles from O. minuta. QTLs from O. minuta introgression could be new sources of natural variation for the genetic improvement of rice.
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Affiliation(s)
- Md Lutfor Rahman
- Department of Plant Science and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Korea
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17
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Jeung JU, Heu SG, Shin MS, Vera Cruz CM, Jena KK. Dynamics of Xanthomonas oryzae pv. oryzae Populations in Korea and Their Relationship to Known Bacterial Blight Resistance Genes. Phytopathology 2006; 96:867-75. [PMID: 18943752 DOI: 10.1094/phyto-96-0867] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
ABSTRACT Developing resistant cultivars requires an understanding of the dynamics of the pathogen populations as well as the genetics of host resistance. Bacterial leaf blight (BB), caused by the vascular pathogen Xanthomonas oryzae pv. oryzae, has become one of the most devastating diseases of rice. We demonstrate here the quantitative analyses of responses of near-isogenic lines carrying various BB resistance (R) genes and R-gene combinations against 16 X. oryzae pv. oryzae isolates representing Korean BB pathotypes. The estimated main effects of each R gene against the 16 isolates identified prominent differences in BB pathotypes between Korea and other countries. Three major aspects of our quantitative observations and statistical analysis are (i) strong and broad resistance of xa5; (ii) independent and additive genetic actions of Xa4, xa5, and Xa21 under digenic or trigenic status; and (iii) a strong quantitative complementation effect contributed by the functional alleles of Xa4 and Xa21. We conclude that the pyramid line containing genes Xa4, xa5, and Xa21 would be the most promising and valuable genotype for improving Korean japonica cultivars for BB resistance.
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18
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Jena KK, Jeung JU, Lee JH, Choi HC, Brar DS. High-resolution mapping of a new brown planthopper (BPH) resistance gene, Bph18(t), and marker-assisted selection for BPH resistance in rice (Oryza sativa L.). Theor Appl Genet 2006; 112:288-97. [PMID: 16240104 DOI: 10.1007/s00122-005-0127-8] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2005] [Accepted: 09/28/2005] [Indexed: 05/04/2023]
Abstract
Brown planthopper (BPH) is a destructive insect pest of rice in Asia. Identification and the incorporation of new BPH resistance genes into modern rice cultivars are important breeding strategies to control the damage caused by new biotypes of BPH. In this study, a major resistance gene, Bph18(t), has been identified in an introgression line (IR65482-7-216-1-2) that has inherited the gene from the wild species Oryza australiensis. Genetic analysis revealed the dominant nature of the Bph18(t) gene and identified it as non-allelic to another gene, Bph10 that was earlier introgressed from O. australiensis. After linkage analysis using MapMaker followed by single-locus ANOVA on quantitatively expressed resistance levels of the progenies from an F2 mapping population identified with marker allele types, the Bph18(t) gene was initially located on the subterminal region of the long arm of chromosome 12 flanked by the SSR marker RM463 and the STS marker S15552. The corresponding physical region was identified in the Nipponbare genome pseudomolecule 3 through electronic chromosome landing (e-landing), in which 15 BAC clones covered 1.612 Mb. Eleven DNA markers tagging the BAC clones were used to construct a high-resolution genetic map of the target region. The Bph18(t) locus was further localized within a 0.843-Mb physical interval that includes three BAC clones between the markers R10289S and RM6869 by means of single-locus ANOVA of resistance levels of mapping population and marker-gene association analysis on 86 susceptible F2 progenies based on six time-point phenotyping. Using gene annotation information of TIGR, a putative resistance gene was identified in the BAC clone OSJNBa0028L05 and the sequence information was used to generate STS marker 7312.T4A. The marker allele of 1,078 bp completely co-segregated with the BPH resistance phenotype. STS marker 7312.T4A was validated using BC2F2 progenies derived from two temperate japonica backgrounds. Some 97 resistant BC2F2 individuals out of 433 screened completely co-segregated with the resistance-specific marker allele (1,078 bp) in either homozygous or heterozygous state. This further confirmed a major gene-controlled resistance to the BPH biotype of Korea. Identification of Bph18(t) enlarges the BPH resistance gene pool to help develop improved rice cultivars, and the PCR marker (7312.T4A) for the Bph18(t) gene should be readily applicable for marker-assisted selection (MAS).
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Affiliation(s)
- K K Jena
- Plant Breeding, Genetics, and Biotechnology Division, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines.
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Jeung JU, Cho SK, Shin JS. A partial-complementary adapter for an improved and simplified ligation-mediated suppression PCR technique. ACTA ACUST UNITED AC 2005; 64:110-20. [PMID: 16005075 DOI: 10.1016/j.jbbm.2005.06.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2005] [Revised: 04/18/2005] [Accepted: 06/06/2005] [Indexed: 11/20/2022]
Abstract
Ligation-mediated suppression PCR (LMS-PCR) is a powerful tool for walking in unknown genomic DNA regions from known adjacent sequences. This approach has made it feasible to obtain promoter sequences and to enable researchers to identify full-length gene sequences or isoforms of multigene families. However, the advantages of LMS-PCR can be obviated by the presence of incomplete base modifications on the suppression adapters. We propose here that a 'partial-complementary adapter' is a more reliable suppression adapter, demanding only 5'-end phosphorylation. We also describe a simplified procedure for the easier preparation of PCR templates with very small quantities of DNA and a fast and direct characterization of the suppression-PCR products. A set of practical guidelines is proposed for pre-checking the efficiency of the adapter modification using two model systems: bacteriophage lambda (lambda) and Arabidopsis.
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Affiliation(s)
- Ji-Ung Jeung
- IRRI-Korea Office, NICS, RDA, Suwon 441-854, Korea
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Jeung JU, Cho SK, Lee SJ, Shin JS. Characterization of Ty3-gypsy-like elements in Hibiscus syriacus. Mol Cells 2005; 19:318-27. [PMID: 15995347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023] Open
Abstract
Southern blot analysis revealed a ubiquitous distribu-tion and high copy number of Ty3-gypsy-like elements in the genome of Hibiscus syriacus. Comparative phylogenetic analysis of the large subunit of Rubisco and the integrase region of Ty3-gypsy elements in various plant species indicated that the retrotransposon-like sequences have different evolutionary histories and their own unique polymorphism in the H. syriacus population. Sequence-tagged site-restriction fragment length polymorphisms (STS-RFLP) analysis also indicated great variability in the numbers and sequences of Ty3-gypsy-like elements within H. syriacus varieties. Ty3-gypsy-like elements may still be active within H. syriacus, since Northern analysis of wounded leaves of H. syriacus variety Saehan with a probe for the integrase domain gave strong hybridization signals. The sequence heterogeneity and ubiquity of the Ty3-gypsy-like elements in H. syriacus genomes could provide reliable DNA markers for line identification as well for the analysis of genetic diversity in H. syriacus.
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Affiliation(s)
- Ji-Ung Jeung
- School of Life Sciences and Biotechnology, Korea University, Seoul 136-701, Korea
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21
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Cho SK, Jung KW, Jeung JU, Kang KH, Shim KS, You MK, Yoo KS, Ok SH, Shin JS. Analysis of differentially expressed transcripts from planthopper-infested wild rice (Oryza minuta). Plant Cell Rep 2005; 24:59-67. [PMID: 15635457 DOI: 10.1007/s00299-004-0905-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2004] [Revised: 11/04/2004] [Accepted: 11/04/2004] [Indexed: 05/24/2023]
Abstract
A subtracted library was constructed from planthopper-infested wild rice (Oryza minuta) by suppression subtractive hybridization in combination with mirror orientation selection. To screen the differentially expressed transcripts in the library, we applied a cDNA microarray containing 960 random clones in a reverse Northern blot analysis using cDNA probes prepared from the mRNAs of control and planthopper-infested samples. On the basis of the signal intensities and expression ratios obtained from experiments performed in triplicate, we selected 383 clones. The elevated expression levels and overall profiles over time were verified by Northern blot analysis. Although Southern blot analysis showed similar copy numbers of the screened genes in O. minuta and O. sativa, it also revealed that the expression profiles had a different pattern. Functional categorization placed the identified transcripts in the categories of subcellular localization, metabolism, and protein fate. The presence of these expressed sequence tags implies that resistance of O. minuta to insect infestation can be achieved not only by an elevated expression of defense-related genes but also by enhanced metabolic activities.
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Affiliation(s)
- S K Cho
- School of Life Sciences and Biotechnology, Korea University, Seoul 136-701, Korea.
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Cho SK, Ok SH, Jeung JU, Shim KS, Jung KW, You MK, Kang KH, Chung YS, Choi HC, Moon HP, Shin JS. Comparative analysis of 5,211 leaf ESTs of wild rice (Oryza minuta). Plant Cell Rep 2004; 22:839-847. [PMID: 14968263 DOI: 10.1007/s00299-004-0764-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2003] [Revised: 01/07/2004] [Accepted: 01/08/2004] [Indexed: 05/24/2023]
Abstract
The expressed sequence tags (ESTs) presented in this report are the first transcriptomes of wild rice. A cDNA library was constructed from 4-week-old leaf samples of greenhouse-grown Oryza minuta. The 5,211 cDNA clones of O. minuta represent 3,401 unique sequences, consisting of 2,787 singletons and 614 assembled sequences. Database comparisons of the cDNAs in GenBank's non-redundant databases using BLAST revealed that 4,957 of the 5,211 cDNAs (95.1%) showed a high degree of sequence homology to genes from other organisms. Most of the transcripts identified were genes related to metabolism, energy, protein biosynthesis and subcellular localization. The metabolism and energy categories of the O. minuta ESTs showed a considerably higher gene expression level than those of O. sativa ESTs. These data and genes can be utilized in rice breeding.
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Affiliation(s)
- S K Cho
- School of Life Sciences and Biotechnology, Korea University, 136-701 Seou, Korea
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Shim KS, Cho SK, Jeung JU, Jung KW, You MK, Ok SH, Chung YS, Kang KH, Hwang HG, Choi HC, Moon HP, Shin JS. Identification of fungal ( Magnaporthe grisea) stress-induced genes in wild rice ( Oryza minuta). Plant Cell Rep 2004; 22:599-607. [PMID: 14648106 DOI: 10.1007/s00299-003-0742-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2003] [Revised: 10/17/2003] [Accepted: 10/18/2003] [Indexed: 05/24/2023]
Abstract
To identify fungal stress-related genes in wild rice, Oryza minuta, we constructed a subtracted library using suppression subtractive hybridization in combination with mirror orientation selection. DNA chips containing 960 randomly selected cDNA clones were applied by reverse Northern analysis to eliminate false positive clones from the library and to prescreen differentially expressed genes. In total, 377 cDNA clones were selected on the basis of their signal intensities and expression ratios. Sequence analyses of these 377 cDNA fragments revealed that 180 of them (47.7%) represented unique genes. Of these 180 cDNAs, 89 clones (49.6%) showed significant homologies to previously known genes, while the remaining 91 did not match any known sequences. The putative functions of the 180 unique ESTs were categorized by aligning them with MIPS data. They were classified into seven different groups using microarray data-derived expression patterns and verified by Northern blotting.
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Affiliation(s)
- K S Shim
- School of Life Sciences and Biotechnology, Korea University, 136-701 Seoul, Korea
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Bahn SC, Bae MS, Park YB, Oh SI, Jeung JU, Bae JM, Chung YS, Shin JS. Molecular cloning and characterization of a novel low temperature-induced gene, blti2, from barley (Hordeum vulgare L.). Biochim Biophys Acta 2001; 1522:134-7. [PMID: 11750066 DOI: 10.1016/s0167-4781(01)00317-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The Suppression Subtractive Hybridization (SSH) was used to isolate large numbers of low temperature-induced genes from the cold-treated winter barley (Hordeum vulgare L. cv. Dongbori). One hundred and sixty blti (barley low temperature-induced) cDNA clones were obtained. Northern blot analyses showed that several blti clones were differentially expressed by treatment of low temperature, NaCl, dehydration and ABA. One of the clones, blti2, was induced from 3 to 72 h after cold treatment while its transcript was detected only at 12 h after ABA treatment, indicating that the expression of blti2 by low temperature was regulated by an ABA-independent pathway. The full-length cDNA sequences were 944 nucleotides long and the open reading frame consisted of 492 nucleotides encoding 164 amino acids. Nucleotide sequences showed no sequence homology with the previously reported low temperature-responsive (LTR) barley genes, and the deduced amino acid sequences revealed that the blti2 contains three membrane-spanning regions. These results suggest that blti2 is a novel transmembrane protein induced by low temperature.
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Affiliation(s)
- S C Bahn
- Graduate School of Biotechnology, Korea University, Seoul, South Korea
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